| Type |
Details |
Score |
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2413
|
| Description: |
receptor-like protein kinase 1; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR025287 (Wall-associated receptor kinase galacturonan-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0030247 (polysaccharide binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2442
|
| Description: |
peptidyl-prolyl cis-trans isomerases; hydrolases; nucleoside-triphosphatases; ATP binding; nucleotide binding; ATPases; IPR021911 (ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0000166 (nucleotide binding), GO:0005524 (ATP binding), GO:0017111 (nucleoside-triphosphatase activity) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3431
|
| Description: |
Protein phosphatase 2A regulatory B subunit family protein; IPR002554 (Protein phosphatase 2A, regulatory B subunit, B56), IPR016024 (Armadillo-type fold); GO:0000159 (protein phosphatase type 2A complex), GO:0005488 (binding), GO:0007165 (signal transduction), GO:0008601 (protein phosphatase type 2A regulator activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
297
|
| Description: |
sugar transport protein 13 [Glycine max]; IPR005828 (General substrate transporter), IPR016196 (Major facilitator superfamily domain, general substrate transporter); GO:0005215 (transporter activity), GO:0006810 (transport), GO:0016020 (membrane), GO:0016021 (integral component of membrane), GO:0022857 (transmembrane transporter activity), GO:0055085 (transmembrane transport) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3607
|
| Description: |
probable ubiquitin conjugation factor E4-like [Glycine max]; IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR019474 (Ubiquitin conjugation factor E4, core); GO:0000151 (ubiquitin ligase complex), GO:0004842 (ubiquitin-protein ligase activity), GO:0006511 (ubiquitin-dependent protein catabolic process), GO:0016567 (protein ubiquitination), GO:0034450 (ubiquitin-ubiquitin ligase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1944
|
| Description: |
asparagine-tRNA ligase; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004816 (asparagine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006421 (asparaginyl-tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2952
|
| Description: |
disease resistance protein (TIR-NBS-LRR class), putative; IPR000157 (Toll/interleukin-1 receptor homology (TIR) domain), IPR000767 (Disease resistance protein), IPR001611 (Leucine-rich repeat), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0005515 (protein binding), GO:0006952 (defense response), GO:0007165 (signal transduction), GO:0043531 (ADP binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2886
|
| Description: |
Protein kinase superfamily protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0006950 (response to stress) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
591
|
| Description: |
threonyl-tRNA synthetase, putative / threonine--tRNA ligase, putative; IPR002320 (Threonine-tRNA ligase, class IIa); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004829 (threonine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006435 (threonyl-tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2135
|
| Description: |
Protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR018392 (LysM domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016998 (cell wall macromolecule catabolic process) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2483
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0006950 (response to stress) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1733
|
| Description: |
uridine kinase-like protein 4-like [Glycine max]; IPR000764 (Uridine kinase), IPR001162 (UvrC family homology region), IPR026008 (Uridine kinase-like protein), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0004849 (uridine kinase activity), GO:0005524 (ATP binding), GO:0008152 (metabolic process), GO:0016301 (kinase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2523
|
| Description: |
receptor-like protein kinase 4; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR025287 (Wall-associated receptor kinase galacturonan-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0030247 (polysaccharide binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2398
|
| Description: |
ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial-like [Glycine max]; IPR004487 (Clp protease, ATP-binding subunit ClpX), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0000166 (nucleotide binding), GO:0005524 (ATP binding), GO:0006457 (protein folding), GO:0017111 (nucleoside-triphosphatase activity), GO:0051082 (unfolded protein binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1936
|
| Description: |
aspartate-tRNA ligase; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004815 (aspartate-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006422 (aspartyl-tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
7231
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR001650 (Helicase, C-terminal), IPR009057 (Homeodomain-like), IPR014012 (Helicase/SANT-associated, DNA binding), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003676 (nucleic acid binding), GO:0003677 (DNA binding), GO:0004386 (helicase activity), GO:0005524 (ATP binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2913
|
| Description: |
receptor-like protein kinase 4; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR025287 (Wall-associated receptor kinase galacturonan-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0030247 (polysaccharide binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3646
|
| Description: |
ubiquitin carboxyl-terminal hydrolase 10-like isoform 1 [Glycine max]; IPR006615 (Peptidase C19, ubiquitin-specific peptidase, DUSP domain), IPR028134 (Ubiquitin carboxyl-terminal hydrolase USP), IPR028889 (Ubiquitin carboxyl-terminal hydrolase-like domain); GO:0004843 (ubiquitin-specific protease activity), GO:0006511 (ubiquitin-dependent protein catabolic process), GO:0016579 (protein deubiquitination) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2315
|
| Description: |
Protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR025287 (Wall-associated receptor kinase galacturonan-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0030247 (polysaccharide binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3102
|
| Description: |
sugar transport protein 10-like [Glycine max]; IPR005828 (General substrate transporter), IPR016196 (Major facilitator superfamily domain, general substrate transporter); GO:0005215 (transporter activity), GO:0006810 (transport), GO:0016020 (membrane), GO:0016021 (integral component of membrane), GO:0022857 (transmembrane transporter activity), GO:0055085 (transmembrane transport) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3031
|
| Description: |
aspartate-tRNA ligase; IPR018150 (Aminoacyl-tRNA synthetase, class II (D/K/N)-like); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004815 (aspartate-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006422 (aspartyl-tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2865
|
| Description: |
ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial-like [Glycine max]; IPR004487 (Clp protease, ATP-binding subunit ClpX), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0000166 (nucleotide binding), GO:0005524 (ATP binding), GO:0006457 (protein folding), GO:0017111 (nucleoside-triphosphatase activity), GO:0051082 (unfolded protein binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
297
|
| Description: |
sugar transport protein 13 [Glycine max]; IPR005828 (General substrate transporter), IPR016196 (Major facilitator superfamily domain, general substrate transporter); GO:0005215 (transporter activity), GO:0006810 (transport), GO:0016020 (membrane), GO:0016021 (integral component of membrane), GO:0022857 (transmembrane transporter activity), GO:0055085 (transmembrane transport) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2792
|
| Description: |
SH2 domain protein B; IPR001217 (Transcription factor STAT), IPR008985 (Concanavalin A-like lectin/glucanases superfamily), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup); GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0004871 (signal transducer activity), GO:0005515 (protein binding), GO:0005634 (nucleus), GO:0007165 (signal transduction) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3152
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0006950 (response to stress) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3473
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR001650 (Helicase, C-terminal), IPR002711 (HNH endonuclease), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003676 (nucleic acid binding), GO:0003677 (DNA binding), GO:0004386 (helicase activity), GO:0004519 (endonuclease activity), GO:0005524 (ATP binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2877
|
| Description: |
Protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR018392 (LysM domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016998 (cell wall macromolecule catabolic process) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1926
|
| Description: |
Protein kinase superfamily protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR018392 (LysM domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0016998 (cell wall macromolecule catabolic process) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
297
|
| Description: |
sugar transport protein 13 [Glycine max]; IPR005828 (General substrate transporter), IPR016196 (Major facilitator superfamily domain, general substrate transporter); GO:0005215 (transporter activity), GO:0006810 (transport), GO:0016020 (membrane), GO:0016021 (integral component of membrane), GO:0022857 (transmembrane transporter activity), GO:0055085 (transmembrane transport) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
4776
|
| Description: |
disease resistance protein (TIR-NBS-LRR class), putative; IPR000157 (Toll/interleukin-1 receptor homology (TIR) domain), IPR000767 (Disease resistance protein), IPR001611 (Leucine-rich repeat), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0005515 (protein binding), GO:0006952 (defense response), GO:0007165 (signal transduction), GO:0043531 (ADP binding) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2484
|
| Description: |
protein kinase family protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR014729 (Rossmann-like alpha/beta/alpha sandwich fold); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0006950 (response to stress) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
900
|
| Description: |
Unknown protein; IPR004162 (E3 ubiquitin-protein ligase SINA like), IPR013083 (Zinc finger, RING/FYVE/PHD-type); GO:0004842 (ubiquitin-protein ligase activity), GO:0005515 (protein binding), GO:0005634 (nucleus), GO:0006511 (ubiquitin-dependent protein catabolic process), GO:0007275 (multicellular organismal development), GO:0008270 (zinc ion binding), GO:0016567 (protein ubiquitination) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Phenylalanyl-tRNA synthetase, class IIc, beta subunit, archaeal/eukaryotic type |
| Type: |
Family |
| Description: |
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].Phenylalanyl-tRNA synthetase (
) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (see
). Reciprocally the large subunit
(pheT gene) can be designated as alpha (E. coli) or beta. In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [].This family describes the beta subunit. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps (see also
). This family represents the subfamily that includes the beta subunit from eukaryotic cytosol, the archaea, and spirochetes.
|
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
DNA-directed RNA polymerase, alpha subunit |
| Type: |
Family |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins [
,
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Phenylalanyl-tRNA synthetase, class IIc, alpha subunit |
| Type: |
Family |
| Description: |
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].Phenylalanyl-tRNA synthetase (
) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit
(pheT gene) can be designated as alpha (E. coli) or beta (see and
). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [
].This family describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this family. |
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| Protein Domain |
| Name: |
DNA topoisomerase, type IIA, subunit B |
| Type: |
Family |
| Description: |
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [
].Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA [
].Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication [
]. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.This entry represents subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), primarily of bacterial origin, and which functions in ATP hydrolysis and subunit interaction. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. |
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| Protein Domain |
| Name: |
DNA-directed RNA polymerase M, 15kDa subunit, conserved site |
| Type: |
Conserved_site |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides.
