The Exo70 protein forms one subunit of the exocyst complex (consist of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70, and Exo84 in budding yeast). First discovered in Saccharomyces cerevisiae [
], it is evolutionarily conserved in eukaryotes. It mediates the tethering of post-Golgi secretory vesicles to the plasmamembrane and promotes the assembly of the SNARE complex for membrane fusion. It also plays a role in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumourigenesis and metastasis [
]. It is a member of the the Complex Associated with Tethering Containing Helical Rods (CATCHRs) family which also includes Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP) and DSL1 complexes, all evolutionarily related and share structural features consisting of α-helical bundles at the C terminus and coiled-coil region at the N terminus [,
,
,
]. Exo70 interacts with phospholipids the Rho3 GTPase [,
]. This interaction with Rho3 mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) [].
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), andare involved in PSII assembly, stabilisation, dimerisation, and photo-protection [
]. This entry represents the intrinsic antenna proteins CP43 (PsbC) and CP47 (PsbB) found in the reaction centre of PSII. These polypeptides bind to chlorophyll a and beta-carotene and pass the excitation energy on to the reaction centre [
]. This entry also includes the iron-stress induced chlorophyll-binding protein CP43' (IsiA), which evolved in cyanobacteria from a PSII protein to cope with light limitations and stress conditions. Under iron-deficient growth conditions, CP43' associates with PSI to form a complex that consists of a ring of 18 or more CP43' molecules around a PSI trimer, which significantly increases the light-harvesting system of PSI. IsiA can also provide photoprotection for PSII [].
Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of
receptors for intracellular transport vesicles. Each target membrane may beidentified by a specific member of the syntaxin family [
].Members of the syntaxin family [,
] have a size ranging from30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well
conserved region SNARE motif, which seems to be in a coiled-coil conformation. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core []. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in α-helical secondary structure. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Epimorphin is related to neuronal and yeast vesicle
targeting proteins.This entry represents the coiled-coil region of these proteins.
Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins
, and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A (
) it is found as three α-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role.
The function of syntaxins is determined by their localisation. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors [
].
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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short β hairpin and an α helix (β/β/α structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 [
]. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved β/β/α structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short α-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets [].This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator [
].
This entry represents the N-terminal domain of Small EDRK-rich factors (SERFs), including SERF1/2 from human. Proteins containing this domain are short proteins that are rich in aspartate, glutamate, lysine and arginine [
]. SERF1/2 are positive regulators of amyloid protein aggregation and proteotoxicity; they induce conformational changes in amyloid proteins, driving them into compact formations preceding the formation of aggregates [,
,
].
The NRL (for NPH3/RPT2-Like) family is formed by signaling molecules specific
to higher plants. Several regions of sequence and predicted structuralconservation define members of the NRL family, with three domains being most
notable: an N-terminal BTB domain, a centrally located NPH3domain, and a C-terminal coiled coil domain. The function of the NPH3 domain
is not yet known [,
,
,
,
,
,
,
].Some proteins known to contain a NPH3 domain include:
Arabidopsis non-phototropic hypocotyl 3 (NPH3), may function as an adapter
or scaffold protein in plants.Arabidopsis root-phototropisme 2 (RPT2), a signal transducer involved in
phototropic response and stomatal opening in association with phototropin 1(phot1).Oriza coleoptile phototropism 1 (CPT1), the rice ortholog of NPH3. It is
required for phototropism of coleoptiles and lateral translocation ofauxin.This entry represents the NPH3 domain.
Adenylate kinase (
) converts ATP + AMP to ADP + ADP, that is, it uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (
) is
, a GTP:AMP phosphotransferase.
This N-terminal domain is found in Nucleolar protein 58/56 from fungi and animals and the homologues form plants. These are RNA-binding proteins of the NOP5 family [
]. Nop56 and Nop58 are components of box C/D small nucleolar ribonucleoprotein (snoRNP) particles [,
]. This domain interacts with Nop1 and forms the box B/C side, in the case of Nop56, or box C'/D side in the case of Nop58, of U3 snoRNP [].
