Cofactor assembly of complex C subunit B, CCB2/CCB4
Type:
Family
Description:
Cofactor maturation pathways such as the CCB system (system IV) for cytochrome c-heme attachment are conserved in all organisms performing oxygenic photosynthesis [
]. The CCB system consists of four proteins: CCB1-4. CCB2 and CCB4 are paralogues derived from a unique cyanobacterial ancestor []. Orthologues are conserved in higher plants [].
Uridylate kinases (also known as UMP kinases) are key enzymes in the synthesis of nucleoside triphosphates. They catalyse the reversible transfer of the gamma-phosphoryl group from an ATP donor to UMP, yielding UDP, which is the starting point for the synthesis of all other pyrimidine nucleotides. The eukaryotic enzyme has a dual specificity, phosphorylating both UMP and CMP, while the bacterial enzyme is specific to UMP. The bacterial enzyme shows no sequence similarity to the eukaryotic enzyme or other nucleoside monophosphate kinases, but rather appears to be part of the amino acid kinase family. It is dependent on magnesium for activity and is activated by GTP and repressed by UTP [
,
]. In many bacterial genomes, the gene tends to be located immediately downstream of elongation factor T and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function is found in the archaea and in spirochetes.Structurally, the bacterial and archaeal proteins are homohexamers centred around a hollow nucleus and organised as a trimer of dimers [
,
]. Each monomer within the protein forms the amino acid kinase fold and can be divided into an N-terminal region which binds UMP and mediates intersubunit interactions within the dimer, and a C-terminal region which binds ATP and contains a mobile loop covering the active site. Inhibition of enzyme activity by UTP appears to be due to competition for the binding site for UMP, not allosteric inhibition as was previously suspected.Uridylate kinase PUMPKIN, chloroplastic from Arabidopsis thaliana is essential for retaining photosynthetic activity in chloroplasts as it is required for specific post-transcriptional processes of many plastid transcripts [
,
]. This entry represents uridine monophosphate kinase predominantly found in bacteria and plant chloroplasts.
The conversion of dTDP-glucose into dTDP-4-keto-6-deoxyglucose by Escherichia coli dTDP-glucose 4,6-dehydratase takes place in the active site in three steps: dehydrogenation to dTDP-4-ketoglucose, dehydration to dTDP-4-ketoglucose-5,6-ene, and rereduction of C6 to the methyl group. The 4,6-dehydratase makes use of tightly bound NAD
+as the coenzyme for transiently oxidizing the substrate, activating it for the dehydration step [
]. This and other 4,6-dehydratases catalyze the first committed step in all 6-deoxysugar biosynthetic pathways described to date. Numerous 6-deoxysugars are used in bacterial lipopolysaccharide production as well as in the biosynthesis of a diverse array of secondary metabolites.
This family includes eukaryotic translation initiation factor 6 (eIF6) as well as presumed archaeal homologues.The assembly of 80S ribosomes requires joining of the 40S and 60S subunits, which is triggered by the formation of an initiation complex on the 40S subunit. This event is rate-limiting for translation, and depends on external stimuli and the status of the cell. Eukaryotic translation initiation factor 6 (eIF6) binds specifically to the free 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit ribosomes [
]. Furthermore, eIF6 interacts in the cytoplasm with RACK1, a receptor for activated protein kinase C (PKC). RACK1 is a major component of translating ribosomes, which harbour significant amounts of PKC. Loading 60S subunits with eIF6 caused a dose-dependent translational block and impairment of 80S formation, which are reversed by expression of RACK1 and stimulation of PKC in vivo and in vitro. PKC stimulation leads to eIF6 phosphorylation and its release, promoting 80S subunit formation. RACK1 provides a physical and functional link between PKC signalling and ribosome activation [,
,
].All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved C-terminal extension which is not required for ribosomal binding, and may have an alternative function [
].
Protein N-terminal asparagine amidohydrolase (NTAN1) acts on the side-chain deamidation of N-terminal asparagine residues to aspartate. It is required for the ubiquitin-dependent turnover of intracellular proteins that initiate with Met-Asn. These proteins are acetylated on the retained initiator methionine and can subsequently be modified by the removal of N-acetyl methionine by acylaminoacid hydrolase (AAH). Conversion of the resulting N-terminal asparagine to aspartate by PNAD renders the protein susceptible to arginylation, polyubiquitination and degradation as specified by the N-end rule. NTAN1 does not act on substrates with internal or C-terminal asparagines and does not act on glutamine residues in any position [
,
].
An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2. Dcp1 is a coactivator that binds to the decapping enzyme Dcp2 and forms a decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation [
]. Yeast Dcp1 interact directly with Dcp2, however, the Dcp1-Dcp2 interaction is promoted by an additional factor, EDC4 []. In the nervous system, it promotes neurons' lifespan through the negative regulation of the insulin-like peptide ins-7 expression [].
This entry represents iron-sulphur domain containing proteins that have a CDGSH sequence motif (although the Ser residue can also be an Ala or Thr), and is found in proteins from a wide range of organisms with the exception of fungi. The CDGSH-type domain binds a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family [
].CDGSH-type domains are found in mitoNEET, an iron-containing integral protein of the outer mitochondrian membrane (OMM). MitoNEET forms a dimeric structure with a NEET fold, and contains two domains: a β-cap region and a cluster-binding domain that coordinated two acid-labile 2Fe-2S clusters (one bound to each protomer) [
]. The CDGSH iron-sulphur domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, () [
,
]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM.
This superfamily represents a domain found in several uncharacterised proteins, including YbeD from Escherichia coli. YbeD shows structural homology to the regulatory domain from 3-phosphoglycerate dehydrogenase, suggesting a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system [
].
This family includes UPF0250 protein YbeD from Escherichia coli and similar prokaryotic proteins. YbeD shows structural homology to the regulatory domain from 3-phosphoglycerate dehydrogenase, which suggests a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system [
]. The protein has been shown to play an important role in enduring high-temperature stress [].
The large subunit (R1) of ribonucleotide reductase (RNR), is an essential enzyme required for DNA replication and DNA repair. In both Escherichia coli and higher organisms, the enzyme consists of two non-identical subunits, a dimer of an 85kDa protein, R1, and a dimer of a 45kDa protein, R2. Both subunits are essential for RNR enzyme activity - R1 contains, in the substrate binding site, the reducing active cysteine pair and R2 provides a catalytically essential organic radical. R1 is able to bind and reduce the four common ribonucleoside diphosphates. Substrate specificity is determined by nucleoside triphosphates binding to a protein site different from the active site and acting as allosteric effectors. Thus the presence of ATP makes the enzyme reduce CDP and UDP, dGTP favours ADP reduction and dTTP favours GDP reduction. dATP is a general inhibitor. This provides a mechanism for a balanced enzymatic production of building blocks for DNA synthesis [
]. This superfamily represents a mainly alpha domain found at the N terminus of the ribonucleotide reductase R1 subunit [
].