It has recently been shown [], [] that small subunits of about 15kDa, found in polymerase types I and II, are highly conserved.The proteins in this entry contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain. The signature for this entry covers the zinc finger. |
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| Protein Domain |
| Name: |
DNA-directed RNA polymerase, 14-18kDa subunit, conserved site |
| Type: |
Conserved_site |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.A component of 14 to 18kDa shared by all three forms of eukaryotic RNA polymerases and which has been sequenced in budding yeast (gene RPB6 or RPO26), in fission yeast (gene rpb6 or rpo15), in human and in African swine fever virus (ASFV) [] is evolutionary related [] to archaeal subunit K (generpoK). The archaeal protein is colinear with the C-terminal part of the eukaryotic subunit.
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| Protein Domain |
| Name: |
Glycine-tRNA ligase, alpha subunit |
| Type: |
Family |
| Description: |
This entry represents the alpha subunit of glycine-tRNA ligase (also known as glycyl-tRNA synthetase alpha subunit). It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.In eubacteria, glycine-tRNA ligase (
) is an alpha2/beta2 tetramer composed of 2 different subunits [
,
,
]. In some eubacteria, in archaea and eukaryota, glycine-tRNA ligase is an alpha2 dimer (see ). It belongs to class IIc and is one of the most complex ligases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha and beta subunits also lack significant sequence similarity. However, they are translated from a single mRNA [
], and a single chain glycine-tRNA ligase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain [].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [
]. |
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| Protein Domain |
| Name: |
DNA topoisomerase I, active site |
| Type: |
Active_site |
| Description: |
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo IB; eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB []. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [,
]. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases [,
].DNA topoisomerase I (
) [
,
,
,
] is one of the two types of enzyme that catalyze the interconversion of topological DNA isomers. Type I topoisomerases act by catalyzing the transient breakage of DNA, one strand at a time, and the subsequent rejoining of the strands. When a eukaryotic type 1 topoisomerase breaks a DNA backbone bond, it simultaneously forms a protein-DNA link where the hydroxyl group of a tyrosine residue is joined to a 3'-phosphate on DNA, at one end of the enzyme-severed DNA strand. In eukaryotes and poxvirus topoisomerases I, there are a number of conserved residues in the region around the active site tyrosine []. |
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| Protein Domain |
| Name: |
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic |
| Type: |
Family |
| Description: |
This entry are mostly eukaryotic cytosolic and archaeal forms of the glutamyl-tRNA synthetase. The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. In many species, the charging of tRNA (gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases, including all known archaeal enzymes may act on both tRNA (gln) and tRNA (glu).Glutamate-tRNA ligase (also known as glutamyl-tRNA synthetase;
) is a class Ic ligase and shows several similarities with glutamate-tRNA ligase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamate-tRNA ligase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I ligases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure [
].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c []. |
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| Protein Domain |
| Name: |
UDP-glucuronosyl/UDP-glucosyltransferase |
| Type: |
Family |
| Description: |
UDP glycosyltransferases (UGT) are a superfamily of enzymes that catalyses the addition of the glycosyl group from a UDP-sugar to a small hydrophobic molecule. This family currently consist of:Mammalian UDP-glucuronosyl transferases (
) (UDPGT) [
]. A large family of membrane-bound microsomal enzymes which catalyse the transfer of glucuronic acid to a wide variety of exogenous and endogenous lipophilic substrates. These enzymes are of major importance in the detoxification and subsequent elimination of xenobiotics such as drugs and carcinogens. These enzymes are also involved in cancer progression and drug resistance [].A large number of putative UDPGT from Caenorhabditis elegans.Mammalian 2-hydroxyacylsphingosine 1-beta-galactosyltransferase [
] () (also known as UDP-galactose-ceramide galactosyltransferase). This enzyme catalyses the transfer of galactose to ceramide, a key enzymatic step in the biosynthesis of galactocerebrosides, which are abundant sphingolipids of the myelin membrane of the central nervous system and peripheral nervous system.
Fungal Sterol 3-beta-glucosyltransferase, which is involved in the degradation of peroxisomes, mitochondria and nuclei [
]. Fungal Enfumafungin synthase efuA [
]. This protein plays a role in the biosynthesis of enfumafungin, a glycosylated fernene-type triterpenoid with potent antifungal activity.Plants Anthocyanidin 3-O-glucosyltransferase, also known as Flavonol O(3)-glucosyltransferase, an enzyme that catalyses the transfer of glucose from UDP-glucose to a flavanol. This reaction is essential and one of the last steps in anthocyanin pigment biosynthesis. Gallate 1-beta-glucosyltransferase (
), a glucosyltransferase that catalyses the formation of 1-O-galloyl-beta-D-glucose, the first committed step of hydrolyzable tannins (HTs) biosynthesis [
].(R)-mandelonitrile beta-glucosyltransferase from almond, which is involved in the biosynthesis of the cyanogenic glycoside (R)-prunasin (stereo-selective), a precursor of (R)-amygdalin which at high concentrations is associated with bitterness in kernels of almond [
].Baculoviruses ecdysteroid UDP-glucosyltransferase (
) [
] (egt). This enzyme catalyses the transfer of glucose from UDP-glucose to ectysteroids which are insect molting hormones. The expression of egt in the insect host interferes with the normal insect development by blocking the molting process.Prokaryotic zeaxanthin glucosyltransferase (
) (gene crtX), an enzyme involved in carotenoid biosynthesis and that catalyses the glycosylation reaction which converts zeaxanthin to zeaxanthin-beta-diglucoside; Enterobactin C-glucosyltransferase iroB which catalyses the successive monoglucosylation, diglucosylation and triglucosylation of enterobactin decreasing the membrane affinity of Enterobactin and increasing the iron acquisition rate [
,
].Streptomyces macrolide glycosyltransferases (
) [
]. These enzymes specifically inactivate macrolide antibiotics via 2'-O-glycosylation using UDP-glucose. |
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| Protein Domain |
| Name: |
Peptidase S51 |
| Type: |
Family |
| Description: |
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [
]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [].Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [
]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [,
].This group of serine peptidases belong to MEROPS peptidase family S51 (clan PC(S)). The type example being dipeptidase E (alpha-aspartyl dipeptidase) from Escherichia coli. The family contains alpha-aspartyl dipeptidases (dipeptidase E) and cyanophycinases.The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E has been determine at 1.2-A resolution. The structure of this 25kDa enzyme consists of two mixed β-sheets forming a V, flanked by six α-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organisation of the catalytic triad differ from those of the known serine proteases. This enzyme appears to represent a new example of convergent evolution of peptidase activity [
].Alpha-aspartyl dipeptidase hydrolyses dipeptides containing N-terminal aspartate residues, asp-|-xaa. It does not act on peptides with N-terminal Glu, Asn or Gln, nor does it cleave isoaspartyl peptides. In the cyanobacteria, cyanophycinase is an exopeptidase that catalyses the hydrolytic cleavage of multi-l-arginyl-poly-l-aspartic acid (cyanophycin; a water- insoluble reserve polymer) into aspartate-arginine dipeptides. |
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| Protein Domain |
| Name: |
Phosphotransferase system, EIIC component, type 1 |
| Type: |
Domain |
| Description: |
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [
,
] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC [
]. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [
,
,
,
]. According to sequence analyses [
,
,
], the PTS EIIC domain can be divided in five groups:The PTS EIIC type 1 domain is found in the Glucose class of PTS and has an average length of about 80 amino acids. The PTS EIIC type 2 domain is found in the Mannitol class of PTS and has an average length of about 90 amino acids.The PTS EIIC type 3 domain is found in the Lactose class of PTS and has an average length of about 100 amino acids. The PTS EIIC type 4 domain is found in the Mannose class of PTS and has an average length of about 160 amino acids. The PTS EIIC type 5 domain is found in the Sorbitol class of PTS and has an average length of about 190 amino acids. This entry represents the type 1 domain. |
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| Protein Domain |
| Name: |
RNA polymerase sigma factor RpoD, C-terminal |
| Type: |
Domain |
| Description: |
The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [
]. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [
,
].This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [
,
]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [,
]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif []. |
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| Protein Domain |
| Name: |
Peptidase M9A/M9B, collagenase, bacterial |
| Type: |
Family |
| Description: |
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role.
Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases [].This entry represents sequences belonging to peptidase family M9, subfamilies M9A and M9B (microbial collagenase, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the metal ligands and active site residues for members of this family and thermolysin occur in the motif HEXXH [
].Microbial collagenases have been identified from bacteria of both the Vibrio and Clostridium genera. Collagenase is used during bacterial attack to degrade the collagen barrier of the host during invasion. Vibrio bacteria are non-pathogenic, and are sometimes used in hospitals to remove dead tissue from burns and ulcers. Clostridium histolyticum is a pathogen that causes gas gangrene; nevertheless, the isolated collagenase has been used to treat bed sores. Collagen cleavage occurs within the Gly-Xaa-Yaa repeats at Xaa+Gly in Vibrio and at Yaa+Gly bonds in Clostridium collagenase.Analysis of the primary structure of the gene product from Clostridium perfringens has revealed that the enzyme is produced with a stretch of 86 residues that contain a putative signal sequence [
]. Within this stretch is found PLGP, an amino acid sequence typical of collagenase substrates. This sequence may thus be implicated in self-processing of the collagenase []. |
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| Protein Domain |
| Name: |
Alpha 2B adrenoceptor |
| Type: |
Family |
| Description: |
The adrenoceptors (or adrenergic receptors) are rhodopsin-like G protein-coupled receptors that are targets of the catecholamines, especially norepinephrine (noradrenaline) and epinephrine (adrenaline). Many cells possess these receptors, and the binding of a catecholamine to the receptor will generally stimulate the sympathetic nervous system, effect blood pressure, myocardial contractile rate and force, airway reactivity, and a variety of metabolic and central nervous system functions. The clinical uses of adrenergic compounds are vast. Agonists and antagonists interacting with adrenoceptors have proved useful in the treatment of a variety of diseases, including hypertension, angina pectoris, congestive heart failure, asthma, depression, benign prostatic hypertrophy, and glaucoma. These drugs are also useful in several other therapeutic situations including shock, premature labour and opioid withdrawal, and as adjuncts to general anaesthetics.There are three classes of adrenoceptors, based on their sequence similarity, receptor pharmacology and signalling mechanisms [
]. These three classes are alpha 1 (a Gq coupled receptor), alpha 2 (a Gi coupled receptor) and beta (a Gs coupled receptor), and each can be further divided into subtypes []. The different subtypes can coexist in some tissues, but one subtype normally predominates.There are three subtpyes of alpha 2 adrenoceptors (2A-C). The receptors are usually found presynaptically, where they inhibit the release of noradrenaline, and thus serve as an important receptor in the negative feedback control of noradrenaline release [
,
,
,
]. Postsynaptic alpha 2 receptors are located on liver cells, platelets, and the smooth muscle of blood vessels. Activation of the receptors causes platelet aggregation [], blood vessel constriction [,
] and constriction of vascular smooth muscle []. Agonists of alpha 2 adrenergic receptors are frequently used in veterinary anaesthesia, where they affect sedation, muscle relaxation and analgesia through their effects on the CNS []. Alpha 2 adrenoceptors are coupled through the Gi/Go mechanism, inhibiting adenylate cyclase activity and downregulating cAMP formation. This entry represents the alpha 2B receptor. It is found in the kidney, brain,
and spinal cord, along with the other alpha 2 subtypes. However, it is the onlysubtype to be found in the heart and liver. Peripheral tissues, predominantly
express the alpha 2A and 2B subtypes, with little alpha 2C. This is in contrastto the CNS, where alpha 2A and 2C are predominantly expressed, with little
alpha 2B [,
]. |
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| Protein Domain |
| Name: |
Chloride channel ClC-4 |
| Type: |
Family |
| Description: |
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport [
].The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata [
], and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains []. Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm [].A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl- channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia [
]. Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms of inherited kidney stone disease []. These mutations have been demonstrated to reduce or abolish CLC function.CLC-4 was initially identified as a putative member of the CLC family
following mappingof the human Xp22.3 chromosome region [
]. Together withCLC-5 and CLC-3, it forms a distinct branch of the CLC gene family. Initial
expression studies of CLC-4 did not yield measurable Cl-currents; however,
recent studies of human CLC-4 have revealed that it gives rise to Cl-currents that rapidly activate at positive voltages, and are sensitive toextracellular pH, with currents decreasing when pH falls below 6.5 [
]. |
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| Protein Domain |
| Name: |
Chloride channel ClC-0 |
| Type: |
Family |
| Description: |
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport [
].The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata [
], and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains []. Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm [].A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl- channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia [
]. Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms of inherited kidney stone disease []. These mutations have been demonstrated to reduce or abolish CLC function.CLC-0 is the principal Cl
-channel of the electric organ of Torpedo
species. These marine electric rays generate high voltage pulses (to stuntheir prey) by the concerted action of Cl
-channels and nicotinic acetylcholine receptors, in specialised cells known as electrocytes. The
properties of the CLC-0 channel (consisting of 805-809 amino acids) havebeen extensively studied after reconstitution into lipid bilayers. It has
a peculiar double-barrelled structure, appearing to have two identical ionpores that close and open independently, but which can be also closed
together by another common gate. Further evidence also suggests it mayfunction as a homodimer [
,
]. |
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| Protein Domain |
| Name: |
Chloride channel ClC-2 |
| Type: |
Family |
| Description: |
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport [
].The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata [
], and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains [
]. Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm [].A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl- channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia [
]. Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms of inherited kidney stone disease []. These mutations have been demonstrated to reduce or abolish CLC function.CLC-2 is a member of the CLC family that is ubiquitously expressed in
mammalian tissues. It is 898 amino acid residues in length (human isoform)and shows ~50% amino acid identity to CLC-1, to which it is most closely
related []. The channel is normally closed at physiological membranepotentials, but can be activated by rather strong hyperpolarisation.
However, it is activated by cell swelling, suggesting a role for it in cellvolume regulation. It is also activated by acidic extracellular pH; the
region of the molecule (near the N terminus) that imparts sensitivity toboth cell swelling and extracellular pH has been elucidated [
]. |
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| Protein Domain |
| Name: |
Nuclear hormone receptor, ligand-binding domain |
| Type: |
Domain |
| Description: |
Nuclear receptors (NRs), such as the receptors for steroids and thyroid hormones, retinoids and vitamin D3, are one of the most abundant classes of transcriptional regulators in animals (metazoans). They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. The most prominent feature differentiating them from other transcription factors is their capacity to bind small hydrophobic molecules specifically. These ligands constitute regulatory signals, which modify the NR transcriptional activity through conformational changes. Prototypical NRs share a common structural organisation with a variable N-terminal domain that contains a constitutively active activation function (AF)-1, a conserved DNA- binding domain (DBD) consisting of two zinc fingers, a linker region, and a C-terminal ligand-binding domain (LBD), also called HOLI domain [
,
,
].The NR LBD plays a crucial role in ligand-mediated NR activity. In addition to its role is ligand recognition, the LBD also contains
a ligand-dependent AF-2. Conformational changes in AF-2 induced by various ligands can modulate interactions with conserved motifs of coregulatoryproteins. Specifically, the binding of ligands to the LBD determines the recruiting of transcriptional coregulators which triggers induction or repression of target genes. The coregulators include coactivators like the p160 factors also referred to as the steroid receptor coactivators (SRC) family, and corepressors such as SMART (silencing mediator for retinoid and thyroid hormone receptors) and N-CoR (nuclear corepressor) [
,
,
,
].The overall structure of NR LBD is composed of about 11-13 α-helices that are arranged into a three-layer antiparallel α-helical sandwich with the three long helices (helices 3, 7, and 10) forming the two outer layers. The middle layer of helices (helices 4, 5, 8 and 9) is present only in the top half of the domain but is missing from the bottom half, thereby creating a cavity, so called ligand-binding pocket, for ligand binding in most receptors. The bound ligands stabilize the NR conformation through direct contacts with multiple structural elements including helices H3, H5, H6, H7, H10, and the loop proceeding the AF-2 helix. The C-terminal activation region also forms an α-helix (AF-2), which can adopt multiple conformation
depending on the nature of the bound ligand. Helices 3,4 and 12 enclose a shallow hydrophobic groove which is the site for coregulator binding. Despite the conserved fold of NR LBDs, the ligand-binding pocket is the least conserved region among different NR LBDs [,
,
]. |
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| Protein Domain |
| Name: |
Estrogen receptor |
| Type: |
Family |
| Description: |
Steroid or nuclear hormone receptors (NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands [
]. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [,
]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.The oestrogen receptors (ERs) are steroid or nuclear hormone receptors that act as transcription regulators involved in diverse physiological functions. Oestrogen receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. The ER consists of three functional and structural domains: an N-terminal modulatory domain, a highly conserved DNA-binding domain that recognises specific sequences (
), and a C-terminal ligand-binding domain (
).
The N-terminal modulatory domain spans the first 180 residues and contains the activation function 1 (AF1) region. Nuclear receptors differ considerably with respect to AF1 activity and regulation, as it is a poorly conserved region [
]. There is another activation function region, namely AF2, which resides in the C-terminal end of the ligand-binding domain. Transcription activation is facilitated by both AF1 and AF2, which appear to act synergistically in the ER complex [,
]. For example, the ER can recruit TIF2 (transcription intermediary factor 2) via the AF1 and AF2 regions, whose synergistic action results in the activation of transcription. |
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| Protein Domain |
| Name: |
Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related |
| Type: |
Family |
| Description: |
Members of this group function in ethanolamine [
,
] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbor these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively.
The EutE protein is a putative CoA-dependent aldehyde dehydrogenase () proposed to catalyse the second step of the coenzyme B12 (adenosylcobalamin, AdoCbl)-dependent pathway of ethanolamine degradation [
], converting acetaldehyde into acetyl-CoA. Mutational analysis has shown that EutE is involved in ethanolamine degradation [] and, on the basis of sequence similarity to AdhE alcohol dehydrogenase/acetaldehyde dehydrogenase () and aldehyde dehydrogenases, it is believed to be an acetaldehyde dehydrogenase. Ethanolamine degradation pathway enzymes, including EutE, are encoded by the eut operon [
,
,
].PduP is encoded by the propanediol (pdu) operon and is involved in propanediol utilization [
]. The pathway of 1,2-propanediol degradation starts with the conversion of 1,2-propanediol to propionaldehyde by an AdoCbl-dependent propanediol dehydratase. Then, propionaldehyde is oxidized by propionaldehyde dehydrogenase to propionyl-CoA. Subsequently, propionyl-CoA can be metabolized either aerobically into pyruvate (presumably in three steps) or anaerobically into propionate (presumably in two steps) []. PduP is closely related to EutE and, therefore, has been predicted to be a CoA-dependent aldehyde dehydrogenase used in the pdu pathway for the conversion of propionaldehyde to propionyl-CoA [].Propanediol utilization is thought to be important for natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [
,
]. More than 1% of the Salmonella enterica genome is devoted to the utilization of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilization genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect []. The pdu operon is contiguous and coregulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [,
].On the basis of sequence analysis, it has been suggested that the pdu/cob genes were lost by a common ancestor of Escherichia coli and Salmonella enterica and were reintroduced as a single fragment into the Salmonella lineage by a single horizontal gene transfer event from an exogenous source [
,
]. |
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|
| Protein Domain |
| Name: |
DNA-directed RNA polymerase, subunit beta-prime, bacterial type |
| Type: |
Family |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw"is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit [
]. |
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| Protein Domain |
| Name: |
Cobalamin-binding domain superfamily |
| Type: |
Homologous_superfamily |
| Description: |
The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [
,
,
]. Proteins containing the cobalamin-binding domain include:Animal and prokaryotic methionine synthase (
), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine.
