| Type |
Details |
Score |
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2520
|
| Description: |
receptor-like protein kinase 2; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2580
|
| Description: |
probable plastid-lipid-associated protein 14, chloroplastic-like isoform X3 [Glycine max]; IPR006843 (Plastid lipid-associated protein/fibrillin conserved domain), IPR011009 (Protein kinase-like domain); GO:0004672 (protein kinase activity), GO:0005198 (structural molecule activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0009507 (chloroplast) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
5220
|
| Description: |
DNA repair protein UVH3-like isoform X1 [Glycine max]; IPR006084 (XPG/Rad2 endonuclease); GO:0003677 (DNA binding), GO:0003697 (single-stranded DNA binding), GO:0003824 (catalytic activity), GO:0004518 (nuclease activity), GO:0004519 (endonuclease activity), GO:0005634 (nucleus), GO:0006281 (DNA repair), GO:0006289 (nucleotide-excision repair) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3632
|
| Description: |
receptor-like protein kinase 2; IPR001611 (Leucine-rich repeat), IPR003591 (Leucine-rich repeat, typical subtype), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2375
|
| Description: |
arginine--tRNA ligase, cytoplasmic-like [Glycine max]; IPR001278 (Arginine-tRNA ligase, class Ia); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004814 (arginine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006420 (arginyl-tRNA aminoacylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1410
|
| Description: |
ADP-ribosylation factor GTPase-activating protein AGD12 isoform X1 [Glycine max]; IPR000008 (C2 domain), IPR001164 (Arf GTPase activating protein); GO:0005515 (protein binding), GO:0008060 (ARF GTPase activator activity), GO:0008270 (zinc ion binding), GO:0032312 (regulation of ARF GTPase activity) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3242
|
| Description: |
homeobox-leucine zipper protein HAT5-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1517
|
| Description: |
homeobox-leucine zipper protein ATHB-13-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
1726
|
| Description: |
homeobox-leucine zipper protein ATHB-6-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
3183
|
| Description: |
receptor-like protein kinase 1; IPR001611 (Leucine-rich repeat), IPR003591 (Leucine-rich repeat, typical subtype), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2309
|
| Description: |
arginine--tRNA ligase, cytoplasmic-like [Glycine max]; IPR001278 (Arginine-tRNA ligase, class Ia); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004814 (arginine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006420 (arginyl-tRNA aminoacylation) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
2847
|
| Description: |
Disease resistance protein (TIR-NBS-LRR class) family; IPR000767 (Disease resistance protein), IPR000858 (S-locus glycoprotein), IPR001480 (Bulb-type lectin domain), IPR003609 (Apple-like), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0006952 (defense response), GO:0043531 (ADP binding), GO:0048544 (recognition of pollen) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
10922
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR001650 (Helicase, C-terminal), 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 arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2322
|
| Description: |
WD repeat-containing protein 61-like isoform 1 [Glycine max]; IPR014906 (Pre-mRNA processing factor 4 (PRP4)-like), IPR015943 (WD40/YVTN repeat-like-containing domain), IPR020472 (G-protein beta WD-40 repeat), IPR027106 (U4/U6 small nuclear ribonucleoprotein Prp4); GO:0005515 (protein binding), GO:0008380 (RNA splicing) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
4919
|
| Description: |
Protein kinase superfamily protein; IPR011009 (Protein kinase-like domain), IPR015943 (WD40/YVTN repeat-like-containing domain), IPR016024 (Armadillo-type fold); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005488 (binding), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1341
|
| Description: |
homeobox-leucine zipper protein ATHB-12-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3048
|
| Description: |
Protein kinase superfamily protein; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2), IPR025875 (Leucine rich repeat 4); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3287
|
| Description: |
homeobox-leucine zipper protein HAT5-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2282
|
| Description: |
homeobox-leucine zipper protein ATHB-6-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1953
|
| Description: |
Unknown protein; 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), GO:0043039 (tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
10949
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR001650 (Helicase, C-terminal), 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: |
1885
|
| Description: |
homeobox-leucine zipper protein ATHB-6-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
5382
|
| Description: |
DNA repair protein UVH3-like isoform X1 [Glycine max]; IPR006084 (XPG/Rad2 endonuclease); GO:0003677 (DNA binding), GO:0003697 (single-stranded DNA binding), GO:0003824 (catalytic activity), GO:0004518 (nuclease activity), GO:0004519 (endonuclease activity), GO:0005634 (nucleus), GO:0006281 (DNA repair), GO:0006289 (nucleotide-excision repair) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1352
|
| Description: |
homeobox-leucine zipper protein ATHB-20-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2032
|
| Description: |
zinc finger CCCH domain-containing protein 69-like isoform X1 [Glycine max]; IPR000571 (Zinc finger, CCCH-type), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR026290 (Putative E3 ubiquitin-protein ligase, makorin-related); GO:0005515 (protein binding), GO:0008270 (zinc ion binding), GO:0046872 (metal ion binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2336
|
| Description: |
arginine--tRNA ligase, cytoplasmic-like [Glycine max]; IPR001278 (Arginine-tRNA ligase, class Ia); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004814 (arginine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006420 (arginyl-tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1406
|
| Description: |