The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators [
].In ribonucleotide reductase protein R1 (
) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices [
]. It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region []. This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.
Ribonucleotide reductase large subunit, C-terminal
Type:
Domain
Description:
Ribonucleotide reductase (RNR,
) [
,
] catalyzes the reductivesynthesis of deoxyribonucleotides from their corresponding ribonucleotides. It 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 in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes.
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 reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals, the function of each metallocofactor is to generate an active site thiyl radical. This thiyl radical then initiates the nucleotide reduction process by hydrogen atom abstraction from the ribonucleotide [
]. The radical-based reaction involves five cysteines: two of these are located at adjacent anti-parallel strands in a new type of ten-stranded alpha/β-barrel; two others reside at the carboxyl end in a flexible arm; and the fifth, in a loop in the centre of the barrel, is positioned to initiate the radical reaction []. There are several regions of similarity in the sequence of the large chain of prokaryotes, eukaryotes and viruses spread across 3 domains: an N-terminal domain common to the mammalian and bacterial enzymes; a C-terminal domain common to the mammalian and viral ribonucleotide reductases; and a central domain common to all three [].
Ribonucleotide reductase large subunit, N-terminal
Type:
Domain
Description:
Ribonucleotide reductase (RNR,
) [
,
] catalyzes the reductivesynthesis of deoxyribonucleotides from their corresponding ribonucleotides. It 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 in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes.
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 reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals, the function of each metallocofactor is to generate an active site thiyl radical. This thiyl radical then initiates the nucleotide reduction process by hydrogen atom abstraction from the ribonucleotide [
]. The radical-based reaction involves five cysteines: two of these are located at adjacent anti-parallel strands in a new type of ten-stranded alpha/β-barrel; two others reside at the carboxyl end in a flexible arm; and the fifth, in a loop in the centre of the barrel, is positioned to initiate the radical reaction []. There are several regions of similarity in the sequence of the large chain of prokaryotes, eukaryotes and viruses spread across 3 domains: an N-terminal domain common to the mammalian and bacterial enzymes; a C-terminal domain common to the mammalian and viral ribonucleotide reductases; and a central domain common to all three [].
This entry represent a domain found in bacterial NnrU proteins. It can also be found in plant 15-cis-zeta-carotene isomerase (Z-ISO). NnrU is thought to be involved in the reduction of nitric oxide. The exact function of NnrU is unclear. It is thought however that NnrU and perhaps NnrT are required for expression of both nirK and nor [
].Plant Z-ISO is an isomerase involved in the biosynthesis of carotenoids. It catalyzes the cis- to trans-conversion of the 15-cis-bond in 9,15,9'-tri-cis-zeta-carotene [
].
This is the conserved barrel domain of the 'cupin' superfamily found in (S)-ureidoglycine aminohydrolase (UGlyAH or UGHY) from E.coli, with a conserved jelly roll-like β-barrel fold capable of homodimerization. This enzyme is involved in the anaerobic nitrogen utilization via the assimilation of allantoin and catalyses the second stereospecific hydrolysis reaction (deamination) of the allantoin degradation pathway, producing S-ureidoglycolate and ammonia from S-ureidoglycine [,
].This domain is also present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity [
]. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins [].
Ketol-acid reductoisomerases (KARI) catalyses two steps in the biosynthesis of branched-chain amino acids. The reaction involves an Mg2+ dependent alkyl migration followed by an NADPH-dependent reduction of the 2-keto group. There are two groups of KARI enzymes: class I is a short form found in fungi and most bacteria, and class II is a long form found in plants and certain bacteria (although their sequences differ) [
,
]. However, there has also been a long form found in certain bacteria, but these differ from class II sequences found in plants.This group represents a ketol-acid reductoisomerase, plant type.
This PH-like domain can be found in the N-terminal region of NECAPs (also known as adaptin ear-binding coat-associated proteins). NECAPs are alpha-ear-binding proteins that enrich on clathrin-coated vesicles (CCVs). NECAP-1 is expressed in brain and non-neuronal tissues and cells while NECAP-2 is ubiquitously expressed. The PH-like domain of NECAPs is a protein-binding interface that mimics the FxDxF motif binding properties of the alpha-ear and is called PHear (PH fold with ear-like function) domain [
].PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes [
,
,
,
,
].
Thioredoxin domain-containing protein 17-like domain
Type:
Domain
Description:
This domain can be found in thioredoxin domain-containing protein 17 (also known as TRP14), which is a highly conserved and ubiquitously expressed oxidoreductase involved in controlling of cellular redox signalling pathways. TXNDC17 has been shown to efficiently reduce l-cystine and can directly reactivate oxidized protein-tyrosine phosphatase PTP1B [
].
This domain is found in GSK3-beta interaction protein (GSKIP), which binds to GSK3beta [
]. It is also found as a short domain towards the N terminus in clustered mitochondria protein, also known as clueless in Drosophila, which is involved in proper cytoplasmic distribution of mitochondria [,
,
].
The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in highly conserved eukaryotic proteins required for correct mitochondrial dispersal [
,
]. The exact function of the domain is unknown [].
The Notch receptor is a large, cell surface transmembrane protein involved in a wide variety of developmental processes in higher organisms [
]. It becomes activated when its extracellular region binds to ligands located on adjacent cells. Much of this extracellular region is composed of EGF-like repeats, many of which can be O-fucosylated. A number of these O-fucosylated repeats can in turn be further modified by the action of a beta-1,3-N-acetylglucosaminyltransferase enzyme known as Fringe []. Fringe potentiates the activation of Notch by Delta ligands, while inhibiting activation by Serrate/Jagged ligands. This regulation of Notch signalling by Fringe is important in many processes [].Four distinct Fringe proteins have so far been studied in detail; Drosophila Fringe (Dfng) and its three mammalian homologues Lunatic Fringe (Lfng), Radical Fringe (Rfng) and Manic Fringe (Mfng). Dfng, Lfng and Rfng have all been shown to play important roles in developmental processes within their host, though the phenotype of mutants can vary between species e.g. Rfng mutants are retarded in wing development in chickens, but have no obvious phenotype in mice [
,
,
]. Mfng mutants have not, so far, been charcterised. Biochemical studies indicate that the Fringe proteins are fucose-specific transferases requiring manganese for activity and utilising UDP-N-acetylglucosamine as a donor substrate []. The three mammalian proteins show distinct variations in their catalytic efficiencies with different substrates.Dfng is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands which is localised to the Golgi apparatus [
] (not secreted as previously thought). Modification of Notch occurs through glycosylation by Dfng. This entry consists of Fringe proteins and related glycosyltransferase enzymes including:
Beta-1,3-glucosyltransferase, which glucosylates O-linked fucosylglycan on thrombospondin type 1 repeat domains [
].Core 1 beta1,3-galactosyltransferase 1, generates the core T antigen, which is a precursor for many extended O-glycans in glycoproteins and plays a central role in many processes, such as angiogenesis, thrombopoiesis and kidney homeostasis development [
].