This family of proteins are about 50 to 77kDa. The central region is well conserved and contains three conserved histidines. Most of these proteins are related at the N-terminal region to the beta-lactamase family. The family has been characterised as ribonuclease J. RNase J cleaves the 5'-leader sequence of certain mRNAs and may play a role in the maturation and stability of specific mRNAs [
]. It is also required for the maturation of the 16S rRNA acting preferentially on 16S rRNA precursors after association of the 30S and 50S ribosomal subunits [,
].
The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in
and are common to all metallo-beta-lactamases. This, the fifth motif [
], appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 [] which are involved in the processing of mRNA [,
]. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3'-end-processing endonucleases [,
,
].
Quinoprotein alcohol dehydrogenases are a family of proteins found in methylotrophic or autotrophic bacteria. These quinoproteins use pyrroloquinoline quinone as their prosthetic group. There are three types of alcohol dehydrogenases: type I includes methanol dehydrogenase and ethanol dehydrogenase, type II includes soluble quinohaemoprotein with a C-terminal containing haem C, and type III includes quinoprotein alcohol dehydrogenase with a C-terminal cytochrome C domain [
]. These quinoproteins contain an 8-bladed β-propeller motif, which is present in the N-terminal domain of quinoprotein alcohol dehydrogenase, ethanol dehydrogenase, and the heavy chain (alpha subunit) of methanol dehydrogenase () [
,
,
].This entry represents quinoprotein alcohol dehydrogenases as well as some other proteins that share a similar structure, including WD repeat-containing protein and echinoderm microtubule-associated protein-like proteins.
Argininosuccinate synthase (
) (AS) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate [
,
].In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation.AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.
Argininosuccinate synthetase, catalytic/multimerisation domain body
Type:
Homologous_superfamily
Description:
The argininosuccinate synthetase (AS) monomer is composed of a nucleotide binding domain and a catalytic/multimerisation domain. The catalytic/multimerisation domain can be subdivided in the body of the domain and a C-terminal tail involved in multimerisation, though this tail is not present in all sequences. This entry represents the body of the catalytic/multimerisation domain. It is a mixed alpha/beta fold consisting of two four-stranded antiparallel beta sheets arranged end-to-end to form a cradle for a cluster of five alpha helices. In general, the alpha helices of the domain are responsible for multimerisation interactions, whereas the beta sheets form the solvent-exposed surface [
].
Argininosuccinate synthase (
) (AS) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate [
,
].In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation.AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.
Argininosuccinate synthase (
) (AS) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate [
,
].In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation.AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.This entry represents argininosuccinate synthase, type 1 subfamily.
The single subunit DNA-directed RNA polymerase (RNAP) that is encoded by bacteriophage T7 is the prototype of a class of relatively simple RNAPs that includes the RNAPs of the related phages T3 and SP6, as well as the mitochondrial and chloroplastic RNAPs [
]. This superfamily represents a helix hairpin structural domain found in this type of RNA polymerases.
Adenylylsulphate kinase (
) catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. It is often found as a fusion protein with sulphate adenylyltransferase. Both enzymes are required for PAPS (phosphoadenosine-phosphosulphate) synthesis from inorganic sulphate [
].
This entry represents glyoxysomal malate synthases and one of two bacterial forms, designated malate synthase A.Malate synthase and isocitrate lyase are the two characteristic enzymes of the glyoxylate cycle. The glyoxylate cycle allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle [
]. Isocitrate lyase, first catalyzes the aldol cleavage of isocitrate to succinate (an intermediate of the tricarboxylic acid cycle) and glyoxylate. Then malate synthase catalyzes the condensation of acetyl CoA with glyoxylate to yield malate (another intermediate of the tricarboxylic acid cycle) [].
Malate synthase (MS) (
) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted α/β domain in MSG that may have regulatory function [
,
]. MSA and MSG consist of an N-terminal α-helical clasp domain, a central TIM-barrel domain and a C-terminal helical plug domain. In malate synthases, the TIM β/α-barrel fold and the C-terminal helical domain are well conserved and the cleft between them forms the active site [,
,
].