ADP-ribosylation factor GTPase-activating protein AGD12 isoform X1 [Glycine max]; IPR000008 (C2 domain), IPR001164 (Arf GTPase activating protein); GO:0005515 (protein binding), GO:0008060 (ARF GTPase activator activity), GO:0008270 (zinc ion binding), GO:0032312 (regulation of ARF GTPase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1623
|
| Description: |
homeobox-leucine zipper protein HAT5-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1298
|
| Description: |
homeobox-leucine zipper protein ATHB-12-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2813
|
| Description: |
Disease resistance protein (TIR-NBS-LRR class) family; IPR000767 (Disease resistance protein), IPR001611 (Leucine-rich repeat), IPR008808 (Powdery mildew resistance protein, RPW8 domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0005515 (protein binding), GO:0006952 (defense response), GO:0043531 (ADP binding) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
804
|
| Description: |
polyadenylate-binding protein 8-like [Glycine max]; IPR000358 (Ribonucleotide reductase small subunit), IPR009078 (Ferritin-like superfamily), IPR012677 (Nucleotide-binding, alpha-beta plait); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0009186 (deoxyribonucleoside diphosphate metabolic process), GO:0016491 (oxidoreductase activity), GO:0055114 (oxidation-reduction process) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1827
|
| Description: |
fasciclin-like arabinogalactan protein 12-like [Glycine max]; IPR000782 (FAS1 domain), IPR001107 (Band 7 protein), IPR011905 (Glutaredoxin-like, plant II), IPR012336 (Thioredoxin-like fold); GO:0009055 (electron carrier activity), GO:0015035 (protein disulfide oxidoreductase activity), GO:0016020 (membrane), GO:0045454 (cell redox homeostasis) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1633
|
| Description: |
dual specificity protein phosphatase 1-like [Glycine max]; IPR000340 (Dual specificity phosphatase, catalytic domain), IPR024950 (Dual specificity phosphatase); GO:0004725 (protein tyrosine phosphatase activity), GO:0006470 (protein dephosphorylation), GO:0008138 (protein tyrosine/serine/threonine phosphatase activity), GO:0016311 (dephosphorylation), GO:0016791 (phosphatase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2333
|
| Description: |
receptor-like protein kinase 4; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3330
|
| Description: |
protein kinase family protein; IPR004000 (Actin-related protein), IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR024788 (Malectin-like carbohydrate-binding domain); GO:0004672 (protein kinase activity), GO:0004674 (protein serine/threonine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3794
|
| Description: |
dynamin-like protein 6; IPR000375 (Dynamin central domain), IPR001401 (Dynamin, GTPase domain), IPR011993 (Pleckstrin homology-like domain), IPR020850 (GTPase effector domain, GED), IPR022812 (Dynamin superfamily), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003924 (GTPase activity), GO:0005525 (GTP binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2327
|
| Description: |
signal recognition particle subunit SRP68-like [Glycine max]; IPR026258 (Signal recognition particle subunit SRP68); GO:0005047 (signal recognition particle binding), GO:0006614 (SRP-dependent cotranslational protein targeting to membrane), GO:0008312 (7S RNA binding), GO:0030942 (endoplasmic reticulum signal peptide binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
930
|
| Description: |
polyadenylate-binding protein 8-like [Glycine max]; IPR000358 (Ribonucleotide reductase small subunit), IPR009078 (Ferritin-like superfamily), IPR012677 (Nucleotide-binding, alpha-beta plait); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0009186 (deoxyribonucleoside diphosphate metabolic process), GO:0016491 (oxidoreductase activity), GO:0055114 (oxidation-reduction process) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2503
|
| Description: |
receptor-like protein kinase 2; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1837
|
| Description: |
tryptophan--tRNA ligase, cytoplasmic-like [Glycine max]; IPR002305 (Aminoacyl-tRNA synthetase, class Ic); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004830 (tryptophan-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006436 (tryptophanyl-tRNA aminoacylation) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1454
|
| Description: |
ADP-ribosylation factor GTPase-activating protein AGD12-like isoform X2 [Glycine max]; IPR000008 (C2 domain), IPR001164 (Arf GTPase activating protein); GO:0005515 (protein binding), GO:0008060 (ARF GTPase activator activity), GO:0008270 (zinc ion binding), GO:0032312 (regulation of ARF GTPase activity) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm3 |
| Annotation: |
ann1 |
| Length: |
732
|
| Description: |
homeobox-leucine zipper protein ATHB-12-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer arietinum |
| Strain: |
CDCFrontier |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1252
|
| Description: |
ADP-ribosylation factor GTPase-activating protein AGD12-like isoform X2 [Glycine max]; IPR000008 (C2 domain), IPR001164 (Arf GTPase activating protein); GO:0005515 (protein binding), GO:0008060 (ARF GTPase activator activity), GO:0008270 (zinc ion binding), GO:0032312 (regulation of ARF GTPase activity) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2179
|
| Description: |
arginine--tRNA ligase, cytoplasmic-like [Glycine max]; IPR001278 (Arginine-tRNA ligase, class Ia); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004814 (arginine-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006420 (arginyl-tRNA aminoacylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3378
|
| Description: |
receptor-like protein kinase 2; IPR001611 (Leucine-rich repeat), IPR003591 (Leucine-rich repeat, typical subtype), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3134
|
| Description: |
Protein kinase family protein; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1547
|
| Description: |
homeobox-leucine zipper protein ATHB-13-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2222
|
| Description: |
RNA-binding protein 39-like isoform X1 [Glycine max]; IPR006529 (U2 snRNP auxilliary factor, large subunit, splicing factor), IPR012677 (Nucleotide-binding, alpha-beta plait); GO:0000166 (nucleotide binding), GO:0003676 (nucleic acid binding), GO:0003723 (RNA binding), GO:0005634 (nucleus), GO:0006397 (mRNA processing) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2156