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 L29e forms part of the 60S ribosomal subunit [
]. This family is found in eukaryotes. There are there are 20 to 22 copies of the L29 gene in Rattus norvegicus (Rat). Rat L29 is related to yeast ribosomal protein YL43 [].
Pyridine nucleotide-disulphide oxidoreductase, class I, active site
Type:
Active_site
Description:
The pyridine nucleotide-disulphide oxidoreductases are FAD flavoproteins which contain a pair of redox-active cysteines involved in the transfer of reducing equivalents from the FAD cofactor to the substrate. On the basis of sequence and structural similarities [
] these enzymes can be classified into two categories. The first category groups together the following enzymes [,
,
,
]:Glutathione reductase (
) (GR).
Higher eukaryotes thioredoxin reductase (
).
Trypanothione reductase (
).
Lipoamide dehydrogenase (
), the E3 component of alpha-ketoacid dehydrogenase complexes.
Mercuric reductase (
).
The sequence around the two cysteines involved in the redox-active disulphide bond is conserved and can be used as a signature pattern.Note: In positions 6 and 7 of the pattern all known sequences have Asn-(Val/ Ile) with the exception of GR from plant chloroplasts and from cyanobacteria which have Ile-Arg [
].
Proteins containing this domain are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In
Bacillus subtilis, TenA is one of a number of proteins that enhance the expression of extracellular enzymes, such asalkaline protease, neutral protease and levansucrase [
] and has been identified as a Thiaminase 2 []. The THI-4 protein, which is involved in thiamine biosynthesis, also contains this domain. The C-terminal part of these proteins consistently show significant sequence similarity to TenA proteins. This similarity was first noted with the Neurospora crassa THI-4 []. This domain is also found in bacterial coenzyme PQQ synthesis protein C or PQQC. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes,including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria [
]. PQQC has been found to be required in the synthesis of PQQ, but its function is unclear.
The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments.Members of the importin-alpha (karyopherin-alpha) family can form heterodimers with importin-beta. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Proteins can contain one (monopartite) or two (bipartite) NLS motifs. Importin-alpha contains several armadillo (ARM) repeats, which produce a curving structure with two NLS-binding sites, a major one close to the N terminus and a minor one close to the C terminus.Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. The N-terminal importin-beta-binding (IBB) domain of importin-alpha contains an auto-regulatory region that mimics the NLS motif [
]. The release of importin-beta frees the auto-regulatory region on importin-alpha to loop back and bind to the major NLS-binding site, causing the cargo to be released [].This entry represents importin alpha.
The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments.Members of the importin-alpha (karyopherin-alpha) family can form heterodimers with importin-beta. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Proteins can contain one (monopartite) or two (bipartite) NLS motifs. Importin-alpha contains several armadillo (ARM) repeats, which produce a curving structure with two NLS-binding sites, a major one close to the N terminus and a minor one close to the C terminus.Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. The N-terminal importin-beta-binding (IBB) domain of importin-alpha contains an auto-regulatory region that mimics the NLS motif [
]. The release of importin-beta frees the auto-regulatory region on importin-alpha to loop back and bind to the major NLS-binding site, causing the cargo to be released [].This entry represents the N-terminal IBB domain of importin-alpha that contains the auto-regulatory region.
Electron transfer flavoprotein, alpha subunit, C-terminal
Type:
Domain
Description:
Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, "housekeeping"ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) [
]. ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP [
,
,
,
,
]. ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical α-β-alpha sandwich fold, while domain II forms an α-β-alpha sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides.This entry represents the C-terminal domain of the alpha subunit of both Group I and Group II ETFs.
Electron transfer flavoprotein, alpha/beta-subunit, N-terminal
Type:
Domain
Description:
Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, "housekeeping"ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) [
]. ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP [
,
,
,
,
]. ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical α-β-alpha sandwich fold, while domain II forms an α-β-alpha sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides.This entry represents the N-terminal domain of both the alpha and beta subunits from Group I and Group II ETFs.
This family consists of various potassium transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J (
). These proteins are involved in active sodium uptake utilizing ATP in the process. TrkH from Escherichia coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in this organism [
,
]. This protein interacts with TrkA and requires TrkE for transport activity [].
This family consists of several hypothetical proteins of around 250 residues in length, which are found in both plants and bacteria. The function of this family is unknown.
3-hydroxyacyl-CoA dehydrogenase (
) (HCDH) [
] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional.In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain [
].The other proteins structurally related to HCDH are:Bacterial 3-hydroxybutyryl-CoA dehydrogenase (
) which reduces 3-hydroxybutanoyl-CoA to acetoacetyl-CoA [
].Eye lens protein lambda-crystallin [
], which is specific to lagomorphes (such as rabbit).There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence.
This domain is found in tubulin-binding cofactor C (or tubulin-specific chaperone C) (TBCC) and in protein XRP2. TBCC is a folding cofactor that participates in tubulin biogenesis along with the other tubulin folding cofactors A (TBCA), B (TBCB), E (TBCE) and D (TBCD), as well as the GTP-binding protein Arl2 [
,
]. XRP2 is a GTPase-activating protein (GAP) involved in intracellular trafficking [].