Animal and prokaryotic methylmalonyl-CoA mutase (
), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle.
Prokaryotic lysine 5,6-aminomutase (
).
Prokaryotic glutamate mutase (
) [
].Prokaryotic methyleneglutarate mutase (
).
Prokaryotic isobutyryl-CoA mutase (
).
The core structure of the cobalamin-binding domain is characterised by a five-stranded α/β (Rossmann) fold, which consists of 5 parallel β-sheets surrounded by 4-5 α-helices in three layers (α/β/α) [
]. Upon binding cobalamin, important elements of the binding site appear to become structured, including an α-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices [].In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (
); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (
) [
]. |
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| Protein Domain |
| Name: |
Haem peroxidase, animal-type |
| Type: |
Family |
| Description: |
Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions.Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, a number of animal haem peroxidases can be categorised as members of a superfamily: myeloperoxidase (MPO); eosinophil peroxidase (EPO); lactoperoxidase (LPO); thyroid peroxidase (TPO); prostaglandin H synthase (PGHS); and peroxidasin [
,
,
]. MPO plays a major role in the oxygen-dependent microbicidal system of neutrophils. EPO from eosinophilic granulocytes participates in immunological reactions, and potentiates tumor necrosis factor (TNF) production and hydrogen peroxide release by human monocyte-derived macrophages [
,
]. In the main, MPO (and possibly EPO) utilises Cl-ions and H
2O
2to form hypochlorous acid (HOCl), which can effectively kill bacteria or parasites. In secreted fluids, LPO catalyses the oxidation of thiocyanate ions (SCN
-) by H
2O
2, producing the weak oxidising agent hypothiocyanite (OSCN
-), which has bacteriostatic activity [
]. TPO uses I-ions and H
2O
2to generate iodine, and plays a central role in the biosynthesis of thyroid hormones T(3) and T(4).
To date, the 3D structures of MPO and PGHS have been reported. MPO is a homodimer: each monomer consists of a light (A or B) and a heavy (C or D) chain resulting from post-translational excision of 6 residues from the common precursor. Monomers are linked by a single inter-chain disulphide. Each monomer includes a bound calcium ion [
]. PGHS exists as a symmetric dimer, each monomer of which consists of 3 domains: an N-terminal epidermal growth factor (EGF) like module; a membrane-binding domain; and a large C-terminal catalytic domain containing the cyclooxygenase and the peroxidase active sites. The catalytic domain shows striking structural similarity to MPO. The cyclooxygenase active site, which catalyses the formation of prostaglandin G2 (PGG2) from arachidonic acid, resides at the apex of a long hydrophobic channel, extending from the membrane-binding domain to the centre of the molecule. The peroxidase active site, which catalyses the reduction of PGG2 to PGH2, is located on the other side of the molecule, at the haem binding site []. Both MPO and the catalytic domain of PGHS are mainly α-helical, 19 helices being identified as topologically and spatially equivalent; PGHS contains 5 additional N-terminal helices that have no equivalent in MPO. In both proteins, three Asn residues in each monomer are glycosylated. |
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| Protein Domain |
| Name: |
P2X purinoreceptor 7, intracellular domain |
| Type: |
Domain |
| Description: |
P2X purinoceptors are cell membrane ion channels, gated by adenosine 5'-triphosphate (ATP) and other nucleotides; they have been found to be widely expressed on mammalian cells, and, by means of their functional properties, can be differentiated into three sub-groups. The first group is almost equally well activated by ATP and its analogue alpha,betamethylene-ATP, whereas, the second group is not activated by the latter compound. A third type of receptor (also called P2Z) is distinguished by the fact that repeated or prolonged agonist application leads to the opening of much larger pores, allowing large molecules to traverse the cell membrane. This increased permeability rapidly leads to cell death, and lysis.Molecular cloning studies have identified seven P2X receptor subtypes, designated P2XR1-P2XR7, however, P2X1R, P2X2R, P2X3R, P2X4R, and P2X7R are functional [
]. These receptors are proteins that share 35-48% amino acid identity, and possess two putative transmembrane (TM) domains, separated by a long (~270 residues) intervening sequence, which is thought to form an extracellular loop. Around 1/4 of the residues within the loop are invariant between the cloned subtypes, including 10 characteristic cysteines.Studies of the functional properties of heterologously expressed P2X receptors, together with the examination of their distribution in native tissues, suggests they likely occur as both homo- and hetero multimers in vivo [
,
]. Stimulation of these receptors induces changes in intracellular ion homeostasis leading to multiple key responses crucial for initiation, propagation, and resolution of inflammation []. The P2X7 subtype has an important role in the activation of lymphocyte, granulocyte, macrophage and dendritic cell responses and, therefor, it may be a promising target for anti-inflammatory therapies.This entry represents the intracellular domain found at the C-terminal domain of P2X7 (also known as P2Z receptor). P2X7 receptor has different functional properties from those of P2X1-P2X6. Key properties of the current produced are little rectification or desensitisation, and strong potentiation of responses when the concentration of extracellular Ca2 and/or Mg2 are reduced. It is also found to be relatively insensitive to ATP. In certain studies, prolonged activation of expressed P2X7 receptors causes cell permeabilization, and lysis. This domain is critical for the receptor to initiate apoptosis and not undergo desensitization. It shows a globular structure and is shaped like a wedge with three β-strands forming an antiparallel β-sheet followed by eight α-helices separated by loops that form a helical bundle [
]. |
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| Protein Domain |
| Name: |
Gastric H+/K+-transporter P-type ATPase, N-terminal |
| Type: |
Domain |
| Description: |
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.P-ATPases (also known as E1-E2 ATPases) ([intenz:3.6.3.-]) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H+, Na
+, K
+, Mg
2+, Ca
2+, Ag
+and Ag
2+, Zn
2+, Co
2+, Pb
2+, Ni
2+, Cd
2+, Cu
+and Cu
2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.
This entry represents the N-terminal domain found in gastric H+/K+-transporter ATPases. This domain adopts an α-helical conformation under hydrophobic conditions. The domain contains tyrosine residues, phosphorylation of which regulates the function of the ATPase. Additionally, the domain also interacts with various structural proteins, including the spectrin-binding domain of ankyrin III [
]. |
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•
|
| Protein Domain |
| Name: |
Haem peroxidase domain superfamily, animal type |
| Type: |
Homologous_superfamily |
| Description: |
Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions.Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, a number of animal haem peroxidases can be categorised as members of a superfamily: myeloperoxidase (MPO); eosinophil peroxidase (EPO); lactoperoxidase (LPO); thyroid peroxidase (TPO); prostaglandin H synthase (PGHS); and peroxidasin [,
,
]. MPO plays a major role in the oxygen-dependent microbicidal system of neutrophils. EPO from eosinophilic granulocytes participates in immunological reactions, and potentiates tumor necrosis factor (TNF) production and hydrogen peroxide release by human monocyte-derived macrophages [
,
]. In the main, MPO (and possibly EPO) utilises Cl-ions and H
2O
2to form hypochlorous acid (HOCl), which can effectively kill bacteria or parasites. In secreted fluids, LPO catalyses the oxidation of thiocyanate ions (SCN
-) by H
2O
2, producing the weak oxidising agent hypothiocyanite (OSCN
-), which has bacteriostatic activity [
]. TPO uses I-ions and H
2O
2to generate iodine, and plays a central role in the biosynthesis of thyroid hormones T(3) and T(4).
To date, the 3D structures of MPO and PGHS have been reported. MPO is a homodimer: each monomer consists of a light (A or B) and a heavy (C or D) chain resulting from post-translational excision of 6 residues from the common precursor. Monomers are linked by a single inter-chain disulphide. Each monomer includes a bound calcium ion [
]. PGHS exists as a symmetric dimer, each monomer of which consists of 3 domains: an N-terminal epidermal growth factor (EGF) like module; a membrane-binding domain; and a large C-terminal catalytic domain containing the cyclooxygenase and the peroxidase active sites. The catalytic domain shows striking structural similarity to MPO. The cyclooxygenase active site, which catalyses the formation of prostaglandin G2 (PGG2) from arachidonic acid, resides at the apex of a long hydrophobic channel, extending from the membrane-binding domain to the centre of the molecule. The peroxidase active site, which catalyses the reduction of PGG2 to PGH2, is located on the other side of the molecule, at the haem binding site []. Both MPO and the catalytic domain of PGHS are mainly α-helical, 19 helices being identified as topologically and spatially equivalent; PGHS contains 5 additional N-terminal helices that have no equivalent in MPO. In both proteins, three Asn residues in each monomer are glycosylated. |
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| Protein Domain |
| Name: |
Conotoxin-I, conserved site |
| Type: |
Conserved_site |
| Description: |
Cone snail toxins, conotoxins, are small peptides with disulphide connectivity, that target ion-channels or G-protein coupled receptors. Based on the number and pattern of disulphide bonds and biological activities, conotoxins can be classified into several families [
]. Omega, delta and kappa families of conotoxins have a knottin or inhibitor cystine knot scaffold. The knottin scaffold is a very special disulphide through disulphide knot, in which the III-VI disulphide bond crosses the macrocycle formed by two other disulphide bonds (I-IV and II-V) and the interconnecting backbone segments, where I-VI indicates the six cysteine residues starting from the N terminus; for further information see the KNOTTIN database (https://www.dsimb.inserm.fr/KNOTTIN/).Conotoxins represent a unique arsenal of neuropharmacologically active peptides that have been evolutionarily tailored to afford unprecedented and exquisite selectivity for a wide variety of ion-channel subtypes. The toxins derived from cone snails are currently being investigated for the treatment of chronic pain, epilepsy, cardiovascular diseases, psychiatric and movement disorders, spasticity, cancer, stroke as well as an anesthetic agent. Several potential analgesic and anti-inflammatory peptides from conotoxin families have been identified and patented [,
], e.g. Conus magus (Magus cone) (Magician's cone snail) omega-conotoxin MVIIa (Ziconotide), which is used for the treatment of chronic pain, Conus catus (Cat cone) omega-conotoxin CVID, which is tested for treating severe morphine-resistant pain stress, and Conus geographus (Geography cone) (Nubecula geographus) omega-conotoxin GVIA, which may exert antagonistic effects against beta-endorphin induced anti-nociception.