Malate synthase (
) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. Malate synthase has a TIM beta/α-barrel fold [
].Malate synthase is a protein of 530 to 570 amino acids whose sequence is highly conserved across species [
]. The signature pattern for this entry is to a very conserved region in the central section of the enzyme.
Malate synthase (MS) (
) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted α/β domain in MSG that may have regulatory function [
,
]. MSA and MSG consist of an N-terminal α-helical clasp domain, a central TIM-barrel domain and a C-terminal helical plug domain. In malate synthases, the TIM β/α-barrel fold and the C-terminal helical domain are well conserved and the cleft between them forms the active site [,
,
].
This entry represents a domain found in RMND1 from mammals, Sif2/Sif3 from fission yeasts and Rmd1/Rmd8/YDR282C (Mrx10) from budding yeasts. RMND1 and its yeast homologue, Mrx10, are mitochondrial proteins required for mitochondrial translation [
,
]. Rmd1 and Rmd8 are cytoplasmic proteins required for sporulation [
].
This is a family of glycine cleavage H-proteins, part of the glycine cleavage system (GCS) found in bacteria, archaea, and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-proteins) which catalyzes the oxidative cleavage of glycine []. The H-protein shuttles the methylamine group of glycine from the P-protein (glycine dehydrogenase) to the T-protein (aminomethyltransferase) via a lipoyl group, attached to a completely conserved lysine residue [].This entry represents the glycine cleavage system H protein. The genome of Aquifex aeolicus contains one protein belonging to this group, and four more related proteins not included here; it seems doubtful that all of these homologues are authentic H proteins. The Chlamydial homologue of the H protein is nearly as divergent as the Aquifex outgroup, is not accompanied by P and T proteins, and is not included in this entry.
This is a family of glycine cleavage H-proteins, part of the glycine cleavage system (GCS) found in bacteria, archaea, and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-proteins) which catalyzes the oxidative cleavage of glycine [
]. The H-protein shuttles the methylamine group of glycine from the P-protein (glycine dehydrogenase) to the T-protein (aminomethyltransferase) via a lipoyl group, attached to a completely conserved lysine residue [].
The single hybrid motif has a β-barrel sandwich hybrid fold, consisting of a sandwich of half-barrel shaped β-sheets. This motif is found in biotinyl/lipoyl-carrier proteins and domains, where the biotin and lipoic acid moieties act as covalently attached coenzyme cofactors in enzymes that catalyse metabolic reactions. For example, this motif can be found in the biotinyl domain of Escherichia coli acetyl-CoA carboxylase [
], protein H of the glycine cleavage system in Pisum sativum (Garden pea) [], the ipoyl domain of dihydrolipoamide acetyltransferase, which is a component of the pyruvate dehydrogenase complex [], the lipoyl domain of the 2-oxoglutarate dehydrogenase complex [], and the lipoyl domain f the mitochondrial branched-chain alpha-ketoacid dehydrogenase.
The 2-oxo acid dehydrogenase multienzyme complexes [
] from bacterial andeukaryotic sources catalyze the oxidative decarboxylation of 2-oxo acids to
the corresponding acyl-CoA. These include: Pyruvate dehydrogenase complex (PDC). 2-oxoglutarate dehydrogenase complex (OGDC). Branched-chain 2-oxo acid dehydrogenase complex (BCOADC). These three complexes share a common architecture: they are composed of
multiple copies of three component enzymes - E1, E2 and E3. E1 is a thiaminepyrophosphate-dependent 2-oxo acid dehydrogenase, E2 a dihydrolipamide
acyltransferase, and E3 an FAD-containing dihydrolipamide dehydrogenase. E2 acyltransferases have an essential cofactor, lipoic acid, which is
covalently bound via a amide linkage to a lysine group. The E2 components ofOGCD and BCOACD bind a single lipoyl group, while those of PDC bind either one
(in yeast and in Bacillus), two (in mammals), or three (in Azotobacter and inEscherichia coli) lipoyl groups [
]. In addition to the E2 components of the three enzymatic complexes described
above, a lipoic acid cofactor is also found in the following proteins: H-protein of the glycine cleavage system (GCS) [
]. GCS is a multienzymecomplex of four protein components, which catalyzes the degradation of
glycine. H protein shuttles the methylamine group of glycine from the Pprotein to the T protein. H-protein from either prokaryotes or eukaryotes
binds a single lipoic group. Mammalian and yeast pyruvate dehydrogenase complexes differ from that of
other sources, in that they contain, in small amounts, a protein of unknownfunction - designated protein X or component X. Its sequence is closely
related to that of E2 subunits and seems to bind a lipoic group []. Fast migrating protein (FMP) (gene acoC) from Ralstonia eutropha (Alcaligenes eutrophus) [
].This protein is most probably a dihydrolipamide acyltransferase involved in
acetoin metabolism. This signature contains the lipoyl-binding lysine residue. The domain surronding this site is evolutionary related to that around the biotin-binding lysine residue of biotin requiring enzymes.
