Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain
Type:
Domain
Description:
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].Glutamate-tRNA ligase (also known as glutamyl-tRNA synthetase;
) is a class Ic ligase and shows several similarities with glutamate-tRNA ligase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamate-tRNA ligase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I ligases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure [
].
Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal
Type:
Domain
Description:
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (
) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [
].
Aminoacyl-tRNA synthetase, class I, conserved site
Type:
Conserved_site
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 [
].This entry represents a conserved sequence in their N-terminal section of class I aminoacyl-tRNA synthetases.
Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways [
]. The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane.The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains [
]. Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar []. Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase.The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues []. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus.Hexokinase (
), a fructose and glucose phosphorylating enzyme, contains two structurally similar domains represented by this family and
. Some hexokinases have two copies of each of these domains. This entry represents the N-terminal domain.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational
error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast 40S ribosomal protein S2 (also known as SUP44).
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.
This entry represents the C-terminal of the ribosomal protein S5, which is related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (
). Ribosomal protein S5 is one of the proteins from the small ribosomal subunit.
In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies.
Ribosomal protein S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino-acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44).This entry represents the conserved site of the ribosomal protein S5. This entry represents the N-terminal domain of ribosomal protein S5, which has an α-β(3)-alpha structure that folds into two layers, alpha/beta.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].Ribosomal protein S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44).This entry represents the N-terminal domain of ribosomal protein S5, which has an α-β(3)-α structure that folds into two layers, α/β.
BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking, are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins [
,
,
,
,
,
,
,
].The BEACH domain is usually followed by a series of WD repeats.
The BEACH domain is found in eukaryotic proteins that have diverse cellular functions ranging from lysosomal traffic to apoptosis and cytokinesisin vesicle trafficking, membrane dynamics, and receptor signaling. The name BEACH is derived from BEige And Chediak-Higashi syndrome. This entry represents a domain with a fold similar to that of the PH (pleckstrin homology) domain, despite displaying little sequence homology with canonical PH domains. Furthermore, this domain is incapable of binding phospholipids [
]. This domain is found preceding the BEACH domain in beige-like and BEACH-domain containing proteins.
Microtubule-associated protein 70 (MAP70) are plant-specific proteins that interact with microtubules. In Arabidopsis thaliana, there are five MAP70 genes (MAP70-1/2/3/4/5). MAP70-1 associates with MAP70-5 and is essential for the normal banding pattern of secondary cell wall and for the proper development of xylem tracheary elements and wood formation [
,
].
This entry represents a subgroup of the class-I aminoacyl-tRNA synthetase family. It includes cysteinyl-tRNA synthetase and the related enzyme mycothiol ligase [
].Cysteine-tRNA ligase (also known as Cysteinyl-tRNA synthetase) (
) is an alpha monomer and belongs to class Ia [
]. It is highly specific despite not possessing the amino acid editing activity characteristic of many other tRNA ligases [
].Mycothiol ligase, also known as L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis [
].
Cysteine-tRNA ligase (also known as Cysteinyl-tRNA synthetase) (
) is an alpha monomer and belongs to class Ia [
]. It is highly specific despite not possessing the amino acid editing activity characteristic of many other tRNA ligases [].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 [].
Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
Type:
Homologous_superfamily
Description:
Aminoacyl-tRNA synthetase (aaRS) is a key enzyme during protein biosynthesis. Each aaRS contains a catalytic central domain (CCD), responsible for activating amino acid, and an anticodon-binding domain (ABD), necessary for binding the anticodon in cognate tRNA. aaRSs are classified into class I and II (aaRS-I and aaRS-II) based on the topologies of CCDs. Whereas the structure of the CCDs is similar among the members of each of the two different aaRS classes, the ABDs are diverse in structure [
].The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases. Both classes of tRNA synthetases have been subdivided into three subclasses, designated Ia, Ib, Ic and IIa, IIb, IIc.This superfamily represents the anticodon binding domain (ABD) of class Ia aminoacyl-tRNA synthetases, and also matches the ABD of glycine tRNA synthetases.
This entry contains a diverse range of flavoprotein enzymes, including epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN [
]. This enzyme catalyzes the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance []. Dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenylacrylic acid decarboxylase [
].
This family summarizes both S1 and P1 nucleases (
) which cleave RNA and single stranded DNA with no base specificity [
]. S1 nuclease is more active on DNA than RNA. Its reaction products are oligonucleotides or single nucleotides with 5' phosphoryl groups []. Although its primary substrate is single-stranded, it may also introduce single-stranded breaks in double-stranded DNA or RNA, or DNA-RNA hybrids. It is used as a reagent in nuclease protection assays and in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA. P1 nuclease cleaves its substrate at every position yielding nucleoside 5' monophosphates, and it does not recognize or act on double-stranded DNA []. It is useful at removing single stranded strands hanging off the end of double stranded DNA and at completely cleaving melted DNA for simple DNA composition analysis.