The disulphide bonding network as well as specific amino acids in inter-cysteine loops provide specificity of conotoxins []. The cysteine arrangement [C-C-CC-C-C]is the same for omega and delta families, which belong to the O-superfamily. The omega conotoxins are calcium channel blockers, whereas delta conotoxins delay the inactivation of sodium channels [
]. The M-superfamily Mu conotoxins have two types of cysteine arrangement [CC-C-C-CC]and [CC-C-C-C-C], but knottin scaffold is not observed. Mu conotoxins target the voltage-gated sodium channels [] and are useful probes for investigating voltage-dependent sodium channels of excitable tissues []. Alpha conotoxins belong to the A-superfamily and have two types of cysteine arrangement [CC-C-C]and [CCC-C-C-C] []. Alpha conotoxins are competitive nicotinic acetylcholine receptor antagonists. The I-superfamily of conotoxins is characterised by a pattern of eight cysteine residues that form four disulphide bridges. The arrangement of cysteine residues is similar to the Janus-faced atracotoxin peptides characterised from spider venoms [,
]. |
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| Protein Domain |
| Name: |
DNA ligase, ATP-dependent, N-terminal |
| Type: |
Domain |
| Description: |
DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (
), the other NAD (
), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [
,
].Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [,
]. This domain is found in many but not all ATP-dependent DNA ligase enzymes (
). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (
), and in Saccharomyces cerevisiae (Baker's yeast) (
), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (
) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation [
]. |
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|
| Protein Domain |
| Name: |
Cobalamin (vitamin B12)-binding domain |
| Type: |
Domain |
| Description: |
The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [
,
,
]. Proteins containing the cobalamin-binding domain include:Animal and prokaryotic methionine synthase (
), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine.
Animal and prokaryotic methylmalonyl-CoA mutase (
), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle.
Prokaryotic lysine 5,6-aminomutase (
).
Prokaryotic glutamate mutase (
) [
].Prokaryotic methyleneglutarate mutase (
).
Prokaryotic isobutyryl-CoA mutase (
).
The core structure of the cobalamin-binding domain is characterised by a five-stranded α/β (Rossmann) fold, which consists of 5 parallel β-sheets surrounded by 4-5 α-helices in three layers (α/β/α) [
]. Upon binding cobalamin, important elements of the binding site appear to become structured, including an α-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices [].In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (
); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (
) [
]. |
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|
| Protein Domain |
| Name: |
Nitrile hydratase, alpha subunit |
| Type: |
Family |
| Description: |
Nitrile hydratases (
) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [
,
]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [,
]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols.Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia [
].The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase [
].This entry represents the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations. |
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|
| Protein Domain |
| Name: |
Phosphotransferase system, EIIC component, type 2 |
| Type: |
Domain |
| Description: |
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [
,
] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [
,
,
,
]. According to sequence analyses [
,
,
], the PTS EIIC domain can be divided in five groups:The PTS EIIC type 1 domain is found in the Glucose class of PTS and has an average length of about 80 amino acids. The PTS EIIC type 2 domain is found in the Mannitol class of PTS and has an average length of about 90 amino acids.The PTS EIIC type 3 domain is found in the Lactose class of PTS and has an average length of about 100 amino acids. The PTS EIIC type 4 domain is found in the Mannose class of PTS and has an average length of about 160 amino acids. The PTS EIIC type 5 domain is found in the Sorbitol class of PTS and has an average length of about 190 amino acids. This entry represents the type 2 domain. |
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|
| Protein Domain |
| Name: |
DNA-directed RNA polymerase, beta subunit, external 1 domain |
| Type: |
Domain |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This entry represents a domain in prokaryotic polymerases that spans the gap between domains 4 and 5 of the protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [
]. |
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|
| Protein Domain |
| Name: |
DNA-directed RNA polymerase, 30-40kDa subunit, conserved site |
| Type: |
Conserved_site |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 12 polypeptides.
It has been shown [,
,
,
] that small subunits of about 30 to 40kDa found in archebacterial and all three types of eukaryotic polymerases are highly conserved. Subunits known to belong to this family are:Saccharomyces cerevisiae RPC5 subunit (or RPC40) from RNA polymerases I and III.Mammalian RPA40 from RNA polymerase I.S. cerevisiae RPB3 subunit from RNA polymerase II.Schizosaccharomyces pombe rpb3 subunit from RNA polymerase II.Mammalian RPB3 (or RPB33) (gene POLR2C) from RNA polymerase II.Conjugation stage-specific protein cnjC from Tetrahymena thermophila, which may be a stage-specific RNA polymerase subunit.Archaebacterial RNA polymerase subunit D (gene rpoD). |
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| Protein Domain |
| Name: |
Diaminopimelate epimerase, active site |
| Type: |
Active_site |
| Description: |
Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see [
].The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria [
]. The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants [].This entry represents diaminopimelate epimerase (
), which catalyses the isomerisation of L,L-dimaminopimelate to meso-DAP in the biosynthetic pathway leading from aspartate to lysine. It is a member of the broader family of PLP-independent amino acid racemases. This enzyme is a monomeric protein of about 30kDa consisting of two domains which are homologus in structure though they share little sequence similarity [
]. Each domain consists of mixed β-sheets which fold into a barrel around the central helix. The active site cleft is formed from both domains and contains two conserved cysteines thought to function as the acid and base in the catalytic reaction []. Other PLP-independent racemases such as glutamate racemase have been shown to share a similar structure and mechanism of catalysis.This signature pattern covers a region surrounding the first of the two active site cysteines. |
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| Protein Domain |
| Name: |
RNA polymerase Rpb4/RPC9, core |
| Type: |
Domain |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.A major role in the regulation of eukaryotic protein-coding genes is played by the gene-specific transcriptional regulators, which recruit the RNA polymerase II holoenzyme to the specific promoter. The Rpb4 and Rpb7 subunits of yeast RNA polymerase II form a heterodimeric complex essential for promoter-directed transcription initiation. The Rpb4-Rpb7 complex is not required for stable recruitment of polymerase to active preinitiation complexes, suggesting that Rpb4-Rpb7 mediates an essential step subsequent to promoter binding [
].This entry represents a domain present in DNA-directed RNA polymerase II subunit Rpb4 and DNA-directed RNA polymerase III subunit RPC9. |
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| Protein Domain |
| Name: |
DNA topoisomerase I, bacterial-type |
| Type: |
Family |
| Description: |
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo IB; eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB [
]. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [,
]. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases [,
].This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I [
]. Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5'-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand []. Topoisomerase I require Mg2+ as a cofactor for catalysis to take place. |
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| Protein Domain |
| Name: |
DNA topoisomerase, type IA, active site |
| Type: |
Active_site |
| Description: |
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks [
]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [,
]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
; topoisomerases II, IV and VI) break double-strand DNA [
].Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo IB; eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB [
]. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [,
]. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases [,
].DNA topoisomerase I (
) is one of the two types of enzyme that catalyze the interconversion of topological DNA isomers [
,
,
]. Type I topoisomerases act by catalyzing the transient breakage of DNA, one strand at a time, and the subsequent rejoining of the strands. When a prokaryotic type I topoisomerase breaks a DNA backbone bond, it simultaneously forms a protein-DNA link where the hydroxyl group of a tyrosine residue is joined to a 5'-phosphate on DNA, at one end of the enzyme-severed DNA strand. Prokaryotic organisms, such as Escherichia coli, have two type I topoisomerase isozymes: topoisomerase I (gene topA) and topoisomerase III (gene topB). Eukaroytes also contain homologues of prokaryotic topoisomerase III. The signature pattern of this entry contains a number of conserved residues and spans the active site tyrosine. |
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•
|
| Protein Domain |
| Name: |
Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit |
| Type: |
Family |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.A RNAP component of 14 to 18kDa is shared by all three forms of eukaryotic RNA polymerases and has been sequenced in budding yeast (gene rpb6 or rpo26), in fission yeast (gene rpb6 or rpo15), in human and in African swine fever virus (ASFV) [
]. It is evolutionary related [] to archaeal Rpo6 subunit (gene rpoK or rpo6). The archaeal protein is colinear with the C-terminal part of the eukaryotic subunit.This family includes both eukaryotic Rpb6 and archaeal Rpo6 subunit, also known as subunit K, as well as the evolutionary related RPB6 homologue from ASFV [
]. |
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| Protein Domain |
| Name: |
Phenylalanyl-tRNA synthetase, class IIc, mitochondrial |
| Type: |
Family |
| Description: |
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].Phenylalanyl-tRNA synthetase (
) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit
(pheT gene) can be designated as alpha (E. coli) or beta (see and
). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [
].This family describes the mitochondrial phenylalanyl-tRNA synthetases. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. |
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| Protein Domain |
| Name: |
Glutamine amidotransferase type 2 domain |
| Type: |
Domain |
| Description: |
A large group of biosynthetic enzymes are able to catalyse the removal of the ammonia group from glutamine and then to transfer this group to a substrate to form a new carbon-nitrogen group. This catalytic activity is known as glutamine amidotransferase (GATase) [
]. The GATase domain exists either as a separate polypeptidic subunit or as part of a larger polypeptide fused in different ways to a synthase domain. On the basis of sequence similarities two classes of GATase domains have been identified [,