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [
]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [].Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [
]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [,
].This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 [
] and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad [
].
After cytochrome c is synthesized in the cytoplasm as apocytochrome c, it is transported through the outer mitochondrial membrane to the intermembrane space, where haem is covalently attached by thioester bonds to two cysteine residues located in the cytochrome c centre. Cytochrome c is required during oxidative phosphorylation as an electron shuttle between Complex III (cytochrome c reductase) and IV (cytochrome c oxidase). In addition, cytochrome c is involved in apoptosis in more complex organisms such as Xenopus, rats and humans. Cellular stress can induce cytochrome c release from the mitochondrial membrane. In mammals, cytochrome c triggers the assembly of the apoptosome, consisting of cytochrome c, Apaf-1 and dATP, which activates caspase-9, leading to cell death [
,
]. There are several different members of the cytochrome c family with different functional roles, for instance cytochrome c549 is associated with photosystem II []. The known structures of c-type cytochromes have six different classes of fold. Of these, four are unique to c-type cytochromes [
,
]. The consensus sequence for the cytochrome c centre is Cys-X-X-Cys-His, where the histidine residue is one of the two axial ligands of the haem iron []. This arrangement is shared by all proteins known to belong to the cytochrome c family, which presently includes both mono-haem proteins and multi-haem proteins. This entry represents mono-haem cytochrome c proteins (excluding class II and f-type cytochromes), such as cytochromes c, c1, c2, c5, c555, c550 to c553, c556, and c6.Cytochrome c-type centres are also found in the active sites of many enzymes, including cytochrome cd1-nitrite reductase as the N-terminal haem c domain, in quinoprotein alcohol dehydrogenase as the C-terminal domain, in Quinohemoprotein amine dehydrogenase A chain as domains 1 and 2, and in the cytochrome bc1 complex as the cytochrome bc1 domain.
This entry represents a group of lipid metabolizing enzymes, including LACT and LPLA2 from humans, and PDAT from plants.Lecithin:cholesterol acyltransferase (LACT), also known as phosphatidylcholine-sterol acyltransferase (
), is involved in extracellular metabolism of plasma lipoproteins, including cholesterol. It esterifies the free cholesterol transported in plasma lipoproteins, and is activated by apolipoprotein A-I. Its structure has been revealed [
]. Defects in LACT cause Fish eye disease and familial LCAT deficiency [].Phospholipid:diacylglycerol acyltransferase (PDAT)(
) is involved in triacylglycerol formation by an acyl-CoA independent pathway. The enzyme specifically transfers acyl groups from the sn-2 position of a phospholipid to diacylglycerol, thus forming an sn-1-lysophospholipid [
].Lysosomal phospholipase A2 (LPLA2) (
) plays important roles for lung surfactant metabolism and maturation of invariant natural killer T cells. Its structure has been revealed [
].
DNA-directed RNA polymerase, 30-40kDa subunit, conserved site
Type:
Conserved_site
Description:
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 12 polypeptides.