The enzymes belonging to this superfamily are involved in phosphate ester hydrolysis and contain a triad of closely spaced zinc ions at their active centres. Both families of enzymes hydrolyse phosphodiesters. Substrates for phospholipase C are phosphatidylinositol and phosphatidylcholine, while P1 nuclease is an endonuclease hydrolysing single stranded ribo- and deoxyribonucleotides. P1 nuclease also has activity as a phosphomonoesterase against 3'-terminal phosphates of nucleotides. The Zn ions in both enzymes form almost identical trinuclear sites [
].
A wide variety of enzymes contain this domain, principally thioesterases. Proteins containing this domain include 4HBT (4-hydroxybenzoyl-CoA thioesterase) (
) which catalyses the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3 [
,
]. It also includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other long chain fatty acyl-CoA thioesters [].
This domain is found in the PAAI protein from Escherichia coli that may be involved in phenylacetic acid degradation and in a few others that may be transcription regulators [
]. Most proteins containing this domain consist almost entirely of a single copy of this domain. A protein from Caenorhabditis elegans consists of two tandem copies of the domain. The domain is also found as the N-terminal region of an apparent initiation factor eIF-2B alpha subunit of Aquifex aeolicus.
Homing endonucleases are rare-cutting enzymes encoded by inteins and introns. They are found inserted within host genes in eukaryotes, bacteria, archaebacteria and viruses [
]. By making a site-specific double-strand break in the intronless or inteinless alleles, these nucleases create recombinogenic ends which engage in a gene conversion process that duplicates the intron or intein [,
]. There are four families of homing endonucleases classified by the conserved sequence motifs LAGLIDADG, GIY-YIG, H-N-H and His-Cys box [,
]. Endonucleases of the DOD family contain one or two copies of the 10-residue sequence known as a dodecapeptide or LAGLIDADG motif. LAGLIDADG endonucleases are either monomers, such as I-SceI, that are composed of two pseudo symmetric subdomains, or homodimers, such as I-CreI. In both cases, the LAGLIDADG endonuclease folds into a β-saddle architecture, a common motif for nucleic acid binding proteins [].This superfamily represents the homing endonuclease domain.
Wall-associated kinases (WAKs) are transmembrane proteins containing a cytoplasmic serine/threonine kinase domain and an extracellular domain in contact with the pectin fraction of the plant cell wall [
]. The cysteine-rich galacturonan-binding domain is located near the N-terminal end of the extracellular domain and binds to the cell-wall pectins [,
].
Homing endonucleases (HEnases) form a large and highly diverse class of proteins
encoded by introns and inteins that confer mobility to their host genetic elements. LAGLIDADG HEnases are structured into two tandemly repeated homing endonuclease-like domains [,
]. This entry represents the homing endonuclease LAGLIDADG domain [].
The P protein is part of the glycine decarboxylase multienzyme complex (GDC), also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T [
]. The P protein () binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. The reaction catalysed by this protein is:
Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 The subunit composition of glycine cleavage system P proteins have been classified into two types. Those from eukaryotes and some of the P proteins from prokaryotes (e.g. Escherichia coli) are in the homodimeric form. The rest of those from prokaryotes are heterotetrameric, with two different subunits which, based on sequence similarities, correspond respectively to the N and C-terminal halves of the eukaryotic subunit [
].
The binding of the LYPxL motif of late HIV p6Gag and EIAV p9Gag to this domain is necessary for viral budding. In ALIX, a component of the ESCRT pathway, this domain is central between an N-terminal Bro1 domain (
) and a C-terminal proline-rich domain. The ALIX central domain is formed by two three-helix bundles disposed in a V shape [
,
]. Retroviruses thus used this domain to hijack the ESCRT system of the cell [].
The BRO1 domain is a protein domain of ~390 residues in length. It occurs in a number of eukaryotic proteins, such as yeast BRO1 and human PDCD6IP/Alix, which are involved in protein targeting to the vacuole or lysosome. The BRO1 domain of fungal and mammalian proteins binds with multivesicular body components (ESCRT-III proteins) such as yeast Snf7 and mammalian CHMP4b, and can function to target BRO1 domain-containing proteins to endosomes [
,
,
].The BRO1 domain has a boomerang shape composed of 14 α-helices and 3 β-sheets. It contains a TPR-like substructure in the central part [
]. The C terminus is less conserved.