|
| Description: |
Protein kinase superfamily protein; IPR011009 (Protein kinase-like domain), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup), IPR016187 (C-type lectin fold); GO:0004672 (protein kinase activity), GO:0004713 (protein tyrosine kinase activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0030246 (carbohydrate binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
5120
|
| Description: |
chromodomain-helicase-DNA-binding protein 1-like isoform X2 [Glycine max]; IPR000330 (SNF2-related), IPR013083 (Zinc finger, RING/FYVE/PHD-type), IPR016197 (Chromo domain-like), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0003677 (DNA binding), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0008270 (zinc ion binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2585
|
| Description: |
Protein kinase superfamily protein; IPR001611 (Leucine-rich repeat), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2), IPR013320 (Concanavalin A-like lectin/glucanase, subgroup); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1741
|
| Description: |
homeobox-leucine zipper protein ATHB-6-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3183
|
| Description: |
receptor-like protein kinase 1; IPR001611 (Leucine-rich repeat), IPR003591 (Leucine-rich repeat, typical subtype), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
3411
|
| Description: |
receptor-like protein kinase 2; IPR001611 (Leucine-rich repeat), IPR003591 (Leucine-rich repeat, typical subtype), IPR011009 (Protein kinase-like domain), IPR013210 (Leucine-rich repeat-containing N-terminal, type 2); GO:0004672 (protein kinase activity), GO:0005515 (protein binding), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
309
|
| Description: |
Unknown protein; IPR008832 (Signal recognition particle, SRP9 subunit), IPR009018 (Signal recognition particle, SRP9/SRP14 subunit); GO:0006614 (SRP-dependent cotranslational protein targeting to membrane), GO:0008312 (7S RNA binding), GO:0045900 (negative regulation of translational elongation), GO:0048500 (signal recognition particle) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1478
|
| Description: |
homeobox-leucine zipper protein ATHB-6-like [Glycine max]; IPR003106 (Leucine zipper, homeobox-associated), IPR009057 (Homeodomain-like); GO:0000976 (transcription regulatory region sequence-specific DNA binding), GO:0003677 (DNA binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2622
|
| Description: |
probable plastid-lipid-associated protein 14, chloroplastic-like isoform X3 [Glycine max]; IPR006843 (Plastid lipid-associated protein/fibrillin conserved domain), IPR011009 (Protein kinase-like domain); GO:0004672 (protein kinase activity), GO:0005198 (structural molecule activity), GO:0005524 (ATP binding), GO:0006468 (protein phosphorylation), GO:0009507 (chloroplast) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
654
|
| Description: |
prolyl-tRNA synthetase family protein; IPR004499 (Proline-tRNA ligase, class IIa, archaeal-type); GO:0000166 (nucleotide binding), GO:0004812 (aminoacyl-tRNA ligase activity), GO:0004827 (proline-tRNA ligase activity), GO:0005524 (ATP binding), GO:0005737 (cytoplasm), GO:0006418 (tRNA aminoacylation for protein translation), GO:0006433 (prolyl-tRNA aminoacylation) |
| Organism: |
Cicer echinospermum |
| Strain: |
S2Drd065 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
2797
|
| Description: |
Disease resistance protein (TIR-NBS-LRR class) family; IPR000767 (Disease resistance protein), IPR001611 (Leucine-rich repeat), IPR008808 (Powdery mildew resistance protein, RPW8 domain), IPR027417 (P-loop containing nucleoside triphosphate hydrolase); GO:0005515 (protein binding), GO:0006952 (defense response), GO:0043531 (ADP binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| mRNA |
| Assembly: |
gnm1 |
| Annotation: |
ann1 |
| Length: |
1858
|
| Description: |
trihelix transcription factor GT-1-like isoform 1 [Glycine max]; IPR009057 (Homeodomain-like), IPR027775 (C2H2- zinc finger protein family); GO:0003677 (DNA binding), GO:0003682 (chromatin binding), GO:0003700 (sequence-specific DNA binding transcription factor activity), GO:0005634 (nucleus), GO:0043565 (sequence-specific DNA binding) |
| Organism: |
Cicer reticulatum |
| Strain: |
Besev079 |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
NADH:ubiquinone oxidoreductase, subunit 1, conserved site |
| Type: |
Conserved_site |
| Description: |
NADH:ubiquinone oxidoreductase (complex I) (
) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) [
]. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [].This entry represents subunit 1 NADH:ubiquinone oxidoreductase [
]. Among the many polypeptide subunits that make up complex I, there are fifteen which are located in the membrane part, seven of which are encoded by the mitochondrial and chloroplast genomes of most species. The most conserved of these organelle-encoded subunits is known as subunit 1 (gene ND1 in mitochondrion, and NDH1 in chloroplast) and seems to contain the ubiquinone binding site.The ND1 subunit is highly similar to subunit 4 of Escherichia coli formate hydrogenlyase (gene hycD), subunit C of hydrogenase-4 (gene hyfC). Paracoccus denitrificans NQO8 and Escherichia coli nuoH NADH-ubiquinone oxidoreductase subunits also belong to this family [
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
S-adenosylmethionine synthetase, conserved site |
| Type: |
Conserved_site |
| Description: |
Two conserved site signatures are present in S-adenosylmethionine synthetase. The more N-terminal site represents a hexapeptide which is thought to be involved in ATP binding whilst the C-terminal conserved site is an almost perfectly conserved glycine-rich nonapeptide. S-adenosylmethionine synthetase (MAT,
) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP [
]. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance [
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Peptidase M28 |
| Type: |
Domain |
| 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 domain is found in metallopeptidases belonging to the MEROPS peptidase family M28 (aminopeptidase Y, clan MH) [
] and in non-peptidase homologues such as transferrin receptor proteins. Members containing this domain, also contain a transferrin receptor-like dimerisation domain () and a protease-associated PA domain (
).