]: class-I (also known as trpG-type or triad) and class-II (also known as purF-type or Ntn). Class-II (or type 2) GATase domains have been found in the following enzymes:Amido phosphoribosyltransferase (glutamine phosphoribosylpyrophosphate amidotransferase). An enzyme which catalyses the first step in purine biosynthesis, the transfer of the ammonia group of glutamine to PRPP to form 5-phosphoribosylamine (gene purF in bacteria, ADE4 in yeast).Glucosamine--fructose-6-phosphate aminotransferase. This enzyme catalyses a key reaction in amino sugar synthesis, the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine (gene glmS in Escherichia coli, nodM in Rhizobium, GFA1 in yeast).Asparagine synthetase (glutamine-hydrolyzing). This enzyme is responsible for the synthesis of asparagine from aspartate and glutamine.Glutamate synthase (gltS), an enzyme which participates in the ammonia assimilation process by catalysing the formation of glutamate from glutamine and 2-oxoglutarate. Glutamate synthase is a multicomponent iron-sulphur flavoprotein and three types occur which use a different electron donor: NADPH-dependent gltS (large chain), ferredoxin-dependent gltS and NADH-dependent gltS [
].The active site is formed by a cysteine present at the N-terminal extremity of the mature form of all these enzymes [
,
,
,
]. Two other conserved residues, Asn and Gly, form an oxyanion hole for stabilisation of the formed tetrahedral intermediate. An insert of ~120 residues can occur between the conserved regions []. In some class-II GATases (for example in Bacillus subtilis or chicken amido phosphoribosyltransferase) the enzyme is synthesised with a short propeptide which is cleaved off post-translationally by a proposed autocatalytic mechanism. Nuclear-encoded Fd-dependent gltS have a longer propeptide which may contain a chloroplast-targeting peptide in addition to the propeptide that is excised on enzyme activation.The 3-D structure of the GATase type 2 domain forms a four layer alpha/beta/beta/alpha architecture which consists of a fold similar to the N-terminal nucleophile (Ntn) hydrolases. These have the capacity for nucleophilic attack and the possibility of autocatalytic processing. The N-terminal position and the folding of the catalytic Cys differ strongly from the Cys-His-Glu triad which forms the active site of GATases of type 1. |
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| Protein Domain |
| Name: |
Pseudouridine synthase, RsuA/RluA-like |
| Type: |
Domain |
| Description: |
Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are [,
]:Pseudouridine synthase I, TruA.Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit) and TruC [
].RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [
,
]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site.RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine:RluB modifies uracil-2605.RluC modifies uracil-955, U-2504, and U-2580.RluD modifies uracil-1911, U-1915, and U-1917.RluE modifies uracil-3457.RluF modifies uracil-2604, and to a lesser extent U-2605.RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [
,
]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. |
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| Protein Domain |
| Name: |
Mononegavirales RNA-directed RNA polymerase catalytic domain |
| Type: |
Domain |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents the catalytic domain RNA-directed RNA polymerase. |
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| Protein Domain |
| Name: |
Nicotinic acetylcholine receptor |
| Type: |
Family |
| Description: |
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [
,
]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [
].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [
].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [
].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [
].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [
,
].Nicotinic acetylcholine receptors are ligand-gated ion channels that mediate signal transduction at the post-synaptic membrane of cholinergic synapses, such as the neuromuscular junction [
]. They belong to a family of neurotransmitter-gated receptors, including glycine, gamma-aminobutyric-acid (GABA), serotonin 5HT3 receptors. These are oligomeric transmembrane (TM) complexes (pentamers of 2 alpha and 1 beta, 1 gamma and 1 delta subunit) that contain a central channel, which transiently opens upon binding of a specific neurotransmitters. Their sequences are related and share the same topology: each has an extracellular, glycosylated N-terminal ligand-binding domain; 3 hydrophobic TM regions, which form the channel; a hydrophilic cytoplasmic domain; followed by a fourth putative TM region []. The nicotinic receptor ligand binding domain is a specialised pocket of aromatic and hydrophobic residues formed at interfaces between protein subunits that changes conformation to convert agonist binding into gating of an intrinsic ion channel []. The expression of acetylcholine receptors is activated during muscle
differentiation and upon denervation of adult muscle []. Receptor function is regulated by phosphorylation and dephosphorylation by kinases and phosphatases present in the post-synaptic membranes []. Most of the phosphorylation sites are located in the major intracellular loop between the third and fourth TM regions and are closely spaced. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, phytoreovirus |
| Type: |
Family |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [
].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents a RNA-directed RNA polymerase, Phytoreovirus type. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, orthobunyavirus |
| Type: |
Family |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents a RNA-directed RNA polymerase, Orthobunyavirus type. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, phlebovirus |
| Type: |
Family |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents a predicted RNA-directed RNA polymerase of Phleboviruses. |
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| Protein Domain |
| Name: |
5-Hydroxytryptamine 2C receptor |
| Type: |
Family |
| Description: |
5-hydroxytryptamine (5-HT) or serotonin, is a neurotransmitter that it is primarily found in the gastrointestinal (GI) tract, platelets, and in the central nervous system (CNS). It is implicated in a vast array of physiological and pathophysiological pathways. Receptors for 5-HT mediate both excitatory and inhibitory neurotransmission, and modulate the release of many neurotransmitters including glutamate, GABA, dopamine, epinephrine/norepinephrine, and acetylcholine, as well as many hormones, including oxytocin, prolactin, vasopressin and cortisol. In the CNS, 5-HT receptors can influence various neurological processes, such as aggression, anxiety and appetite and, as a, result are the target of a variety of pharmaceutical drugs, including many antidepressants, antipsychotics and anorectics [
]. The 5-HT receptors are grouped into a number of distinct subtypes, classified according to their antagonist susceptibilities and their affinities for 5-HT. With the exception of the 5-HT3 receptor, which is a ligand-gated ion channel [
], all 5-HT receptors are members of the rhodopsin-like G protein-coupled receptor family [], and they activate an intracellular second messenger cascade to produce their responses. The 5-HT2 receptors mediate many of the central and peripheral physiologic functions of 5-hydroxytryptamine. The original 5HT2 receptor (now renamed as the 5-HT2A receptor) was initially classified according to its ability to display micromolar affinity for 5-HT, to be labelled with [3H]spiperone and by its susceptibility to 5-HT antagonists. At least 3 members of the 5HT2 receptor subfamily exist (5-HT2A, 5-HT2B, 5-HT2C), all of which share a high degree of sequence similarity and couple to Gq/G11 to stimulate the phosphoinositide pathway and elevate cytosolic calcium. Cardiovascular effects include contraction of blood vessels and shape changes in platelets; central nervous system effects include neuronal sensitisation to tactile stimuli and mediation of some of the effects of phenylisopropylamine hallucinogens. 5-HT2 receptors display functional selectivity in which the same agonist in different cell types or different agonists in the same cell type can differentially activate multiple, distinct signalling pathways [
].The distribution of 5-HT2C is limited to the CNS and choroid plexus [
]. Activation of the receptor has been shown to exert an inhibitory influence upon frontocortical dopaminergic and adrenergic, but not serotonergic transmission and, in part, to play a role in neuroendocrine function [,
,
,
]. Additional characteristic behavioural responses attributed to 5-HT2C receptor activation include hypoactivity [,
,
], feeding [,
,
,
,
], reproductive behaviour [] and thermoregulation []. Chronic treatment with antipsychotic drugs that are 5-HT2 antagonists results in downregulation of both 5-HT2A and 5-HT2C receptors, as does chronic treatment with SSRIs and 5-HT agonists []. However, chronic SSRI treatment may increase 5-HT2C expression, specifically in the choroid plexus []. |
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| Protein Domain |
| Name: |
5-Hydroxytryptamine 6 receptor |
| Type: |
Family |
| Description: |
5-hydroxytryptamine (5-HT) or serotonin, is a neurotransmitter that it is primarily found in the gastrointestinal (GI) tract, platelets, and in the central nervous system (CNS). It is implicated in a vast array of physiological and pathophysiological pathways. Receptors for 5-HT mediate both excitatory and inhibitory neurotransmission, and modulate the release of many neurotransmitters including glutamate, GABA, dopamine, epinephrine/norepinephrine, and acetylcholine, as well as many hormones, including oxytocin, prolactin, vasopressin and cortisol. In the CNS, 5-HT receptors can influence various neurological processes, such as aggression, anxiety and appetite and, as a, result are the target of a variety of pharmaceutical drugs, including many antidepressants, antipsychotics and anorectics [
]. The 5-HT receptors are grouped into a number of distinct subtypes, classified according to their antagonist susceptibilities and their affinities for 5-HT. With the exception of the 5-HT3 receptor, which is a ligand-gated ion channel [
], all 5-HT receptors are members of the rhodopsin-like G protein-coupled receptor family [], and they activate an intracellular second messenger cascade to produce their responses. 5-HT6 receptors are positively coupled to adenylyl cyclase. They are expressed almost exclusively in the brain [
] and prominently expressed in the caudate nucleus [,
,
]. Based on their abundance in extrapyramidal, limbic and cortical regions of the brain, it has been suggested that the 5-HT6 receptors play a role in functions like motor control, emotionality, cognition and memory [,
,
]. Blockade of central 5-HT6 receptors has been shown to increase glutamatergic and cholinergic neurotransmission in various brain areas [,
,
], whereas activation enhances GABAergic signaling in a widespread manner []. Antagonism of 5-HT6 receptors also facilitates dopamine and norepinephrine release in the frontal cortex [,
], while stimulation has the opposite effect []. 5-HT6 receptors have high affinity for several typical and atypical antipsychotic agents, including clozapine, olanzapine fluperlapine and seroquel [
,
]. This attribute has led to speculation of potential involvement of the 5-HT6 receptor in the pathogenesis of psychiatric disorders. 5-HT6 receptor antagonists have been demonstrated to be active in rodent models of depression, anxiety and obsessive-compulsive disorder, and such agents may be useful treatments for these conditions [,
]. There is also some evidence of enhanced retention of spatial learning following treatment with such compounds [,