The ~100-residue ERV/ALR sulphydryl oxidase domain is a versatile module adapted for catalysis of disulphide bond formation in various organelles and biological settings. The ERV/ALR sulphydryl oxidase domain has a Cys-X-X-Cys dithiol/disulphide motif adjacent to a bound FAD cofactor, enabling transfer of electrons from thiol substrates to non-thiol electron acceptors. ERV/ALR family members differ in their N- or C-terminal extensions, which typically contain at least one additional disulphide bond, the hypothesised 'shuttle' disulphide. In yeast ERV1, a mitochondrial enzyme, the shuttle disulphide is N-terminal to the catalytic core; in yeast ERV2, present in the endoplasmic reticulum, it is C-terminal. The N- and C-terminal extensions can be entire domains, such as the thioredoxin-like domains () or short segments that do not seem to be distinct domains. Proteins of the ERV/ALR family are encoded by all eukaryotes and cytoplasmic DNA viruses (poxviruses, African swine fever virus, iridoviruses, and Paramecium bursaria Chlorella virus 1) [
,
,
,
,
].The ERV/ALR sulphydryl oxidase domain contains a four-helix bundle (helices alpha1-alpha4) and an additional single turn of helix (alpha5) packed perpendicular to the bundle [
,
]. The FAD prosthetic group is housed at the mouth of the 4-helix bundle and communicates with the pair of juxtaposed cysteine residues that form the proximal redox active site [].
Ribose 5-phosphate isomerase, also known as phosphoriboisomerase, catalyses the reversible conversion of D-ribose 5-phosphate to D-ribulose 5-phosphate, the first step in the non-oxidative branch of the pentose phosphate pathway [
]. This reaction enables ribose to be synthesized from sugars, as well as the recycling of sugars during the degradation of nucleotides. There are two unrelated types of ribose 5-phosphate isomerases: type A (RpiA) is the most common and is found in most organisms, while type B (RpiB) is restricted to specific eukaryotic and prokaryotic species. Escherichia coli produces both RpiA and RpiB (also known as AlsB), although RpiA accounts for 99% of total RPI enzymes []. This entry represents type A (RpiA) enzymes found in eukaryotes (plants, Metazoa and fungi), bacteria and archaea.
Ribose 5-phosphate isomerase, also known as phosphoriboisomerase, catalyses the reversible conversion of D-ribose 5-phosphate to D-ribulose 5-phosphate, the first step in the non-oxidative branch of the pentose phosphate pathway [
]. This reaction enables ribose to be synthesized from sugars, as well as the recycling of sugars during the degradation of nucleotides. There are two unrelated types of ribose 5-phosphate isomerases: type A (RpiA) is the most common and is found in most organisms, while type B (RpiB) is restricted to specific eukaryotic and prokaryotic species. Escherichia coli produces both RpiA and RpiB (also known as AlsB), although RpiA accounts for 99% of total RPI enzymes []. This entry represents a subgroup of type A ribose-5-phosphate isomerase that is found in bacteria, archaea and eukaryotes (plants and Metazoa), but excluding those found in fungi.
Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold [
]. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation [
]. Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.DnaJ comprises a 70-residue N-terminal domain
(the J-domain); a 30-residue glycine-rich region (the G-domain); a centraldomain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a
120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryoticproteins [
], either together or separately.The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Only some homologues are included in this family.
Phosphatidyl serine synthase is also known as serine exchange enzyme (
). This family represents eukaryotic PSS I and II, membrane bound proteins that catalyse the replacement of the head group of a phospholipid
(phosphotidylcholine or phosphotidylethanolamine) by L-serine [].Proteins in this entry include Pss from Drosophila melanogaster. Pss has been shown to regulate cell growth, lipid storage and mitochondrial function [
].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [
], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [
,
,
]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents class E cytochrome P450 proteins that fall into sequence cluster group IV. Group IV comprises the CYP7 (cholesterol 7-alpha-hydroxylase) and CYP51 (lanosterol 14-alpha-demethylase) families, which show significant sequence similarity even though there is no apparent functional resemblance. The CYP8 (prostacyclin synthase) family also falls into this group, and shows high sequence similarity to CYP7 members [
]. Proteins required in the biosynthesis of fungal mycotoxins are also included: cytochrome P450 monooxygenases gloO and gloP from Glarea lozoyensis are required for synthesis of lipohexapeptides of the echinocandin family that prevent fungal cell wall formation by non-competitive inhibition of beta-1,3-glucan synthase [].
Fructose-bisphosphate aldolase (
) [
,
] is a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. There are two classes of fructose-bisphosphate aldolases with different catalytic mechanisms: class I enzymes [
] do not require a metal ion, and are characterised by the formation of a Schiff base intermediate between a highly conserved active site lysine and a substrate carbonyl group, while the class II enzymes require an active-site divalent metal ion. This entry represents the class I enzymes.In vertebrates, three forms of this enzyme are found: aldolase A is expressed in muscle, aldolase B in liver, kidney, stomach and intestine, and aldolase C in brain, heart and ovary. The different isozymes have different catalytic functions: aldolases A and C are mainly involved in glycolysis, while aldolase B is involved in both glycolysis and gluconeogenesis. Defects in aldolase A cause
Glycogen storage disease 12 (GSD12) [], while defects in aldolase B result in hereditary fructose intolerance [].
Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase, (
) [
,
] catalyses the reductive synthesisof deoxyribonucleotides from their corresponding ribonucleotides:
2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H2O = ribonucleoside diphosphate + reduced thioredoxin
RNR provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a
diiron-tyrosyl radical, Class II RNRs, found in bacteria,bacteriophage, algae and archaea, use coenzyme B12
(adenosylcobalamin, AdoCbl). Class III RNRs, found inanaerobic bacteria and bacteriophage, use an FeS cluster and
S-adenosylmethionine to generate a glycyl radical. Manyorganisms have more than one class of RNR present in their
genomes. Class I ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain [
]. The small chain binds two iron atoms [] (three Glu, one Asp, and two His areinvolved in metal binding) and contains an active site tyrosine radical. The
regions of the sequence that contain the metal-binding residues and the activesite tyrosine are conserved in ribonucleotide reductase small chain from
prokaryotes, eukaryotes and viruses.This family consist of the small subunit of class I ribonucleotide reductases. It also includes R2-like ligand-binding oxidase, which is homologous to the ribonucleotide reductase small subunit (R2), but whose function is still unknown [
,
].
Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [
,
,
]. A number of bacterial quinoproteins belong to this family.Enzymes in this group have repeats of a beta propeller.
Sec-independent periplasmic protein translocase, conserved site
Type:
Conserved_site
Description:
Proteins encoded by the mttABC operon (formerly yigTUW), mediate a novel Sec-independent membrane targeting and translocation system in Escherichia coli that interacts with cofactor-containing redox proteins having a S/TRRXFLK "twin arginine"leader motif. This family contains the E. coli mttB gene (TATC) [
].A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N and C termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N terminus and the first cytoplasmic loop region of the E. coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon [
,
].This entry represents a conserved site from the central section of these proteins.
Sec-independent periplasmic protein translocase TatC
Type:
Family
Description:
Proteins encoded by the mttABC operon (formerly yigTUW), mediate a novel Sec-independent membrane targeting and translocation system in Escherichia coli that interacts with cofactor-containing redox proteins having a S/TRRXFLK "twin arginine"leader motif. This family contains the E. coli mttB gene (TATC) [
].A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N and C termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N terminus and the first cytoplasmic loop region of the E. coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon [
,
].
This superfamily represents a four helix up-down bundle domain found in a number of proteins including PsbQ from chloroplast and cyanobacterial photosystem II, and cyclocphilins involved in the assembly and maintenanace of phtosystem II [
,
,
].
Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product.PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [
,
,
]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants [
].This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (
) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [
].
This entry represents various acyl-acyl carrier protein (ACP) thioesterases (TE) which terminate fatty acyl group extension via hydrolysing an acyl group on a fatty acid [
]. These proteins contain a duplication of two 4HBT-like domains.
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [
,
].In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit [
].In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory.The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal β-barrel, a central domain containing the nucleotide-binding site and a C-terminal α-bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho.
This entry represents the beta subunit found in the F1 complex of F-ATPases.F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (
) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [
]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit [
,
].
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [
,
].In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit [
].In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory.The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal β-barrel, a central domain containing the nucleotide-binding site and a C-terminal α-bundle domain [
]. This entry represents the N-terminal domain, which forms a closed β-barrel with Greek-key topology.
F-type ATPases have 2 components, CF1 - the catalytic core - and CF0 - the membrane proton channel. CF1 has five subunits: alpha3, beta3, gamma1, delta1, epsilon1. CF0 has three main subunits: a, b and c. This entry represents the beta subunit of the F1 component.The NMR solution structure of the protein in SDS micelles was found to contain two helices, an N-terminal amphipathic α-helix and a C-terminal α-helix separated by a large unstructured internal domain. The N-terminal α-helix is the Tom20 receptor binding site whereas the C-terminal α-helix is located upstream of the mitochondrial processing peptidase cleavage site [
].
ATPase, alpha/beta subunit, nucleotide-binding domain, active site
Type:
Active_site
Description:
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [
,
]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [
]. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [
,
].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.This group of proteins include the alpha and beta subunits found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively (sometimes called the A and B subunits in V- and A-ATPases), as well as Type 3 secretion system ATPase and Flagellum-specific ATP synthase. This entry represents a 10 amino acid signature. The signature pattern contains two conserved serines. The first serine seems to be important for catalysis - in the ATPase alpha-chain at least - as its mutagenesis causes catalytic impairment.