|
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
DNA topoisomerase, type IIA-like domain superfamily |
| Type: |
Homologous_superfamily |
| Description: |
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 superfamily represents the C-terminal of subunit B (gyrB and parE) and the N-terminal of subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent region in eukaryotic topoisomerase II composed of a single polypeptide. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Profilin |
| Type: |
Family |
| Description: |
This entry represents the Profilin family, which are small eukaryotic proteins that have different functions. In plants, they are major allergens present in pollens [
].The majority of the Profilin family members binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). They can also in certain circumstance promote actin polymerisation [
]. However, some Profilin family members, such as Profilin4 from mammals, does not binds to actin and may have functions distinct from regulating actin dynamics []. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain []. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway [,
].This entry also includes Asgard archaea profilins (Thor profilin, Loki profilin-1 and Loki profilin-2), which bind to actin and regulate the structure of the cytoskeleton. This indicates that Asgard archaea have a functional eukaryotic-like actin machinery [
].Some Profilins can also bind to polyphosphoinositides such as PIP2 [
]. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. The N-terminal region is thought to be involved in actin binding. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Tafazzin |
| Type: |
Family |
| Description: |
This entry includes tafazzin and its homologues, such as Taz1 from yeasts and N-acylphosphatidylethanolamine synthase from plants. Tafazzin is an enzyme involved in the cardiolipin remodelling pathway [
,
]. The phospholipid cardiolipin is an important component of the inner mitochondrial membrane that is involved in mitochondrial energy production and apoptosis []. In humans tafazzin is expressed at high levels in cardiac and skeletal muscle. As many as 10 isoforms can be present in different amounts in different tissues. Isoforms with hydrophobic N-termini are thought to be membrane anchored, while shorter forms, lacking the hydrophobic stretch, may be cytoplasmic (these latter are found in leukocytes and fibroblasts, but not in heart and skeletal muscle). A central hydrophilic domain may serve as an exposed loop that interacts with other proteins. Defects in the taz gene are the cause of Barth syndrome, a severe inherited disorder, often fatal in childhood. The disease is characterised by cardiac and skeletal myopathy, short stature and neutropenia [].In flies tafazzin is a CoA-independent, acyl-specific phospholipid transacylase with substrate preference for cardiolipin and phosphatidylcholine [
].Budding yeast Taz1 is a lyso-phosphatidylcholine acyltransferase that is required for normal phospholipid content of mitochondrial membranes, whose acyl specificity in the reaction relies on lipid chemical composition [
,
]. Arabidopsis N-acylphosphatidylethanolamine synthase (NAPE synthase, At1g78690) is an acyltransferase that catalyses the N-acylation of phosphatidylethanolamine to form N-acylphosphatidylethanolamine (N-acyl-PE) [
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Condensin subunit 1 |
| Type: |
Family |
| Description: |
This entry includes condensin subunit 1 (CND1). CND1 is a regulatory subunit of the condensin complex (contains the SMC2 and SMC4 heterodimer, and three non SMC subunits that probably regulate the complex: NCAPH/BRRN1, NCAPD2/CAPD2 and NCAPG), a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes [
]. The condensin complex probably introduces positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerases [,
,
,
]. Condensin is a multi-subunit protein complex that acts as an essential regulator of chromosome condensation [
,
]. It contains both SMC (structural maintenance of chromosomes) and non-SMC subunits. Condensin plays an important role during mitosis in the compaction and resolution of chromosomes to remove and prevent catenations that would otherwise inhibit segregation. This is thought to be achieved by the introduction of positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerases. During interphase condensin promotes clustering of dispersed loci into subnuclear domains and inhibits associations between homologues. In meiosis, condensin has been shown to influence the number of crossover events by regulating programmed double-strand breaks. Roles in gene regulation and lymphocyte development have also been defined. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
DNA polymerase delta, subunit 4 |
| Type: |
Family |
| Description: |
DNA polymerase delta (Pol delta) is responsible for effective DNA replication, playing a key role in the elongation of both the leading and the lagging strands of DNA and the maturation of Okazaki fragments [
]. It consists of four subunits: the catalytic and largest subunit p125, p50 that interacts with p125 to form the core enzyme, p68 which interacts with p50, and a fourth subunit, p12, that bridges p125 and p50, stabilising its interaction [,
].This entry represents the p12 subunit (also called subunit 4), which increases the rate of DNA synthesis and decreases fidelity by regulating POLD1 polymerase and proofreading 3' to 5' exonuclease activity in the Pol delta4 tetramer complex [,
,
]. p12 is PCNA-binding protein, as it contains a N-terminal PCNA-binding motif. Under conditions of DNA replication stress, it is required for the repair of broken replication forks through break-induced replication (BIR), a mechanism that may induce segmental genomic duplications of up to 200 kb []. This subunit is involved in Pol-delta4 translesion synthesis (TLS) of templates carrying O6-methylguanine or abasic sites []. p12 plays a major role in Pol delta4 catalytic functions while its degradation is required for the conversion of Pol delta4 to Pol delta3 in the cellular response to DNA damage, as Pol delta3 has an enhanced proofreading activity []. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Adenylate kinase, active site lid domain |
| Type: |
Domain |
| Description: |
Adenylate kinases (ADK;
) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other [
]. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains.Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [
]. |
|
•
•
•
•
•
|
| Protein Domain |
| Name: |
Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily |
| Type: |
Homologous_superfamily |
| 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 [
]. |
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| Protein Domain |
| Name: |
DNA-directed DNA polymerase, family B, conserved site |
| Type: |
Conserved_site |
| Description: |
DNA is the biological information that instructs cells how to exist in an
ordered fashion: accurate replication is thus one of the most importantevents in the life cycle of a cell. This function is performed by DNA-
directed DNA-polymerases () by adding nucleotide triphosphate (dNTP) residues
to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain
elongation, although terminal proteins may also be used for the de novosynthesis of a DNA chain.
Even though there are 2 different methods of priming, these are mediated by 2 very similar
polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped
under the designation of DNA polymerase family B.Six regions of similarity (numbered from I to VI) are found in all or a subset
of the B family polymerases. The most conserved region (I) includes a conservedtetrapeptide with two aspartate residues. Its function is not yet known.
However, it has been suggested [] that it may be involved in binding amagnesium ion. All sequences in the B
family contain a characteristic DTDS motif, and possess many functionaldomains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [
],a DNA binding domain, and binding domains for both dNTP's and pyrophosphate [
]. |
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| Protein Domain |
| Name: |
DNA-directed DNA polymerase, family B |
| Type: |
Family |
| Description: |
DNA is the biological information that instructs cells how to exist in an
ordered fashion: accurate replication is thus one of the most importantevents in the life cycle of a cell. This function is performed by DNA-
directed DNA-polymerases () by adding nucleotide triphosphate (dNTP) residues
to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain
elongation, although terminal proteins may also be used for the de novosynthesis of a DNA chain.