]. However, it should be noted that the rodent brain has a notably different regional pattern of 5-HT6 receptor expression in comparison to humans, and little data has been generated in actual clinical populations. |
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| Protein Domain |
| Name: |
Chloride channel ClC-1 |
| Type: |
Family |
| Description: |
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport [].The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata [
], and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains []. Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm [].A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl- channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia [
]. Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms of inherited kidney stone disease []. These mutations have been demonstrated to reduce or abolish CLC function.CLC-1 was the first member of the CLC family cloned from mammalian species
[], and has 998 amino acid residues (human isoform). It is principallyexpressed in skeletal muscle, but low transcript levels can be detected in
kidney, heart and smooth muscle. In skeletal muscle, it gives rise to themajority of the muscle membrane Cl
-conductance (which accounts for ~70-80%
of the total resting conductance). These channels are partially open underresting conditions, and it is likely that following a prolonged series of
muscle action potentials, they act to reduce excitability, limiting tetanicactivation. As mentioned above, mutations in CLC-1 can cause recessive
(Becker) as well as dominant (Thomsen) myotonia. Such mutations reducechannel function, rendering skeletal muscle hyperexcitable. This leads to
defective muscle relaxation after voluntary contraction. |
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| Protein Domain |
| Name: |
Gamma-aminobutyric acid A receptor/Glycine receptor alpha |
| Type: |
Family |
| Description: |
Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) [
]. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels [
]. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [,
]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [
], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. This entry also includes glycine receptor subunit alpha [
]; subunits of the acetylcholine-gated chloride channel (ACC), Acetylcholine-gated ion channel acc-4 and Serotonin-gated chloride channel mod-1 in the nematode Caenorhabditis elegans; and Glutamate-gated chloride channel from Drosophila melanogaster (DrosGluCl). ACC is a heteropentamer consisting of ACC-1 and ACC-3, ACC-1 and ACC-4, ACC-2 and ACC-3 or ACC-2 and ACC-4. It is triggered in response to acetylcholine, but not GABA, glutamate, glycine, histamine or dopamine []. DrosGluCl plays an important role in the visual response by regulating the activity of ON/OFF-selective neurons []. |
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| Protein Domain |
| Name: |
Glutamyl-tRNA synthetase |
| Type: |
Domain |
| Description: |
This entry represents the discriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain. The discriminating form of GluRS is only found in bacteria and cellular organelles. GluRS is a monomer that attaches Glu to the appropriate tRNA. Like other class I tRNA synthetases, GluRS aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I 'HIGH' and 'KMSKS' motifs, which are involved in ATP binding [
].Glutamate-tRNA ligase (also known as glutamyl-tRNA synthetase;
) is a class Ic ligase and shows several similarities with glutamate-tRNA ligase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamate-tRNA ligase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I ligases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure [
].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c []. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, reovirus |
| Type: |
Domain |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents the Reoviridae family of dsRNA viruses. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, catalytic domain, bacteriophage |
| Type: |
Domain |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This entry represents the catalytic (palm) domain from the RNA-containing bacteriophage enzymes. |
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| Protein Domain |
| Name: |
Peroxisome proliferator-activated receptor, beta |
| Type: |
Family |
| Description: |
Steroid or nuclear hormone receptors (NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands [
]. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [,
]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.Peroxisome proliferator-activated receptors (PPAR) are ligand-activated
transcription factors that belong to the nuclear hormone receptor superfamily. Three cDNAs encoding PPARs have been isolated from Xenopus laevis: xPPAR alpha, beta and gamma [
]. All three xPPARs appear to be activated by both synthetic peroxisome proliferators and naturally occurring fatty acids, suggesting a common mode of action for all members of this subfamily of receptors []. Furthermore, the multiplicity of the receptors suggests the existence of hitherto unknown cellular signalling pathways for xenobiotics and putative endogenous ligands []. A PPAR alpha-related cDNA from mouse (designated PPAR delta, and
subsequently renamed beta) has been cloned and characterised. The alpha, beta and gamma PPAR isoforms display widely divergent patterns of expression
during embryogenesis and in the adult []. PPAR gamma and beta are not activated by pirinixic acid, a potent peroxisome proliferator and activator of PPAR alpha; they are, however, activated by the structurally distinct peroxisome proliferator LY-171883 and linoleic acid, respectively, indicating that each isoform can act as a regulated activator of
transcription []. Thus tissue-specific responsiveness to peroxisome proliferators, including certain fatty acids, may be partly a consequence of differential expression of multiple, pharmacologically distinct PPAR isoforms []. |
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| Protein Domain |
| Name: |
Peroxisome proliferator-activated receptor gamma |
| Type: |
Family |
| Description: |
Peroxisome proliferator-activated receptors (PPAR) are ligand-activated
transcription factors that belong to the nuclear hormone receptor superfamily. Three subtypes of this receptor have been discovered: PPAR alpha, beta and gamma [
]. They control a variety of target genes involved in lipid homeostasis, diabetes and cancer []. A human cognate of the mouse PPAR-gamma (hPPAR gamma) has been cloned from
a placental cDNA library []. Sequence analysis reveals a high degree of similarity to the mouse receptor (mPPAR) and, like other PPARs, hPPAR gamma forms heterodimers with RXR alpha. hPPAR gamma is expressed strongly in adipose tissue, but significant levels are also detectable in placenta, lung and ovary [
]. In vitrotrans-activation data suggest hPPAR gamma is only poorly activated by xenobiotic peroxisome proliferators, although certain fatty acids and eicosanoids are potent activators of this receptor. Both mPARR and hPPAR gamma may be activated by thiazolidinedione drugs, although the receptors appear to differ in their sensitivity to these compounds. These data suggest a high degree of structural and functional similarity between mPARR and hPPAR gamma, and provide evidence for variation in human receptor structure that may result in differential sensitivity to
activators []. Steroid or nuclear hormone receptors (NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands [
]. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [,
]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members. |
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| Protein Domain |
| Name: |
T cell antigen CD28 |
| Type: |
Family |
| Description: |
Antigen (Ag) recognition by the T cell receptor (TCR) induces activation of
T lymphocytes. However, TCR-mediated signals alone are insufficient forefficient T cell activation, and additional co-stimulatory signals are
required. One of the most important surface molecules that delivers co-stimulatory signals for T cells is CD28. The human T lymphocyte Ag CD28
(Tp44) is a homodimeric 90kDa glycoprotein expressed on the surface of themajority of human peripheral T cells and lymphocytes. Stimulation of CD4+ T
cells in the absence of CD28 co-signalling causes impaired proliferation, reduced cytokine production and altered generation of helper T cell subsets.
Co-stimulation via CD28 promotes T cell viability, clonal expansion,cytokine production and effector functions, while also regulating apoptosis
of activated T cells, suggesting its importance in regulating long-term T cell survival [
,
,
,
].Ligands for CD28 and the structurally related CTLA-4 (CD152) are the
molecules B7.1 (CD80) and B7.2 (CD86). B7.1 and B7.2 are expressed onprofessional antigen presenting cells (APCs) and their expression is up-regulated during an immune response. Ligation of CD28 by its natural ligands
results in tyrosine phosphorylation at a YMNM motif within its cytoplasmictail. The phosphorylated motif subsequently interacts with the Src homology
2 domain in the p85 regulatory subunit of P13K, activating the p110 catalytic subunit. One of the P13K-dependent downstream targets, resulting
from the antibody cross-linking of CD28, is the phoshporylation and activation of Akt (or PKB). Constitutively active Akt is able to substitute
for CD28 signals, and stimulates IL-2 production when introduced into matureCD28-deficient cells. Another molecule affected by CD28 stimulation is the
proto-oncogene Vav, which acts as a guanine-nucleotide exchange factor forRac and CDC42, allowing these molecules to switch from the inactive GDP-
bound state to the active GTP-bound state [,
].Another interesting feature of CD28, is its ability to induce expression of
PDE7, a cAMP phosphodiesterase, thus reducing cellular cAMP levels. cAMP hasbeen reported to affect nearly every pathway important for lymphocyte
activation, leading to inhibition of T cell proliferation. Specifically,increased intracellular cAMP has been implicated in the induction of T cell
anergy, a non-responsive state that occurs after T cells are stimulatedthrough TCR/CD3 in the absence of co-stimulation. This can have therapeutic
implications, in that blockage of CD28 co-stimulation can be profoundlyimmunosuppressive, preventing induction of pathogenic T cell responses in
autoimmune disease models, and allowing for prolonged acceptance of allografts in models of organ transplantation [
]. Finally, CD28 co-stimulation directly controls T cell cycle progression by
down-regulating the cdk inhibitor p27kip1, which actually integratesmitogenic MEK and P13K-dependent signals from both TCR and CD28 [
]. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, tospovirus |
| Type: |
Family |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This group represents a RNA-directed RNA polymerase, Tospovirus type. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase, nairovirus |
| Type: |
Family |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [
,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This group represents a RNA-directed RNA polymerase, Nairovirus type. |
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| Protein Domain |
| Name: |
Precorrin-3B C17-methyltransferase domain |
| Type: |
Domain |
| Description: |
This entry represents a domain found in CobJ and CbiH precorrin-3B C(17)-methyltransferase (
). In the aerobic pathway, once CobG has generated precorrin-3b, CobJ catalyses the methylation of precorrin-3b at C-17 to form precorrin-4 (the extruded methylated C-20 fragment is left attached as an acyl group at C-1) [
]. In the corresponding anaerobic pathway, CbiH carries out this ring contraction, using cobalt-precorrin-3b as a substrate to generate a tetramethylated delta-lactone []. In Mycobacterium this domain fuses with the Pprecorrin-2 C(20)-methyltransferase domain (
) into a bifunctional enzyme known as cobIJ.