Arp2/3 binds to pre-existing actin filaments and nucleates new daughter filaments, and thus becomes incorporated into the dynamic actin network at the leading edge of motile cells and other actin-based protrusive structures [
]. In order to nucleate filaments, Arp2/3 must bind to a member of the N-WASp/SCAR family protein []. Arp2 and Arp3 are thought to be brought together after activation, forming an actin-like nucleus for actin monomers to bind and create a new actin filament. In the absence of an activating protein, Arp2/3 shows very little nucleation activity. Recent research has focused on the binding and hydrolysis of ATP by Arp2 and Arp3 [], and crystal structures of the Arp2/3 complex have been solved [].The human Arp2/3 complex consists of ARP2, ARP3, ARPC1B/p41-ARC, ARPC2/p34-ARC, ARPC3/p21-ARC, ARPC4/p20-ARC and ARPC5/p16-ARC. This family represents the ARPC5/p16-ARC subunit.
The Tre2/Bub2/Cdc16 (TBC), lysin motif (LysM), domain catalytic (TLDc) domain is present in all eukaryotes, and its primary sequence is highly conserved among species. The TLDc domain is present in several proteins that share a protective function against oxidative stress (OS). The TLDc domain alone is able to confer oxidative resistance properties to all the TLDc members. The TLDc domain-containing proteins could influence the expression of key oxygen free-radical scavengers that, in turn, reduce the levels of ROS in the cell [
,
,
,
]. The TLDc domain is a conserved protein motif of ~200 amino acids whose overall structure is globular. Two antiparallel β-sheets form a central beta- sandwich, surrounded by two helices and two one-turn helices. Each β-sheet is composed of six and four strands. The two sheets organize as a pseudo-orthogonal β-sandwich and interact with each other only by hydrophobic interactions [].
This entry represents the N-terminal domain of ELL-associated factor (Eaf) proteins, which act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II (Pol II) transcriptional elongation factors [
,
,
,
]. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis []. EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues [,
].
This entry represents the ELL-associated factor (Eaf) family of proteins. They interact with ELL and ELL2, which are RNA polymerase II elongation factors. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation [
]. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis [].
This entry includes Vps55 from budding yeasts and obesity receptor gene-related protein (OB-RGRP or LEPROT) from animals. Both Vps55 and OB-RGRP are important for functioning membrane trafficking to the vacuole/lysosome of eukaryotic cells [
].Vps55 is involved in the secretion of the Golgi form of the soluble vacuolar carboxypeptidase Y, but not the trafficking of the membrane-bound vacuolar alkaline phosphatase [
]. The leptin receptor overlapping transcript (LEPROT) is co-transcribed with Leptin receptor (LepR) but without similarity to the LepR. Mammals have a single LEPROT homologue called LEPROT like-1 (LEPROTL1), which is also included in this entry. LepROT plays roles in insulin pathway [
]. LEPROT and LEPROTL1 have also been shown to influence liver growth hormone signaling in mice [].
This group of sequences contain a conserved C-terminal domain which is found in the Schizosaccharomyces pombe (Fission yeast) protein Cwf19 (
) and its homologues. Cwf19 is part of the Cdc5p complex involved in mRNA splicing [
]. CWF19-like protein DRN1 from Saccharomyces cerevisiae () is involved branched RNA metabolism, modulating the turnover of lariat-intron pre-mRNAs by the lariat-debranching enzyme DBR1 (
) [
]. This domain is found in association with , which is generally N-terminal and adjacent to this domain, and contain evolutionarily conserved cysteine and histidine residues in an arrangement similar to the CCCH-class of zinc fingers [
].
This group of sequences contain a conserved C-terminal domain which is found in the Schizosaccharomyces pombe (Fission yeast) protein Cwf19 (
) and its homologues. Cwf19 is part of the Cdc5p complex involved in mRNA splicing [
]. CWF19-like protein DRN1 from Saccharomyces cerevisiae () is involved branched RNA metabolism, modulating the turnover of lariat-intron pre-mRNAs by the lariat-debranching enzyme DBR1 (
) [
]. This domain is found in association with , which is generally C-terminal and adjacent to this domain. These domains contain evolutionarily conserved cysteine and histidine residues in an arrangement similar to the CCCH-class of zinc fingers [
].
The histidine triad motif (HIT) consists of the conserved sequence HXHXHXX (where X is a hydrophobic amino acid) at the enzymatic catalytic centre, in which the second histidine is strictly conserved and participates in catalysis with the third histidine [
,
,
]. Proteins containing HIT domains form a superfamily of nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides [,
]. They are highly conserved from archaea to humans and are involved in galactose metabolism, DNA repair, and tumor suppression []. HIT-containing proteins can be divided in five families based on catalytic specificities, sequence compositions, and structural similarities of its members: Hint family of protein kinase-interacting proteins, the most ancient class in this superfamily. These include adenosine 5'-monophosphoramide hydrolases (e.g. HIT-nucleotide-binding protein, or HINT) [
,
]. They also have a conserved zinc-binding motif C-X-X-C (where C is a cysteine residue and X is a hydrophobic residue), and a zinc ion is coordinated by these cysteine residues, together with the first histidine residue [].Fragile HIT protein, or FINT, whose name is due to its high rate of mutation at its locus on chromosome 3 in many cancers has been characterised as a tumor suppressor and plays a role in the hydrolysis of dinucleotide polyphosphates [
,
]. HINT and FINT HIT domains have a topology similar to that found in the N-terminal of protein kinases [].GalT family. These include specific nucleoside monophosphate transferases (e.g. galactose-1-phosphate uridylyltransferase, diadenosine tetraphosphate phosphorylase, and adenylyl sulphate:phosphate adenylytransferase). These HIT domains are a duplication consisting of 2 HIT-like motifs. This family binds zinc and iron [
,
].Aprataxin, which hydrolyses both dinucleotide polyphosphates and phophoramidates, and is involved in DNA repair systems [
,
].mRNA decapping enzyme family. These include enzymes such as DcpS and Dcp2. The HIT-domain is usually C-terminal in these proteins [
,
].