Even though there are 2 different methods of priming, these are mediated by 2 very similar
polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped
under the designation of DNA polymerase family B.Six regions of similarity (numbered from I to VI) are found in all or a subset
of the B family polymerases. The most conserved region (I) includes a conservedtetrapeptide with two aspartate residues. Its function is not yet known.
However, it has been suggested [] that it may be involved in binding amagnesium ion. All sequences in the B
family contain a characteristic DTDS motif, and possess many functionaldomains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [
],a DNA binding domain, and binding domains for both dNTP's and pyrophosphate [
]. |
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| Protein Domain |
| Name: |
Peptide methionine sulphoxide reductase MsrA domain |
| Type: |
Domain |
| Description: |
Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine [
]. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [,
].The domains MsrA and MsrB reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution [
]. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (
) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate.
In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. |
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| Protein Domain |
| Name: |
Tetrapyrrole methylase, subdomain 1 |
| Type: |
Homologous_superfamily |
| Description: |
Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [
]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [].This entry represents the N-terminal subdomain 1 from several tetrapyrrole methylases, which consist of two non-similar domains. These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:Uroporphyrinogen III methyltransferase (
) (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [
].Precorrin-2 C20-methyltransferase CobI/CbiL (
), which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [
]. In some species, this enzyme is part of a bifunctional protein.Precorrin-4 C11-methyltransferase CobM/CbiF (
), which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [
].Sirohaem synthase CysG (
), domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [
].Diphthine synthase (
), which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.
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| Protein Domain |
| Name: |
Tetrapyrrole methylase, subdomain 2 |
| Type: |
Homologous_superfamily |
| Description: |
Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [
]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [].This entry represents the C-terminal subdomain 2 from several tetrapyrrole methylases, which consist of two non-similar domains. These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:Uroporphyrinogen III methyltransferase (
) (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [
].Precorrin-2 C20-methyltransferase CobI/CbiL (
), which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [
]. In some species, this enzyme is part of a bifunctional protein.Precorrin-4 C11-methyltransferase CobM/CbiF (
), which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [
].Sirohaem synthase CysG (
), domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [
].Diphthine synthase (
), which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.
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| Protein Domain |
| Name: |
Tetrapyrrole methylase |
| Type: |
Domain |
| Description: |
Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [
]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [].These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:Uroporphyrinogen III methyltransferase (
) (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [
].Precorrin-2 C20-methyltransferase CobI/CbiL (
), which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [
]. In some species, this enzyme is part of a bifunctional protein.Precorrin-4 C11-methyltransferase CobM/CbiF (
), which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [
].Sirohaem synthase CysG (
), domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [
].Diphthine synthase (
), which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.
This entry represents a tetrapyrrole methylase domain, which consist of two non-similar subdomains [
]. |
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| Protein Domain |
| Name: |
Ubiquitin-activating enzyme, SCCH domain |
| Type: |
Domain |
| Description: |
Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2) [
]. This domain carries the last of five conserved cysteines that is part of the active site of the enzyme, responsible for ubiquitin thiolester complex formation, the active site being represented by the sequence motif PICTLKNFP []. Not all proteins in this entry contain a functional active site.The catalytic cysteine domain contains the E1 active site cysteine, and is divided in two half-domains, FCCH and SCCH, for 'first' and 'second' catalytic cysteine half-domain, respectively. This domain represents the domain 5 found in Ub-activating enzyme E1, the SCCH in which resides the catalytic cysteine [
]. This domain has an α-helical structure and likely to exist in equilibrium of open (adenylation active) and closed (thioester bond formation active) conformations. SCCH, FCCH (the first catalytic cysteine half-domain) and UFD (ubiquitin fold domain) are connected to the AAD (active adenylation domain) through flexible loops that allow the conformational changes and rotations of these domains essential for catalysis of Ub activation and transfer of activated UB from E1 to E2 []. |
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| Protein Domain |
| Name: |
Phosphotransferase system, IIB component, type 1 |
| Type: |
Domain |
| Description: |
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [
,
] is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC) [] which 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) carries the first permease-specific phoshorylation site, a histidine, which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the permease. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate in a process catalyzed by the IIC domain; this process is coupled to the transmembrane transport of the sugar.Several PTS permease families are currently recognised, namely, the (i) glucose (including glucoside), (ii) fructose (including mannitol), (iii) lactose (including N,N-diacetylchitobiose), (iv) galactitol, (v) glucitol, (vi) mannose, and (vii) l-ascorbate families [
].This entry represents the component IIB of the glucose family of PTS systems (type 1). |
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| Protein Domain |
| Name: |
Peptidase S49, N-terminal proteobacteria |
| Type: |
Domain |
| 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 domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also
) [
,
]. |
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| Protein Domain |
| Name: |
Integrase-like, catalytic domain superfamily |
| Type: |
Homologous_superfamily |
| Description: |
Phage integrases are enzymes that mediate unidirectional site-specific recombination between two DNA recognition sequences, the phage attachment site, attP, and the bacterial attachment site, attB [
]. Integrases may be grouped into two major families, the tyrosine recombinases and the serine recombinases, based on their mode of catalysis. Tyrosine family integrases, such as lambda integrase, utilise a catalytic tyrosine to mediate strand cleavage, tend to recognise longer attP sequences, and require other proteins encoded by the phage or the host bacteria.