The tubulin heterodimer consists of one alpha- and one beta-tubulin polypeptide. In humans, five tubulin-specific chaperones termed TBCA/B/C/D/E are essential for bring the alpha- and beta-tubulin subunits together into a tightly associated heterodimer. Following the generation of quasi-native beta- and alpha-tubulin polypeptides (via multiple rounds of ATP-dependent interaction with the cytosolic chaperonin), TBCA and TBCB bind to and stabilise newly synthesised beta- and alpha-tubulin, respectively. The exchange of beta-tubulin between TBCA and TBCD, and of alpha-tubulin between TBCB and TBCE, resulting in the formation of TBCD/beta and TBCE/alpha. These two complexes then interact with each other and form a supercomplex (TBCE/alpha/TBCD/beta). Interaction of the supercomplex with TBCC causes the disassembly of the supercomplex and the release of E-site GDP-bound alpha/beta tubulin heterodimer, which becomes polymerization competent following spontaneous exchange with GTP [
].This entry represents tubulin-specific chaperone C (TBCC, also known as tubulin-folding cofactor C), which is involved in the final step of the tubulin folding pathway [
,
]. In Arabidopsis thaliana, it is required for continuous microtubule cytoskeleton organisation, mitotic division, cytokinesis, and to couple cell cycle progression to cell division in embryos and endosperms [,
].
This entry includes a group of heat shock protein interacting proteins, including AHSA1/2 from animals and Aha1/Hch1 from budding yeasts, and it represents a domain found at the N-terminal of Aha1 and AHSA1/2, while in Hch1 is the only domain. Aha1 adopts a secondary structure consisting of an N-terminal α-helix leading into a four-stranded meandering antiparallel β-sheet, followed by a C-terminal α-helix. The two α-helices are packed together, with the β-sheet curving around them. The N-terminal domain of Aha1 interacts with the central segment of Hsp90 which induces the conformational rearrangements of Hsp90 that favor the N-terminal domain-dimerized state of the chaperone and ends leads to the stimulation of its ATPase activity []. Activator of 90kDa heat shock protein ATPase Aha1/AHSA1 (AHSA1/p38,
) is known to interact with the middle domain of Hsp90, and stimulate its ATPase activity [
,
], where one Aha1/AHSA1 molecule per Hsp90 dimer is sufficient for this stimulation. It is probably a general up regulator of Hsp90 function, particularly contributing to its efficiency in conditions of increased stress []. It is also known to interact with the cytoplasmic domain of the VSV G protein, and may thus be involved in protein transport []. It has also been reported as being under expressed in Down's syndrome.In budding yeasts, both Hch1 and Aha1 bind to the middle domain of Hsp90 and stimulate ATPase activity [
,
]. However, Aha1 but not Hch1 stimulated the intrinsic ATPase activity of Hsp90 5-fold []. Hch1 and Aha1 may regulate Hsp90 function in distinct ways [].
Isoleucine-tRNA ligase (also known as Isoleucyl-tRNA synthetase)(
) is an alpha monomer that belongs to class Ia. The enzyme, isoleucine-tRNA ligase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing"step, the ligase itself rapidly hydrolyses only the valylated products [
,
] as shown from the crystal structures. The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [
,
]. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [,
,
]. However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [].In eukaryotes, two forms of isoleucine-tRNA synthetase exist, a cytoplasmic form and a mitochondrial form [
]. Type 1 includes bacterial and mitochondrial (gene iars2) isoleucine-tRNA ligases.
This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc.DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (
) and AP lyase activity (
) [
]. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity;
). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge [
]. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [,
]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (
) [
,
]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) [].
Isoleucine-tRNA ligase (also known as Isoleucyl-tRNA synthetase)(
) is an alpha monomer that belongs to class Ia. The enzyme, isoleucine-tRNA ligase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing"step, the ligase itself rapidly hydrolyses only the valylated products [
,
] as shown from the crystal structures. 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 domain found in a group of plant proteins, including DNA oxidative demethylase ALKBH2 from Arabidopsis thaliana , a dioxygenase that repairs alkylated DNA containing 1-methyladenine and 1-ethenoadenine by oxidative demethylation [
].
Late embryogenesis abundant protein, LEA_3 subgroup
Type:
Family
Description:
LEA (late embryogenesis abundant) proteins were first identified in land plants. Plant LEA proteins have been found to accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. Later, LEA homologues have also been found in various species [
,
]. They have been classified into several subgroups in Pfam and according to Bray and Dure [].This entry represents Pfam LEA_3, or LEA5 (D-73) from Dure. Proteins in this entry includes LEA-5 from Citrus sinensis [
], whose expression is induced by salt, drought and heat stress []. This entry also includes At4g02380 (SAG21), At1g02820 (LEA2), At3g53770 (LEA37) and At4g15910 (LEA41) from Arabidopsis [].
This family of proteins is found in eukaryotes. Proteins in this family are typically between 173 and 294 amino acids in length. This family includes Human C1orf131.
This is a domain of unknown function found on the C-terminal of C7orf25 protein UPF0415. The C-terminal domain is homologous to the known PIN-like domains. The PIN-like domain is widespread among eukaryotes, including animals, plants, and fungi, but also present in some cyanobacteria, Deinococcus, and dsDNA viruses from the Mimiviridae family. The domain retains up to four potential catalytic residues, thus, depending on the protein is predicted to be an active or inactive nuclease and in a majority of the family members, the PIN-like domain is N-terminally fused with a potentially active PD-(D/E)XK-like domain
[
].
Alkaptonuria (AKU), a rare hereditary disorder, was the first disease to be interpreted as an inborn error of metabolism. The deficiency causes homogentisic aciduria, ochronosis, and arthritis. AKU patients are deficient for homogentisate 1,2 dioxygenase (HGD) (
), the enzyme that mediates the conversion of homogentisate to maleylacetoacetate, a step in the catabolism of both tyrosine and phenylalanine. The structure of this protein shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers [
,
].This group of proteins includes human HDG and homologues from eukaryotes, bacteria and some archaeal species.
This is a region of myo-inositol-1-phosphate synthases that is related to the glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain. 1L-myo-Inositol-1-phosphate synthase (
) catalyzes the conversion of D-glucose 6-phosphate to 1L-myo-inositol-1-phosphate, the first committed step in the production of all inositol-containing compounds, including phospholipids, either directly or by salvage. The enzyme exists in a cytoplasmic form in a wide range of plants, animals, and fungi. It has also been detected in several bacteria and a chloroplast form is observed in alga and higher plants. Inositol phosphates play an important role in signal transduction.
In Saccharomyces cerevisiae (Baker's yeast), the transcriptional regulation of the INO1 gene has been studied in detail [
] and its expression is sensitive to the availability of phospholipid precursors as well as growth phase. The regulation of the structural gene encoding 1L-myo-inositol-1-phosphate synthase has also been analyzed at the transcriptional level in the aquatic angiosperm, Spirodela polyrrhiza (Giant duckweed) and the halophyte, Mesembryanthemum crystallinum (Common ice plant) [].