The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation.
The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator [
].
This entry represents a domain found in the HABP4 protein family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role
in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan [
]. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability []. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function.Hyaluronan/mRNA-binding protein may be involved in nuclear functions such as the remodeling of chromatin and the regulation of transcription [
,
].
This domain is found at the N-terminal region of the Stm1 and similar proteins. Stm1 is a G4 quadraplex and purine motif triplex nucleic acid-binding protein. It has been implicated in many biological processes including apoptosis and telomere biosynthesis. Stm1 is known to interact with Cdc13 [
], and is known to associate with ribosomes and nuclear telomere cap complexes []. This domain is also found at the N-terminal of some 'RGG repeats nuclear RNA binding proteins' [].
This family includes ribosomal L4/L1 from most organellar forms, but excludes homologues from the eukaryotic cytoplasm and from archaea. The L4 protein from yeast has been shown to bind rRNA [
]. Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This family includes ribosomal L4/L1 from eukaryotes and plants and L4 from bacteria. L4 from yeast has been shown to bind rRNA [
]. These proteins have 246 (plant) to 427 (human) amino acids.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].This superfamily represents a domain found in ribosomal protein L4. Its structure consists of three layers (alpha/beta/alpha) with parallel β-sheet of four strands.
This entry represents a family of GTPases associated with ribosome biogenesis, as typified by YsxC from Bacillus subtilis [
]. This family is widely distributed among bacteria, being found in around eighty percent of currently sequenced bacterial genomes. The proteins are commonly annotated as EngB based on their homology to EngA, one of several other GTPases involved in ribosome biogenesis. Some eukaryotic proteins are included in this entry and probably represent organellar sequences.
Several proteins have recently been shown to contain the 5 structural motifs characteristic
of GTP-binding proteins []. These include murine DRG protein; GTP1 proteinfrom Schizosaccharomyces pombe; OBG protein from Bacillus subtilis [
]; ferrous iron transport protein B [
] and several others.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups:
Bacterial L21.Marchantia polymorpha chloroplast L21.Cyanelle L21.Plant chloroplast L21 (nuclear-encoded).Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.
Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups:
Bacterial L21.Marchantia polymorpha chloroplast L21.Cyanelle L21.Plant chloroplast L21 (nuclear-encoded).Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. RNA 3'-terminal phosphate cyclase (
) [
,
] catalyses the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA.ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
These enzymes might be responsible for production of the cyclic phosphate RNA ends that are known to be required by many RNA ligases in both prokaryotes and eukaryotes.RNA cyclase is a protein of from 36 to 42kDa. The best conserved region is a
glycine-rich stretch of residues located in the central part of the sequence and which is reminiscent of various ATP, GTP or AMP glycine-rich loops.The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller insert domain disrupts the large domain, and uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin [
]. Although the active site of this enzyme could not be unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources []. This entry represents the small insert domain that interrupts the large repetitive domain.
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. Type 1 RNA 3'-terminal phosphate cyclases (
) [
,
] catalyse the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA:ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
The physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclisation of the 3' end of U6 snRNA [
].A second subfamily of RNA 3'-terminal phosphate cyclases (type 2) that do not have cyclase activity have been identified in eukaryotes. They are localised to the nucleolus and are involved in ribosomal modification [
].
RNA 3'-terminal phosphate cyclase-like, conserved site
Type:
Conserved_site
Description:
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. Type 1 RNA 3'-terminal phosphate cyclases (
) [
,
] catalyse the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA:ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
The physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclisation of the 3' end of U6 snRNA [].A second subfamily of RNA 3'-terminal phosphate cyclases (type 2) that do not have cyclase activity have been identified in eukaryotes. They are localised to the nucleolus and are involved in ribosomal modification [
].RNA 3'-terminal phosphate cyclases contain a conserved glycine-rich stretch of residues located in the central part of the sequence, which is reminiscent of various ATP, GTP or AMP glycine-rich loops, and may be involved in AMP binding. This entry represents the conserved site.