The 356 amino acid lambda integrase consists of two domains: an N-terminal domain that includes residues 1-64 and is responsible for binding the arm-type sites of attP, and a C-terminal domain (CTD) that binds the lower affinity core-type sites and contains the catalytic site. The CTD can be further divided into the core-type binding domain (residues 65-169) and the catalytic core domain (170-356), the later representing this entry. The catalytic core adopts an alpha3-beta3-alpha4 fold, where one side of the beta sheet is exposed.The recombinases Cre from phage P1, XerD from Escherichia coli and Flp from yeast are members of the tyrosine recombinase family, and have a two-domain motif resembling that of lambda integrase, as well as sharing a conserved binding mechanism [
]. The structural fold of their catalytic core domains resemble that of Lambda integrase. |
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| Protein Domain |
| Name: |
KdsC family |
| Type: |
Family |
| Description: |
This entry is a part of the haloacid dehalogenase (HAD) superfamily of hydrolases, mainly from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. All characterised members of the HAD-superfamily hydrolase, subfamily IIIA and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [
], all of which are found conserved in this family.Lipopolysaccharides of Gram-negative bacteria consist of a heteropolysaccharide component (O-antigen) and a hydrophobic component (lipid A). Linking the two portions is 3-Deoxy-D-manno-octulosonate (KDO), an 8-carbon sugar. Biosynthesis of KDO linked to lipid A proceeds via five steps, one of which involves removal of a phosphate from KDO 8-P via the action of KDO 8-P phosphatase () [
]. This entry includes two homologues with divergent functions: 2-keto-3-deoxy-d-manno-octulosonate 8-phosphate phosphohydrolase (KDO8P phosphatase, KDO8PP, KdsC) and 2-keto-3-deoxy-9-O-phosphonononic acid phosphohydrolase (KDN9P phosphatase, KDN9PP). KDO8PP and KDN9PP catalyze the final step in the synthesis of KDO and the 9-carbon derivative KDN, respectively [,
].One member of this family, the YrbI protein from Haemophilus influenzae has been cloned, expressed, purified and found to be an active phosphatase. Furthermore, its crystal structure has been determined [
]. The sequence from Methanosarcina acetivorans, , is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (
) and is annotated as acylneuraminate cytidylyltransferase.
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| Protein Domain |
| Name: |
Lipid A biosynthesis myristoyltransferase |
| Type: |
Family |
| Description: |
Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS moleculesare variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A [
]. The polysaccharide component consists of a variable repeat-structure polysaccharide known as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS []. The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids []. These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units.This family consists of Lipid A biosynthesis myristoyltransferase (LpxM, also known as MsbB) in Escherichia coli and closely related proteins in other species. LpxM is homologous to HtrB (
) and acts immediately after it in the biosynthesis of KDO-2 lipid A (also called Re LPS and Re endotoxin). These two enzymes act after creation of KDO-2 lipid IV-A by addition of the KDO sugars. |
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| Protein Domain |
| Name: |
Restriction endonuclease, type II, HindIII superfamily |
| Type: |
Homologous_superfamily |
| Description: |
Type II restriction endonucleases (
) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin [
]. However, there is still considerable diversity amongst restriction endonucleases [,
]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the HindIII restriction endonuclease which recognises and cleaves A^AGCTT. |
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| Protein Domain |
| Name: |
RF2-like transcription factor, bZIP domain |
| Type: |
Domain |
| Description: |
This is the bZIP domain found in plant transcription factors with similarity to Oryza sativa RF2a and RF2b, which are important for plant development. RF2a and b interact, as homodimers or heterodimers, with each other, and activate transcription from the RTBV (rice tungro bacilliform virus) promoter, which is regulated by sequence-specific DNA-binding proteins that bind to the essential cis element BoxII. They show differences in binding affinities to BoxII, expression patterns in different rice organs, and subcellular localisation. Transgenic rice with increased RF2a and RF2b display increased resistance to rice tungro disease (RTD) with no impact on plant development [
,
].bZIP domains from Arabidopsis have been classified into 11 groups (groups A-I and S), the ones included in this entry belong to group I such as VIP1 or PosF21 (also known as bZIP transcription factor 59) [
,
,
,
].bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription []. |
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| Protein Domain |
| Name: |
Carbonic anhydrase, CA4/CA15 |
| Type: |
Family |
| Description: |
Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues [
,
].This subgroup of carbonic anhydrases, restricted to animals, contains isozyme IV and similar proteins such as mouse CA XV. Isozymes IV is attached to membranes via a glycosylphosphatidylinositol (GPI) tail. In mammals, Isozyme IV plays crucial roles in kidney and lung function, among others [
]. This subgroup also contains the dual domain CA from the giant clam, Tridacna gigas. T. gigas CA plays a role in the movement of inorganic carbon from the surrounding seawater to the symbiotic algae found in the clam's tissues []. CA XV is expressed in several species but not in humans or chimps. Similar to isozyme CA IV, CA XV attaches to membranes via a GPI tail []. |
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| Protein Domain |
| Name: |
DNA polymerase 1 |
| Type: |
Family |
| Description: |
DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 3'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities [
,
]. Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C [], are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a β-strand and an α-helix; motif B contains an α-helix with positive charges; and motif C has a doublet of negative charges, located in a β-turn-beta secondary structure []. |
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| Protein Domain |
| Name: |
Restriction endonuclease, type II, PvuII superfamily |
| Type: |
Homologous_superfamily |
| Description: |
Type II restriction endonucleases (
) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin [
]. However, there is still considerable diversity amongst restriction endonucleases [,
]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the type II restriction endonuclease PvuII, which recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3 [
]. |
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| Protein Domain |
| Name: |
Fis-like DNA-binding domain-containing signal transduction response regulator, predicted |
| Type: |
Family |
| Description: |
Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions [
]. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [
,
].This entry represents predicted response regulators with Fis-like DNA-binding domain. |
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| Protein Domain |
| Name: |
Deoxycytidylate hydroxymethylase |
| Type: |
Family |
| Description: |
In bacteriophage T4, a specific DNA modification system has evolved in order to protect its own DNA from degradation by host nucleases [
]. Firstly, the cytosine base in dCMP is hydroxymethylated by the T4 enzyme deoxycytidylate hydroxymethylase to produce hydroxymethyl-dCMP (Hm-dCMP). This product is subsequently converted to Hm-dCTP by the combined action of T4 deoxynucleoside monophosphate kinase and host nucleoside diphosphate kinase. Hm-dCTP is then incorporated into T4 DNA by the phage DNA polymerase enzyme. Glucosylation of the Hm-dCTP residues within the phage DNA by glucosyltransferases completes the modification. Degradation of host dCTP by a T4 dCTPase ensures that no unmodified cytosine residues are incorporated in the phage genome.This entry represents the deoxycytidylate hydroxymethylase enzyme catalysing the first step in T4 the cytosine modification system. This enzyme is a dimer which, despite a low sequence identity, forms a similar fold to that of thymidylate synthases [
]. Each monomer consists of several alpha helices surrounding a six-stranded β-sheet which forms the dimerisation interface. The active site is formed in a deep pocket, with the sugar and phosphate-binding residues in a similar configuration to that of thymidylate synthase, while the residues presumed to bind cytosine and the folate cofactor are more divergent. The enzyme has been shown to interact with proteins in the T4 deoxyribonucleoside triphosphate synthetase complex [,
]. |
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| Protein Domain |
| Name: |
Pollen allergen Poa p IX/Phl p VI |
| Type: |
Domain |
| Description: |
Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation.Proteins in this family belong to the Poa p (Poa pratensis or Kentucky bluegrass) IX and Phl p (Phleum pratense) VI allergen family, and include allergens with the following designations: Lol p 5, Pha a 5, Phl p 6, and Poa p 9. Phl p 5b has been shown to possess ribonuclease activity []. Grass pollen allergens are one of the major causes of type I allergies (including allergic rhinoconjunctivitis, allergic bronchial asthma and hayfever), afflicting 15-20% of a genetically predisposed population []. These allergens exhibit an entirely α-helical structure with a four-helical bundle topology [
]. |
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| Protein Domain |
| Name: |
TagA/B/C/D, peptidase domain |
| Type: |
Domain |
| Description: |
In Dictyostelium discoideum, unique members of the ABCB transporter subfamily, TagB and TagC, appear responsible for peptide signal export during development. These Tag proteins are required for cell differentiation in Dictyostelium and have the potential to carry out the processing and transport of peptide signals since they possess an N-terminal serine protease domain and a C-terminal transporter domain [
]. Other family members include TagA, which is required for the specification of an initial population of prespore cells in which tagA is expressed [].This entry represents the N-terminal serine protease domain, which is is part of a family of domains found in serine peptidases belonging to the MEROPS peptidase families S8 (subfamilies S8A (subtilisin) and S8B (kexin)) and S53 (sedolisin), both of which are members of clan SB [
,
,
,
].Peptidases S8 (or subtilases serine endo- and exo-peptidase clan) have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values [
,
,
,
]. |
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| Protein Domain |
| Name: |
Integrin beta subunit, cytoplasmic domain |
| Type: |
Domain |
| Description: |
Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [
,
]. An integrin receptor is a heterodimer composed of alpha and beta subunits. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus.Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits [
]. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans []. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule []. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another.This entry represents the cytoplasmic domain of integrin beta subunits [
]. |
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| Protein Domain |
| Name: |
3-isopropylmalate dehydratase, fused small/large subunit |
| Type: |
Family |
| Description: |
3-isopropylmalate dehydratase (or isopropylmalate isomerase;
) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family [
]. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S]cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [
,
]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase , converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis [
]. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast [].This group represents 3-isopropylmalate dehydratase: with fused small and large subunits [
,
]. |
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| Protein Domain |
| Name: |
Peptide methionine sulphoxide reductase MsrA superfamily |
| Type: |
Homologous_superfamily |
| Description: |
Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine [
]. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [,
].The domains MsrA and MsrB reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution [
]. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (
) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. |
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| Protein Domain |
| Name: |
Transcription elongation factor S-II, central domain superfamily |
| Type: |
Homologous_superfamily |
| Description: |
Transcription factor S-II (TFIIS) induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius [
]. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [,
].TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III [
]. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding β-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre.The superfamily represents the central domain of transcription elongation factor S-II and similar domains. |
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| Protein Domain |
| Name: |
Glycerol-3-phosphate dehydrogenase, GlpA subunit |
| Type: |
Family |
| Description: |
In bacteria, glycerol uptake is mediated by the glycerol diffusion facilitator, an integral membrane protein catalysing the rapid equilibration of concentration gradients of glycerol across the cytoplasmic membrane. Intracellular glycerol is converted to glycerol-3-phosphate that is further metabolised to dihydroxyacetone phosphate (DHAP) by either of two membrane-bound enzymes, depending on the growth conditions.Under aerobic growth conditions, in the presence of glycerol, a glycerol-3-phopshate dehydrogenase (encoded by the glpD gene) is induced, which passes the reducing equivalents to an electron transport chain terminating with oxygen as the electron acceptor. Under anaerobic growth conditions, in the presence of glycerol and fumarate, a different dehydrogenase is induced [