1L-myo-Inositol-1-phosphate synthase (
) catalyzes the conversion of D-glucose 6-phosphate to 1L-myo-inositol-1-phosphate, the first committed step in the production of all inositol-containing compounds, including phospholipids, either directly or by salvage. The enzyme exists in a cytoplasmic form in a wide range of plants, animals, and fungi. It has also been detected in several bacteria and a chloroplast form is observed in alga and higher plants. Inositol phosphates play an important role in signal transduction.
In Saccharomyces cerevisiae (Baker's yeast), the transcriptional regulation of the INO1 gene has been studied in detail [
] and its expression is sensitive to the availability of phospholipid precursors as well as growth phase. The regulation of the structural gene encoding 1L-myo-inositol-1-phosphate synthase has also been analyzed at the transcriptional level in the aquatic angiosperm, Spirodela polyrrhiza (Giant duckweed) and the halophyte, Mesembryanthemum crystallinum (Common ice plant) [].
Most members of this family are phosphoglycerate mutase (
). This enzyme interconverts 2-phosphoglycerate and 3-phosphoglycerate.
2-phospho-D-glycerate + 2,3-diphosphoglycerate = 3-phospho-D-glycerate + 2,3-diphosphoglycerate.The enzyme is transiently phosphorylated on an active site histidine by 2,3-diphosphoglyerate, which is both substrate and product. Some members of this family have are phosphoglycerate mutase as a minor activity and act primarily as a bisphoglycerate mutase, interconverting 2,3-diphosphoglycerate and 1,3-diphosphoglycerate (
).
NO signalling/Golgi transport ligand-binding domain superfamily
Type:
Homologous_superfamily
Description:
This superfamily represents a domain is found in different trafficking protein particle complex (TRAPP) subunits involved in vesicular transport from the endoplasmic reticulum to Golgi [
]. It is also found in soluble guanylate cyclases, where it binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.
TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterised TRAPP proteins and has a dimeric structure [
] with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi [].
This entry includes Bet3 (also known as TRAPPC3) and Bet3-like (TRAPPC3L) proteins from eukaryotes. They seem to be involved in vesicle-mediated transport.
Yeast Bet3 is a core component of transport protein particle (TRAPP) complexes I-III. The TRAPPI complex recognises the coat (COPII) on ER-derived vesicles, whereas the TRAPPII complex recognises the coat (COPI) on Golgi-derived vesicles [
]. TRAPPIII is responsible for vesicular transport from early endosomes to Golgi, facilitating Atg9 cycling in autophagy [].Mammalian TRAPPs complexity is increased by the presence of multiple TRAPP homologues and novel subunits or binding proteins that are not part of the yeast
TRAPP complexes []. Bet3 and its homologue Bet3-like are both components of the mammalian TRAPP complex [].
A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related [
,
,
,
]. All these enzymes share the same catalytic mechanism: they bind PEP and transfer the phosphoryl group from it to a histidine residue. The sequence around that residue is highly conserved. This C-terminal domain has been shown to be the PEP-binding domain []. It is often found associated with the pyruvate phosphate dikinase, AMP/ATP-binding domain () at its N terminus and the PEP-utilizing enzyme mobile domain.
Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum (Bacteroides symbiosus), PPDK uses Mg2+ and NH4+ ions as cofactors [
]. The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres.In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis [
]. PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role [].
This enzyme catalyses the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP) [
]. This domain is present at the N terminus of some PEP-utilizing enzymes, and has been shown to be the AMP/ATP-binding domain [].
A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related [
,
,
,
]. These enzymes are: Pyruvate,orthophosphate dikinase (
) (PPDK). PPDK catalyzes the reversible phosphorylation of pyruvate and phosphate by ATP to PEP and diphosphate. In plants PPDK function in the direction of the formation of PEP, which is the primary acceptor of carbon dioxide in C4 and crassulacean acid metabolism plants. In some bacteria, such as Bacteroides symbiosus, PPDK functions in the direction of ATP synthesis.
Phosphoenolpyruvate synthase (
) (pyruvate,water dikinase). This enzyme catalyzes the reversible phosphorylation of pyruvate by ATP to form PEP, AMP and phosphate, an essential step in gluconeogenesis when pyruvate and lactate are used as a carbon source.
Phosphoenolpyruvate-protein phosphatase (
). This is the first enzyme of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from PEP is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease. The entry signature pattern represents a conserved region in the C-terminal part of the PEP-utilizing enzymes. The biological significance of this region is not yet known.
RNA (C5-cytosine) methyltransferases (RCMTs) catalyse the transfer of a methyl group to the 5th carbon of a cytosine base in RNA sequences to produce C5-methylcytosine. RCMTs use the cofactor S-adenosyl-L-methionine (SAM) as a methyl donor [
]. The catalytic mechanism of RCMTs involves an attack by the thiolate of a Cys residue on position 6 of the target cytosine base to form a covalent link, thereby activating C5 for methyl-group transfer. Following the addition of the methyl group, a second Cys residue acts as a general base in the beta-elimination of the proton from the methylated cytosine ring. The free enzyme is restored and the methylated product is released [].Numerous putative RCMTs have been identified in archaea, bacteria and eukaryota [
,
]; most are predicted to be nuclear or nucleolar proteins []. The Escherichia coli Ribosomal RNA Small-subunit Methyltransferase Beta (RSMB) FMU (FirMicUtes) represents the first protein identified and characterised as a cytosine-specific RNA methyltransferase. RSMB was reported to catalyse the formation of C5-methylcytosine at position 967 of 16S rRNA [,
].A classification of RCMTs has been proposed on the basis of sequence similarity [
]. According to this classification, RCMTs are divided into 8 distinct subfamilies []. Recently, a new RCMT subfamily, termed RCMT9, was identified []. Members of the RCMT contain a core domain, responsible for the cytosine-specific RNA methyltransferase activity. This 'catalytic' domain adopts the Rossman fold for the accommodation of the cofactor SAM []. The RCMT subfamilies are also distinguished by N-terminal and C-terminal extensions, variable both in size and sequence [].The prototypical member of the Nuclear protein 1 RCMT subfamily, the S. cerevisiae NCL1 (also known as Trm4), has been demonstrated to methylate cytosine to C5-methylcytosine at positions 34, 40, 48 and 49 in different intron- containing tRNAs and tRNA precursors [
]. Its human homologue, MISU/NSUN2, was found to catalyse the formation of C5-methylcytosine at position 34 of intron-containing pre-tRNAs []; it was not able to modify tRNAs at positions 48 or 49. It was also shown to be involved in Myc-mediated proliferation of cancer cells [].