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. Type 1 RNA 3'-terminal phosphate cyclases (
) [
,
] catalyse the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA:ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
The physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclisation of the 3' end of U6 snRNA [
].A second subfamily of RNA 3'-terminal phosphate cyclases (type 2) that do not have cyclase activity have been identified in eukaryotes. They are localised to the nucleolus and are involved in ribosomal modification [
].This entry represents the type 2 RNA 3'-terminal phosphate cyclases, also known as RNA'-terminal-phosphate-cyclase-like (Rcl) proteins [
].
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. Type 1 RNA 3'-terminal phosphate cyclases (
) [
,
] catalyse the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA:ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
The physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclisation of the 3' end of U6 snRNA [
].A second subfamily of RNA 3'-terminal phosphate cyclases (type 2) that do not have cyclase activity have been identified in eukaryotes. They are localised to the nucleolus and are involved in ribosomal modification [
].The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller domain uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin [
]. Although the active site of this enzyme has not been unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources [].
This superfamily represents an alpha/beta domain consisting of alternating β-strands and alpha helices in two layer. This domain is found in RNA 3'-terminal phosphate cyclase (RPTC), where it occurs as a duplication of three repeats of this fold packed together around a pseudo three-fold axis [
]. RNA cyclases are a family of RNA-modifying enzymes that catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA. These cyclases contain an insert alpha/beta domain with a thioredoxin topology (
).
This domain is also found in enolpyruvate transferase, where it occurs as a duplication of six repeats of this fold organised into two RPTC-like domains [
,
]. Enolpyruvate transferase is the first enzyme in bacterial peptidoglycan biosynthesis, catalysing the transfer of enolpyruvate from phosphoenolpyruvate to UDP-N-acetyl-glucosamine.
PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as α-β-β-β-α-β. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core β-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding α-helix []. The family is not in general fused with any other domains, so its function cannot be predicted [].This family of uncharacterised plant proteins are defined by a region found toward the C terminus. This region is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [
]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].A number of eukaryotic, bacterial and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of:Mammalian L30 [
].Leishmania major L30.Yeast YL32 [
].Bacillus subtilis proteins YbxF and YlxQ [
].Thermococcus celer L30 [
].A probable ribosomal protein (ORF 1) from Methanococcus vannielii [
].A probable ribosomal protein (ORF 104) from Sulfolobus acidocaldarius [
].These proteins, of the L30e family, have 82 to 114 amino-acid residues.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [
].
Extensins are plant cell-wall proteins; they can account for up to 20% of
the dry weight of the cell wall. They are highly-glycosylated, possiblyreflecting their interactions with cell-wall carbohydrates. Amongst their
functions is cell wall strengthening in response to mechanical stress (e.g.,during attack by pests, plant-bending in the wind, etc.).
By contrast with extensin genes, pistil-specific extensin-like genes arenot induced under stress conditions. Gene expression is organ-specific
and temporally regulated during pistil development. After pollination, transcript levels of pistil-specific extensin-like genes change relative to
levels in unpollinated pistils []. The protein sequence is characterisedby multiple tandem ser-pro-pro-pro-pro pentapeptide repeats.
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 ofthe 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 speciesnames have identical designations, they are discriminated from one another
by adding one or more letters (as necessary) to each species designation.A number of plant pollen proteins, whose biological function is not yet
known, are structurally related [].These proteins are most probably secreted and consist of about 145 residues.
There are six cysteineswhich are conserved in the sequence of these proteins. They seem to be
involved in disulphide bonds. The pollen allergens in this family belong to the Ole e 1 family and include Ole e 1, Pla l 1, Che a 1, Phl p 11 and Lig v 1.
The plant RAPID ALKALINIZATION FACTOR (RALF) family consists of extracellular peptides that serve as extracellular signals. RALF1, a 5kDa ubiquitous polypeptide in plants, arrests root growth and development [
,
]. RALF4/19 peptides interact with LRX proteins to control pollen tube growth [].
Protein phosphatase 2A (PP2A) is a major intracellular protein
phosphatase that regulates multiple aspects of cell growth and metabolism.The ability of this widely distributed heterotrimeric enzyme to act on a
diverse array of substrates is largely controlled by the nature of itsregulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [
].
This entry represents the N-terminal domain of acyl-ATP thioesterases from bacteria and eukaryotes. These proteins are typically between 120 and 131 amino acids in length. The plant acyl-acyl carrier protein (ACP) thioesterases (TEs) play an essential role in chain termination during de novo fatty acid synthesis [
].
This entry represents a conserved region approximately 60 residues long within the eukaryotic targeting protein for Xklp2 (TPX2). Xklp2 is a kinesin-like protein localised on centrosomes throughout the cell cycle and on spindle pole microtubules during metaphase. In Xenopus, it has been shown that Xklp2 protein is required for centrosome separation and maintenance of spindle bi-polarity [
,
]. TPX2 is a microtubule-associated protein that mediates the binding of the C-terminal domain of Xklp2 to microtubules. It is phosphorylated during mitosis in a microtubule-dependent way [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [
], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [
,
,
]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents class B cytochrome P450 proteins, which are part of 3-component systems in bacteria, mitochondria and certain fungal enzymes.