These proteins belong to the superfamily of tetrapyrrole (corrin/porphyrin) methylases (
), which includes methylases that use S-adenosylmethionine (S-AdoMet) in the methylation of diverse substrates. A number of other methylases in the cobalamin biosynthesis pathway also belong to this domain superfamily (precorrin-3 methylase,
,
, amongst others), and a fusion of precorrin-3B C17-methyltransferases with precorrin isomerase is represented by
.
Nomenclature note: precorrin-3B C17-methyltransferase is one of the two methyltransferases often referred to as precorrin-3 methylase (the other is precorrin-4 C11-methyltransferase,
).
Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria [
]:Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway [
]; found in Pseudomonas denitrificans and Rhodobacter capsulatus.Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis [
,
]; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) [
]. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. |
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| Protein Domain |
| Name: |
Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type |
| Type: |
Family |
| Description: |
Phenylalanine-tRNA ligase (
) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (see
). Reciprocally the large subunit
(pheT gene) can be designated as alpha (E. coli) or beta. In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanine-tRNA ligase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other ligases [].This family describes the beta subunit. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps (see also
).
This family represents the subfamily that includes the beta subunit from bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the N-terminal.The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [
]. |
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| Protein Domain |
| Name: |
RNA-directed RNA polymerase beta-chain |
| Type: |
Family |
| Description: |
RNA-directed RNA polymerase (RdRp) (
) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [,
]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product [
]. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb [
]. Only the catalytic palm subdomain, composed of a four-stranded antiparallel β-sheet with two α-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA [].The domain organisation [
] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues.There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage:
Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families.Mononegavirales (negative-strand RNA viruses with non-segmented genomes).Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses.Birnaviridae family of dsRNA viruses.The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups:All positive-strand RNA eukaryotic viruses with no DNA stage.All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages).Reoviridae family of dsRNA viruses.This is a family of Leviviridae RNA replicases. |
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| Protein Domain |
| Name: |
Glycyl-tRNA synthetase |
| Type: |
Family |
| Description: |
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].In eubacteria, glycine-tRNA ligase (
) is an α2/β2 tetramer composed of 2 different subunits [
,
,
]. In some eubacteria, in archaea and eukaryota, glycine-tRNA ligase is an α2 dimer, this family. It belongs to class IIc and is one of the most complex ligases. What is most interesting is the lack of similarity between the two types: divergence at the sequencelevel is so great that it is impossible to infer descent from common genes. The alpha (see
) and beta subunits (see
) also lack significant sequence similarity. However, they are translated from a single mRNA [
], and a single chain glycine-tRNA ligase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain [
].The sequence and crystal structure of the homodimeric glycine-tRNA ligase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel β-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA ligase due to the conserved nature of the class II active site [
,
]. |
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| Protein Domain |
| Name: |
Lysyl-tRNA synthetase, class II, C-terminal |
| Type: |
Domain |
| Description: |
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].Lysine-tRNA synthesis is catalysed by two unrelated families of tRNA ligases: class-I or class-II. In eubacteria and eukaryota lysine-tRNA ligases belong to class II, the same family as aspartyl tRNA ligase. The lysine-tRNA ligase class Ic family is present in archaea and some eubacteria [
]. Moreover in some eubacteria there is a gene X, which is similar to a part of lysine-tRNA ligase from class II.Lysine-tRNA ligase is duplicated in some species with, for example in Escherichia coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots"of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding []. |
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| Protein Domain |
| Name: |
DNA-directed RNA polymerase subunit/transcription factor S |
| Type: |
Family |
| Description: |
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides.This entry represents the conserved small (~15kDa), zinc ribbon-containing, subunit which is found in archaeal and eukaryotic polymerases and forms part of the catalytic core of the enzyme [
,
,
]. This entry also includes transcription factor S (TFS), a protein related in size and sequence to DNA-directed RNA polymerase subunit M, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase (known as archaeal DNA-directed RNA polymerase subunit M), it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase [,
,
]. |
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| Protein Domain |
| Name: |
Lysine-tRNA ligase, class II |
| Type: |
Family |
| Description: |
This entry represents lysine-tRNA ligase class II.Lysine-tRNA synthesis is catalysed by two unrelated families of tRNA ligases: class-I or class-II. In eubacteria and eukaryota lysine-tRNA ligases belong to class II, the same family as aspartyl tRNA ligase. The lysine-tRNA ligase class Ic family is present in archaea and some eubacteria [
]. Moreover in some eubacteria there is a gene X, which is similar to a part of lysine-tRNA ligase from class II.Lysine-tRNA ligase is duplicated in some species with, for example in Escherichia coli, as a constitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots"of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [
].The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c []. |
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| Protein Domain |
| Name: |
5-Hydroxytryptamine 2B receptor |
| Type: |
Family |
| Description: |
5-hydroxytryptamine (5-HT) or serotonin, is a neurotransmitter that it is primarily found in the gastrointestinal (GI) tract, platelets, and in the central nervous system (CNS). It is implicated in a vast array of physiological and pathophysiological pathways. Receptors for 5-HT mediate both excitatory and inhibitory neurotransmission, and modulate the release of many neurotransmitters including glutamate, GABA, dopamine, epinephrine/norepinephrine, and acetylcholine, as well as many hormones, including oxytocin, prolactin, vasopressin and cortisol. In the CNS, 5-HT receptors can influence various neurological processes, such as aggression, anxiety and appetite and, as a, result are the target of a variety of pharmaceutical drugs, including many antidepressants, antipsychotics and anorectics [
]. The 5-HT receptors are grouped into a number of distinct subtypes, classified according to their antagonist susceptibilities and their affinities for 5-HT. With the exception of the 5-HT3 receptor, which is a ligand-gated ion channel [
], all 5-HT receptors are members of the rhodopsin-like G protein-coupled receptor family [], and they activate an intracellular second messenger cascade to produce their responses. The 5-HT2 receptors mediate many of the central and peripheral physiologic functions of 5-hydroxytryptamine. The original 5HT2 receptor (now renamed as the 5-HT2A receptor) was initially classified according to its ability to display micromolar affinity for 5-HT, to be labelled with [3H]spiperone and by its susceptibility to 5-HT antagonists. At least 3 members of the 5HT2 receptor subfamily exist (5-HT2A, 5-HT2B, 5-HT2C), all of which share a high degree of sequence similarity and couple to Gq/G11 to stimulate the phosphoinositide pathway and elevate cytosolic calcium. Cardiovascular effects include contraction of blood vessels and shape changes in platelets; central nervous system effects include neuronal sensitisation to tactile stimuli and mediation of some of the effects of phenylisopropylamine hallucinogens. 5-HT2 receptors display functional selectivity in which the same agonist in different cell types or different agonists in the same cell type can differentially activate multiple, distinct signalling pathways [].The 5-HT2B receptor has been shown to be distributed in a range of tissues, including human gut, brain and the cardiovascular system [
,
,
,
]. In the cardiovascular system the 5-HT2B receptor regulates cardiac structure and function []. 5-HT2B receptor stimulation can also lead to pathological proliferation of cardiac valve fibroblasts [], which, with chronic overstimulation, can lead to a severe valvulopathy. In addition, the 5-HT2B receptor has been shown to be involved in pulmonary hypertension via vasoconstriction []. As a result 5-HT2B antagonists have been developed as treatments for chronic heart disease [,
]. In the CNS the 5-HT2B receptor has been shown to be involved in presynaptic inhibition, leading to behavioural effects [], since it is important to the normal regulation of serotonin levels in the blood plasma [] and abnormal release produced by drugs such as MDMA []. |
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| Protein Domain |
| Name: |
Chloride channel ClC-K |
| Type: |
Family |
| Description: |
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport [
].The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata [
], and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains []. Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm [].A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl- channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia [
]. Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms of inherited kidney stone disease []. These mutations have been demonstrated to reduce or abolish CLC function.Two highly similar members of the CLC family have been cloned that appear
to be kidney-specific isoforms. These are known as CLC-Ka and CLC-Kb inhumans and are ~90% identical (at the amino acid level); in other species,
they are named CLC-K1 and CLC-K2 [,
]. Within species, the two isoformsshow differing distribution patterns in the kidney, possibly suggesting
diferent roles in renal function. To date, attempts at functional expressionof CLC-K isoforms have not yielded measurable Cl
-currents; however, that
they play a key role in normal kidney function had been made clear by thefact that naturally occurring mutations in the human gene CLCNKB (encoding
CLC-Kb) lead to a form of Bartter's syndrome, an inherited kidney diseasecharacterised by hypokalaemic alkalosis [
]. Similarly, transgenic mice,whose CLC-K1 channel has been rendered dysfunctional by targeted gene
disruption, develop overt diabetes, suggesting that these channelsare
important for urinary concentration []. |
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