The proteins in this entry are variously annotated as iron-sulphur cluster insertion protein or Fe/S biogenesis protein. They appear to be involved in Fe-S cluster biogenesis. This family includes IscA, HesB, YadR and YfhF-like proteins. The hesB gene is expressed only under nitrogen fixation conditions [
]. IscA, an 11kDa member of the hesB family of proteins, binds iron and [2Fe-2S]clusters, and participates in the biosynthesis of iron-sulphur proteins. IscA is able to bind at least 2 iron ions per dimer [
]. Other members of this family include various hypothetical proteins that also contain the NifU-like domain (
) suggesting that they too are able to bind iron and are involved in Fe-S cluster biogenesis. The HesB family are found in species as divergent as Homo sapiens (Human) and Haemophilus influenzae suggesting that these proteins are involved in basic cellular functions [
].
These proteins in this entry are small (106 to 135 amino-acid residues in bacteria, about 200 residues in fungi) that contain a number of conserved regions. They appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation [
]. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The Escherichia coli SufA protein is associated with SufS, a NifS homologue and SufD which are involved in the FeS cluster assembly of the FhnF protein []. The Azotobacter protein IscA (homologues of which are also found in E. coli) is associated which IscS, another NifS homologue and IscU, a nifU homologue as well as other factors consistent with a role in FeS cluster chemistry []. A homologue from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.This entry represents a conserved site in the C-terminal extremity, it contains two conserved cysteines.
Proteins in this entry include HesB, IscA, SufA and ErpA, and appear to be scaffold proteins upon which 2Fe-2S clusters are assembled and subsequently transferred to acceptor proteins. Several multiprotein complexes, referred to as ISC, SUF, and NIF, are known to be necessary for building and inserting Fe-S clusters into cellular targets [
]. The HesB proteins are associated with the nif gene cluster. The Escherichia coli SufA protein is associated with SufS, a NifS homologue, and SufD which are involved in the FeS cluster assembly of the FhnF protein []. The Azotobacter protein IscA (homologues of which are also found in E. coli) is associated which IscS, another NifS homologue, and IscU, a NifU homologue, as well as other factors consistent with a role in FeS cluster chemistry []. ErpA is required, together with IscA, for the delivery of iron-sulphur clusters to the hydrogen-oxidizing [NiFe]-hydrogenases in Escherichia coli [
,
].
Defects in the spatacsin gene are the cause of spastic paraplegia 11, a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs [
]. Human and rat spacticin protein has been shown to be expressed in the central nervous system, particularly in cortical and spinal motor neurons as well as in retina [].
MICOS complex subunit MIC60 (also known as Mitofilin) is a component of the MICOS complex which controls mitochondrial cristae morphology, maintenance of junctions, inner membrane architecture, and formation of contact sites to the outer membrane [
,
]. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex []. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence (residues 1-43) rich in positive-charged and hydroxylated residues and a membrane anchor domain (residues 47-66). In addition, it has three centrally located coiled coil domains (residues 200-240, 280-310 and 400-420) [].
Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species [
,
,
]. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components []. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and P2B, which form P1A/P2B and P1B/P2A heterodimers []. Some plants have a third P-protein, called P3, which is not homologous to P1 and P 2 [].In humans, P1 and P2 are strongly autoimmunogenic. They play a significant role in the etiology and pathogenesis of systemic lupus erythema (SLE). In addition, the ribosome-inactivating protein trichosanthin (TCS) interacts with human P0, P1, and P2, with its primary binding site in the C-terminal region of P2. TCS inactivates the ribosome by depurinating a specific adenine in the sarcin-ricin loop of 28S rRNA [
].Archaeal L12 is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12 is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative [
].This entry includes eukaryotic 60S acidic ribosomal protein P1/P2 , as well as archaeal 50S ribosomal protein L12. These proteins play an important role in the elongation step of protein synthesis [
,
].
Glycosylphosphatidylinositol-mannosyltransferase I, PIG-X/PBN1
Type:
Family
Description:
Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I [
]. These enzymes are involved in the transfer of sugar molecules. They probably act by stabilizing the mannosyltransferase PIG-M (GPI14 in yeast) [,
].
D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules. Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA [
,
].
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 L1 is the largest protein from the large ribosomal subunit. The L1 protein contains two domains: 2-layer alpha/beta domain and a 3-layer alpha/beta domain (interrupts the first domain). In Escherichia coli, L1 is known to bind to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [,
], groups:Eubacterial L1Algal and plant chloroplast L1Cyanelle L1Archaebacterial L1Vertebrate L10AYeast SSM1
Serine/threonine-protein kinase Bud32 is conserved from Archaea to human. In many Archaeal genomes, Kae1 and Bud32 are fused [
]. The complex is homologous to the Kae1 and Bud32 subunits of the eukaryotic KEOPS complex (composed of Bud32, Kae1, Cgi121, Pcc1 and Gon7), an apparently ancient protein kinase-containing molecular machine that is essential for t6A tRNA modification [,
].
Homologous recombination is an evolutionarily conserved mechanism for the repair of double-strand breaks in DNA and the generation of genetic diversity. The primary function of homologous recombination in mitotic cells is to repair double-strand breaks or single-strand gaps that form as a result of replication fork collapse, from processing of spontaneous damage, and from exposure to DNA-damaging agents. During meiosis, homologous recombination is essential to establish a physical connection between homologous chromosomes to ensure their correct disjunction at the first meiotic division. In addition, the high frequency of meiotic recombination contributes to diversity by creating new linkage arrangements between genes, or parts of genes [
].The central step of homologous recombination is synapsis, the process of bringing together the two homologous strands. Rad51, a eukaryotic homologue of the prokaryotic recombinase RecA, mediates this process in eukaryotes [
]. Firstly a single-stranded DNA tail is coated by ATP-bound Rad51 to yield a nucleoprotein filament. This filament then searches for a homologous sequence within double-stranded DNA, and catalyses the exchange of strands between the single-stranded and double-stranded DNA substrates. The original broken end of the resulting branched DNA is now aligned with an appropriate matching sequence in an intact duplex, and is further processed by other enzymes [].Rad51 contains an N-terminal α-helical DNA binding domain not found in RecA, and a RecA-like C-terminal ATPase domain [
,
]. The active form of this protein is a long helical filament where the catalytically active unit is a homodimer [].