]. Electrons derived from this reaction are ultimately passed to fumarate as the terminal electron acceptor. The enzyme is composed of three subunits, encoded by the glpABC operon, which are all essential for anaerobic growth on glycerol-3-phosphate []. GlpA and B form the soluble subunit which carries the catalytic site of glycerol-3-phosphate oxidation; while GlpC forms a membrane-bound iron-sulphur subunit, which may act as an anchor for the soluble subunit, and is thought to function in electron transfer from GlpAB to the terminal electron acceptor.This entry represents the GlpA subunit. An archaeal homologue has also recently been characterised [
], which appears to be used under aerobic conditions in halophilic archaea. |
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| Protein Domain |
| Name: |
Vascular endothelial growth factor receptor 2 (VEGFR2) |
| Type: |
Family |
| Description: |
Vascular endothelial growth factor (VEGF) is a potent and specific endothelial cell mitogen that regulates blood and lymphatic vessel development and homeostasis [
,
]. EGFs are predominantly produced by endothelial, hematopoietic, and stromal cells in response to hypoxia and upon stimulation by growth factors such as transforming growth factor beta (TGFbeta), interleukins, or platelet-derived growth factors []. VEGFs specifically interact with one or several receptor tyrosine kinases, VEGF receptors, and with distinct co-receptors such as neuropilins or heparan sulphate glycosaminoglycans. The VEGF receptor family consists of three members, VEGFR1 (FLT1), VEGFR2 (KDR/FLK1) and VEGFR3 (FLT4) []. Among these receptors, VEGFR1 binds strongest to VEGF, VEGF2 binds more weakly, and VEGFR3 shows essentially no binding, although it does bind to other members of the VEGF family. VEGF receptors have a characteristic structure, with 7 Ig-like domains in the extracellular domain and a cytoplasmic tyrosine kinase domain with a long kinase insert region. VEGF receptors are activated upon ligand-mediated dimerisation.This entry represents VEGFR2 proteins. The tyrosine kinase domain of VEGFR2 tranduces signals for endothelial cells with a greater efficacy than VEGFR1. VEGFR2 expression in adult endothelial cells appears to account for most of the mitogenic and chemotactic effects of VEGF [
]. At the post-receptor level, activation of endothelial cells by VEGF leads to the autophosphorylation of VEGFR2 and the subsequent tyrosine phosphorylation of numerous downstream targets. |
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| Protein Domain |
| Name: |
Glycerol-3-phosphate dehydrogenase, GlpB subunit |
| Type: |
Family |
| Description: |
In bacteria, glycerol uptake is mediated by the glycerol diffusion facilitator, an integral membrane protein catalysing the rapid equilibration of concentration gradients of glycerol across the cytoplasmic membrane. Intracellular glycerol is converted to glycerol-3-phosphate that is further metabolised to dihydroxyacetone phosphate (DHAP) by either of two membrane-bound enzymes, depending on the growth conditions.Under aerobic growth conditions, in the presence of glycerol, a glycerol-3-phopshate dehydrogenase (encoded by the glpD gene) is induced, which passes the reducing equivalents to an electron transport chain terminating with oxygen as the electron acceptor. Under anaerobic growth conditions, in the presence of glycerol and fumarate, a different dehydrogenase is induced [
]. Electrons derived from this reaction are ultimately passed to fumarate as the terminal electron acceptor. The enzyme is composed of three subunits, encoded by the glpABC operon, which are all essential for anaerobic growth on glycerol-3-phosphate []. GlpA and B form the soluble subunit which carries the catalytic site of glycerol-3-phosphate oxidation; while GlpC forms a membrane-bound iron-sulphur subunit, which may act as an anchor for the soluble subunit, and is thought to function in electron transfer from GlpAB to the terminal electron acceptor.This entry represents the GlpB subunit. An archaeal homologue has also recently been characterised [
], which appears to be used under aerobic conditions in halophilic archaea. |
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| Protein Domain |
| Name: |
Potassium channel toxin gamma/Ergtoxin |
| Type: |
Family |
| Description: |
The Ergtoxin (ErgTx) family is a class of peptides from scorpion venom that specifically block ERG (ether-a-go-go-related gene) K+ channels of the nerve, heart and endocrine cells [
,
,
]. Peptides of the ErgTx family have from 42 to 47 amino acid residues cross-linked by four disulphide bridges. The four disulphide bridges have been assigned as C1-C4, C2-C6, C3-C7 and C5-C8 (see the schematic representation below) [
]. ErgTxs consist of a triple-stranded β-sheet and an α-helix, as is typical of K+ channel scorpion toxins. There is a large hydrophobic patch on the surface of the toxin, surrounding a central lysine residue located near the β-hairpin loop between the second and third strands of the β-sheet. It has been postulated that this hydrophobic patch is likely to form part of the binding surface of the toxin []. Peptides of the ErgTx family possess a Knottin scaffold (see https://www.dsimb.inserm.fr/KNOTTIN/). Some proteins known to belong to the ErgTx family are listed below: ErgTx1, ErgTx2 and ErgTx3 from Centruroides elegans (Bark scorpion). ErgTx1, ErgTx2, ErgTx3 and ErgTx4 from Centruroides exilicauda (Bark scorpion). ErgTx1, ErgTx2 and ErgTx3 from Centruroides gracilis (Slenderbrown scorpion) (Florida bark scorpion). ErgTx1, ErgTx2, ErgTx3 and ErgTx4 from Centruroides limpidus limpidus (Mexican scorpion). ErgTx1, ErgTx2, ErgTx3, ErgTx4, ErgTx5 and gamma-KTx 4.12 from Centruroides sculpturatus (Bark scorpion). ErgTx, ErgTx2, ErgTx3, ErgTx4 and ErgTx5 from Centruroides noxius (Mexican scorpion). |
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| Protein Domain |
| Name: |
SYK/ZAP-70, N-terminal SH2 domain |
| Type: |
Domain |
| Description: |
ZAP-70 and Syk comprise a family of hematopoietic cell specific protein tyrosine kinases (PTKs) that are required for antigen and antibody receptor function. ZAP-70 is expressed in T and natural killer (NK) cells and Syk is expressed in B cells, mast cells, polymorphonuclear leukocytes, platelets, macrophages, and immature T cells. They are required for the proper development of T and B cells, immune receptors, and activating NK cells [
]. They consist of two N-terminal Src homology 2 (SH2) domains and a C-terminal kinase domain separated from the SH2 domains by a linker or hinge region. Phosphorylation of both tyrosine residues within the Immunoreceptor Tyrosine-based Activation Motifs (ITAM; consensus sequence Yxx[LI]x(7,8)Yxx[LI]) by the Src-family PTKs is required for efficient interaction of ZAP-70 and Syk with the receptor subunits and for receptor function []. ZAP-70 forms two phosphotyrosine binding pockets, one of which is shared by both SH2 domains. In Syk the two SH2 domains do not form such a phosphotyrosine-binding site. The SH2 domains here are believed to function independently. In addition, the two SH2 domains of Syk display flexibility in their relative orientation, allowing Syk to accommodate a greater variety of spacing sequences between the ITAM phosphotyrosines and singly phosphorylated non-classical ITAM ligands [
]. This entry contains the N terminus SH2 domains of both Syk and Zap70. |
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