Many members of this family have no known function and are predicted to be integral membrane proteins.One member of the family has been characterised as protein PGR (AtPGR). PGR is suggested to be a potential glucose-responsive regulator in carbohydrate metabolism in plants. This entry also includes protein VTE6, which is a Pphytyl-phosphate kinase catalyzing the conversion of phytyl-monophosphate to phytyl-diphosphate [
].
This entry includes a variety of exonuclease proteins, such as ribonuclease T [
] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.
Iwr1 is involved in transcription from polymerase II promoters; it interacts with with most of the polymerase II subunits [
]. Deletion of this protein results in hypersensitivity to the K1 killer toxin []. This entry represents a domain found in Iwr1. This domain can also be found in SLC7A6OS and RDM4 (At2g30280). RDM4 is a regulatory factor for several RNA polymerases [
].
O-Glycosyl hydrolases (
) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [
,
]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.Glycoside hydrolase family 1
comprises enzymes with a number of known activities; beta-glucosidase (
); beta-galactosidase (
); 6-phospho-beta-galactosidase (
); 6-phospho-beta-glucosidase (
); lactase-phlorizin hydrolase (
), (
); beta-mannosidase (
); myrosinase (
).
Bile acid:sodium symporter/arsenical resistance protein Acr3
Type:
Family
Description:
This family of proteins are found both in prokaryotes and eukaryotes. They are related to the human bile acid:sodium symporters (TC 2.A.28), which are transmembrane proteins functioning in the liver in the uptake of bile acids from portal blood plasma, a process mediated by the co-transport of Na
+[
].This entry also includes members of the ACR3 family of arsenite (As(III)) permeases, which confer resistance to arsenic by extrusion from cells [
]. They exist in prokaryotes and eukaryotes (lower plants and fungi) [,
]. The ACR3 permeases have ten-transmembrane span topology []. Corynebacterium glutamicum has three Acr3 proteins, CgAcr3-1, CgAcr3-2, and CgAcr3-3. CgAcr3-1 is thought to be an antiporter that catalyses arsenite-proton exchange [].The Shewanella oneidensis Acr3 is not able to transport As(III) and confers resistance only to arsenate (As(V)) [
], whereas the Acr3 orthologue from Synechocystis mediates tolerance to As(III), As(V) and antimonite (Sb(III)) [].In budding yeast, overexpression of the Acr3 gene confers an arsenite- but not an arsenate-resistance phenotype [
]. Saccharomyces cerevisiae Acr3 is a plasma membrane metalloid/H+ antiporter that transports arsenite and antimonite [].
This entry represents the subunit 2 (beta) from DNA-directed RNA polymerases.DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits. The clamp is a mobile structure that grips DNA during elongation [
,
,
,
,
,
,
,
,
].
RNA polymerases (
) catalyse the DNA dependent polymerisation of RNA.
Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (notincluding mitochondrial and chloroplast polymerases). This domain represents the
hybrid-binding domain and the wall domain []. Thehybrid-binding domain binds the nascent RNA strand/template DNA strand in the
Pol II transcription elongation complex. This domain contains the important structuralmotifs, switch 3 and the flap loop and binds an active site metal ion [
]. This domain is also involved in binding to Rpb1 and Rpb3[
]. Many of the bacterial members contain large insertionswithin this domain, which are known as dispensable region 2 (DRII).
RNA polymerases (
) catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This entry describes a structural region consisting of an OB-fold beta barrel that is found in RNA polymerase II Rpb2 [
,
].
RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed switch 4. The switches within the polymerase are thought to signal different stages of transcription [
].
RNA polymerases (
) catalyse the DNA dependent polymerisation of RNA.
Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (notincluding mitochondrial. and chloroplast polymerases). This domain represents the
hybrid binding domain and the wall domain []. Thehybrid-binding domain binds the nascent RNA strand / template DNA strand in the
Pol II transcription elongation complex. This domain contains the important structuralmotifs, switch 3 and the flap loop and binds an active site metal ion [
]. This domain is also involved in binding to Rpb1 and Rpb3[
]. Many of the bacterial members contain large insertionswithin this domain, which is known as dispensable region 2 (DRII).
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain [
]. The other lobe, RNA polymerase Rpb2, domain 2, is nested within this domain.
RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. It is also known as the lobe domain [
]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, a region known as dispensable region 1 (DRI).
DNA-directed RNA polymerase I subunit RPA2, domain 4
Type:
Domain
Description:
This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [
].
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 3, is also known as the fork domain and is proximal to catalytic site [
].