This entry includes Conserved oligomeric Golgi complex subunit 3 (COG3, also known as Sec34), a component of the peripheral membrane COG complex that is involved in intra-Golgi protein trafficking [
]. COG is a member of the complexes associated with tethering containing helical rods (CATCHR) family which also includes the exocyst, GARP and DSL1 complexes, which are evolutionarily related and share structural features consisting of α-helical bundles towards the C-terminal and an N-terminal coiled-coil region [,
].
The protein sequences of d15 from various strains of Haemophilus influenzae are highly conserved, with only a small variable region identified near the carboxyl terminus of the protein [
]. D15 is a highly conserved antigen that is protective in animal models and it may be a useful component of a universal subunit vaccine against Haemophilus infection and disease []. Membrane proteins from other bacteria have been shown to elicit protective immunity. Oma87 is a protective outer membrane antigen of Pasteurella multocida [].
The FMN-binding domain has a split β-barrel structure with a Greek-key topology that is related in structure to the ferredoxin reductase-like FAD-binding domain. The FMN-binding split barrel domain is found in pyridoxine 5'-phoshate oxidase (PNP oxidase), FMN-binding protein, ferric reductase, and in phenol 2-hydroxylase component B (PheA2).PNP oxidase (
) is an FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in Escherichia coli, and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells [
,
]. The binding sites for FMN and for substrate have been highly conserved throughout evolution. The FMN-binding protein (FMN-bp) is one of the smallest proteins known to bind FMN. FMN-bp appears to participate in the electron-transfer pathway, and may have a structural relationship to the C-terminal domain of chymotrypsin [
,
].Microbial ferric reductases are essential for generating more soluble ferrous iron to use in cellular proteins (assimilatory ferric reductases), and as terminal reductases of iron respiratory pathway of certain bacteria (dissimilatory iron reductases). Most assimilatory iron reductases are flavin enzymes [
].
This domain is found mainly in proteins from phages and type II, type III and type IV secretion systems [
,
,
,
].Bacterial lytic transglycosylases degrade murein via cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine, with the concomitant formation of a 1,6-anhydrobond in the muramic acid residue. There are both soluble (Slt enzymes) and membrane-bound (Mlt enzymes) lytic transglycosylases that differ in size, sequence, activity, specificity and location. The multi-domain structure of the 70 Kd soluble lytic transglycosylase Slt70 is known [
]. Slt70 has 3 distinct domains, each rich in alpha helices: an N-terminal superhelical U-shaped domain, a superhelical linker domain (L-domain, ), and a C-terminal catalytic domain (
). Both the U- and L-domain share a similar superhelical structure. These two domains are connected, and together form a closed ring with a large central hole; the catalytic domain is packed on top of, and interacts with, this ring. The catalytic domain has a lysosome-like fold.
SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far [
]. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex []. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [].
Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase
Type:
Family
Description:
This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1/alkaline phosphodiesterase I/nucleotide pyrophosphatase (nppase). These enzymes catalyze the cleavage of phosphodiester and phosphosulphate bonds in NAD, deoxynucleotides and nucleotide sugars [
,
]. Another member of this family is ATX an autotaxin, tumor cell motility-stimulating protein which exhibits type I phosphodiesterases activity [,
]. The alignment encompasses the active site [,
]. Also present within this family is 60kDa Ca2-ATPase from Myroides odoratus [].This entry also hits a number of ethanolamine phosphate transferase involved in glycosylphosphatidylinositol-anchor biosynthesis [
,
].
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important.
SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of
chromatin, subfamily A-like1), also known as DNA-dependent ATPase A and HARP(Hep-A-related proteins), maintains genome integrity during DNA replication.
SMARCAL1 has ATP-dependent annealing helicase activity, which helps tostabilise stalled replication forks and facilitate DNA repair during
replication. Biochemically, SMARCAL1 can bind to DNA that contains single- anddouble-stranded regions such as forks and DNA hairpins. DNA binding activates
its ATPase activity, and this activity promotes DNA single-stranded annealing[
,
].SMARCAL1 is a multifunctional protein. The ATPase domain, which lies in the C-terminal half of the protein, is split into two regions of primary amino acid
sequence by a 115-amino-acid linker sequence. The N-terminalhalf of the protein contains a highly sequence conserved ssDNA-binding protein
replication protein A (RPA)-binding domain, and one or two HARP domain(s). Theevolutionarily conserved HARP domain determines the annealing helicase
activity required for the in vivo and in vitro functions of SMARCAL1 [,
,
].
The BON domain is typically ~60 residues long and has an α/β fold. There is a conserved glycine residue and several hydrophobic regions which suggests a binding function, and, actually, it contains a phospholipid-binding site
,
]. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins [,
,
]; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [
].In the potassium binding protein Kbp, this domain is able to bind K [
].This domain is also found in ArfA, a membrane protein required for supporting bacterial growth in acidic environments [
].
This entry represents an ATPase that includes both a MinD-type, and FleN-type.MinD is a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE [
]. MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD []. Homologues can also be found in archaea, their exact role unknown.FleN is involved in the maintenance of flagellar number in Pseudomonas aeruginosa
. It has been shown to be an anti-activator against FleQ, an important transcriptional regulator of flagellar genes
.
This entry describes MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE [
]. MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD []. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate entry.
This C-terminal domain is found in peptidases belonging to MEROPS peptidase family M1, particularly: aminopeptidase-1 of Caenorhabditis elegans, aminopeptidase O, aminopeptidase B and the bifunctional leukotriene A4 (LTA-4) hydrolase/aminopeptidase. The domain adopts a structure consisting of two layers of parallel α-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. It is required for the formation of a deep cleft harbouring the catalytic Zn2+ site in leukotriene A4 hydrolase [
].
Snapin is a component of the biogenesis of lysosomal organelles complex-1 (BLOC-1), a complex required for the normal biogenesis of lysosome-related organelles, such as melanosomes and platelet dense granules [
], and endosomal cargo sorting [].Snapin binds to SNAP-25, part of the SNARE complex that mediates the synaptic vesicle docking and fusion [
]. Snapin may modulate a step between vesicle priming, fusion and calcium-dependent neurotransmitter release through its ability to potentiate the interaction of synaptotagmin with the SNAREs and the plasma-membrane-associated protein SNAP25 []. Its phosphorylation state influences exocytotic protein interactions and may regulate synaptic vesicle exocytosis [,
]. It may also have a role in the mechanisms of SNARE-mediated membrane fusion in non-neuronal cells [].
Ribosomal protein S1 [
] contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo []. It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities [
]. Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region [
]. There may be a flexible region between the two domains permitting free movement of the domains relative to each other.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 [
,
].
Vertebrate BCNT (named after Bucentaur) protein is found in the nucleus and
cytosol. Gene duplication of the ancestral BCNT gene leads to the h-type BCNTor craniofacial development protein 1 (CFDP1) gene and the ruminant-specific
p97BCNT or craniofacial development protein 2 (CFDP2) gene. The h-type BCNTproteins contain a highly conserved 82-amino acid region at the C terminus
(BCNT-C) that is not present in p97BCNT. Instead ruminant p97BCNT contains aregion derived from the endonuclease domain of a retrotransposable element
RTE-1 [,
].In addition to h-type BCNT proteins, a BCNT-C domain is also
found in Drosophila YETI, a protein that binds to a microtubule-based motorkinesin-1, and the yeast SWR1-complex protein 5 (SWC5) or AOR1 (actin
overexpression resistant 1), a component of the SWR1 chromatin remodelingcomplex [
,
].The entry represents the entire BCNT-C domain.
These sequences represent dihydrolipoamide dehydrogenase, a flavoprotein that acts in a number of ways. It is the E3 component of dehydrogenase complexes for pyruvate, 2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can also serve as the L protein of the glycine cleavage system. This family includes a few members known to have distinct functions (ferric leghemoglobin reductase and NADH:ferredoxin oxidoreductase) but that may be predicted by homology to act as dihydrolipoamide dehydrogenase as well. The motif GGXCXXXGCXP near the N terminus contains a redox-active disulphide.
Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [
,
,
]. This entry represents the N terminus of the 31kDa subunit (42kDa in Drosophila) of transcription initiation factor IID (TAFII31), also known as transcription initiation factor TFIID subunit 9 (TAF9). It has been shown that TAF9 interacts directly with different transcription factors such as p53, herpes simplex virus activator vp16 and the basal transcription factor TFIIB. Binding to p53 is an essential requirement for p53 mediated transcription activation.TAF9 is a component other TBP-free TAF complexes containing the GCN5-type histone acetyltransferase. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three α-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. TFIID has a histone octamer-like substructure. TAF9 is a shared subunit of both, histone acetyltransferase complex (SAGA) and TFIID complexes. TAF9 domain interacts with TAF6 to form a novel histone-like heterodimer that is structurally related to the histone H3 and H4 oligomer [
,
,
,
].
Galactokinase catalyses the first reaction in the galactose metabolism pathway, the
ATP-dependent phosphorylation of galactose, yielding galactose-1-phosphate [,
].Deficiency in this enzyme results in the disease galactosemia, which is responsible for the
formation of cataracts in newborn babies, and is possibly responsible for presenile cataracts inadults [
]. In yeast, the GAL3 gene product is required for the GAL4-mediated inductionof other enzymes involved in galactose metabolism. The induction of GAL1 production then reinforces
this process, increasing the expression of other galactose-inducible genes. GAL3 has been shown tobe similar to the GAL1 protein [
].This entry represents a conserved signature pattern located in the N-terminal domain of galactokinases.
Galactokinase catalyses the first reaction in the galactose metabolism pathway, the
ATP-dependent phosphorylation of galactose, yielding galactose-1-phosphate [,
].Deficiency in this enzyme results in the disease galactosemia, which is responsible for the
formation of cataracts in newborn babies, and is possibly responsible for presenile cataracts inadults [
]. In yeast, the GAL3 gene product is required for the GAL4-mediated inductionof other enzymes involved in galactose metabolism. The induction of GAL1 production then reinforces
this process, increasing the expression of other galactose-inducible genes. GAL3 has been shown tobe similar to the GAL1 protein [
].
The galacto- (
), homoserine (
), mevalonate (
) and phosphomevalonate (
) kinases contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP [
,
]. This group of kinases has been called 'GHMP' (from the first letter of their substrates).This site is also found in some diphosphomevalonate decarboxylases, which are structurally related members of the GHMP superfamily [
], but do not possess kinase activity.
This entry represents ER membrane protein complex subunit 6 (Emc6). Emc6 is a component of the ER membrane protein complex (EMC), which is composed of Emc1, Emc2, Emc3, Emc4, Emc5 and Emc6 in budding yeast [
]. The EMC complex is required for efficient folding of proteins in the ER [,
].
The MCM2-7 complex consists of six closely related proteins that are highly conserved throughout the eukaryotic kingdom. In eukaryotes, Mcm2 is a component of the MCM2-7 complex (MCM complex), which consists of six sequence-related AAA + type ATPases/helicases that form a hetero-hexameric ring [
]. MCM2-7 complex is part of the pre-replication complex (pre-RC). In G1 phase, inactive MCM2-7 complex is loaded onto origins of DNA replication [,
,
]. During G1-S phase, MCM2-7 complex is activated to unwind the double stranded DNA and plays an important role in DNA replication forks elongation [].The components of the MCM2-7 complex are: DNA replication licensing factor MCM2, DNA replication licensing factor MCM3, DNA replication licensing factor MCM4, DNA replication licensing factor MCM5, DNA replication licensing factor MCM6, DNA replication licensing factor MCM7, In addition to its role in initiation of DNA replication, Mcm2 is able to
inhibit the Mcm4,6,7 helicase. Studies on murine Mcm2 indicate that itsC terminus is required for interaction with MCM4, as well as for inhibition
of the DNA helicase activity of the Mcm4,6,7 complex. The N-terminal region,which contains an H3-binding domain and a region required for nuclear
localisation, is required for the phosphorylation by CDC7 kinase.
Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (
) or ammonia (
), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [
,
]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase () (ACC), propionyl-CoA carboxylase (
) (PCCase), pyruvate carboxylase (
) (PC) and urea carboxylase (
).
Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain [
]. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein [
]. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents glutamine-dependent CPSase (
) from prokaryotes and eukaryotes (CPSase II).
This entry represents Ribosomal RNA-processing protein 1 (RPP1) from yeast and its homologues, such as RRP1A/B from mammals and RRP1L from Drosophila. In Saccharomyces cerevisiae, RPP1 is required for 27S rRNA processing to 25S and 5.8S. In humans, RRP1A (also known as) Nop52 is believed to be involved in the generation of 28S rRNA [
].
Ctf8 is a component of the RFC-like complex CTF18-RFC which is required for efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC [,
].