It has been shown [,
,
,
] that small subunits of about 30 to 40kDa found in archebacterial and all three types of eukaryotic polymerases are highly conserved. Subunits known to belong to this family are:Saccharomyces cerevisiae RPC5 subunit (or RPC40) from RNA polymerases I and III.Mammalian RPA40 from RNA polymerase I.S. cerevisiae RPB3 subunit from RNA polymerase II.Schizosaccharomyces pombe rpb3 subunit from RNA polymerase II.Mammalian RPB3 (or RPB33) (gene POLR2C) from RNA polymerase II.Conjugation stage-specific protein cnjC from Tetrahymena thermophila, which may be a stage-specific RNA polymerase subunit.Archaebacterial RNA polymerase subunit D (gene rpoD).
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 (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact [
].The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (
), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (
), dividing it into two halves [
]. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.
RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and the prokaryotic RNAP alpha subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact [
]. These different subunits share regions of homology. Rpb11 contains a domain (Rpb11-like domain) that is required for dimerisation, and binds to a homologous region on Rpb3. The Rpb11-like domain in Rpb11 and archaeal L subunits is contiguous, whereas in Rpb3, archaeal D, and prokaryotic alpha subunits (), the Rpb11-like domain is interrupted by an insert domain (
). In the prokaryotic RNAP alpha subunit, the Rpb11-like domain and the insert domain form two subregions of the N-terminal domain.
The structure of the Rpb11-like domain consists of a two-layer alpha/beta fold consisting of β(2)-α-β(2)-α. Rpb3 and Rpb11 in yeast RNAP [,
,
] have been shown to share a high degree of sequence and structural similarity to the alpha subunit of bacterial RNAP [,
].
The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact, and plays a direct role in promoter recognition [
]. In eukaryotes, RNA polymerase (RNAP) II is responsible for all mRNA synthesis. RNAP-II consists of 12 subunits, where subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the bacterial RpoA homodimer []. Archaeal RNAP closely resembles eukaryotic RNAP-II, and is composed of 12 subunits, of which D and L form a heterodimer resembling the Rpb3/Rpb11 and RpoA/RpoA dimers [].The bacterial RpoA, eukaryotic Rpb3 and archaeal D subunits share sequence and structural motifs, and can be placed into a single family. These subunits also have unique sequence motifs, especially at their C-terminal ends, which are involved in promoter specificity, for example the CTD of the bacterial RNAP alpha subunit (
).
Bud site selection protein 13, also known as pre-mRNA-splicing factor CWC26, belongs to the pre-mRNA retention and splicing (RES) complex. May also be involved in positioning the proximal bud pole signal [
,
,
]. The presence of RES subunit homologues in numerous eukaryotes suggests that its function is evolutionarily conserved [].
Kti12 associates with Elongator complex, a six-subunit histone acetytransferase complex that functions with the elongating form of RNA polymerase II during transcription [
]. It is not a structural subunit but may play a regulatory role in Elongator function []. It has been shown that Kti12 is associated with chromatin throughout the genome, even in non-transcribed regions and in the absence of Elongator []. It is required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA [].L-seryl-tRNA(Sec) kinase (PSTK) specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis [
].
Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localize to both poles of the predivisional cell following completion of DNA replication [
]. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4 [
].
Sulfiredoxins
belong to the oxidoreductase family, which are involved in cellular responses to oxidative stress [
]. They catalyse the reaction peroxiredoxin-(S-hydroxy-S-oxocysteine) + ATP + 2 R-SH = peroxiredoxin-(S-hydroxycysteine) + ADP + phosphate + R-S-S-RIt is a member of a conserved family of eukaryotic antioxidants and contains a conserved C-terminal cysteine which is essential for its antioxidant function.Sulfiredoxin (Srx) plays a role in signalling through the catalytic reduction of oxidative modifications. It is responsible for the regulation of peroxiredoxin (Prx) by catalysing reduction of the conserved cysteine from sulfinic to sulfenic acid. This reduction prevents further reduction to sulfonic acid, which ultimately results in degradation.Srx also has a role in glutathionylation.
This family contains small uncharacterised proteins of 14 to 16kDa mainly from bacteria although the signatures also occur in a hypothetical protein from archaea and eukaryotes. Members of this protein family, designated YjbQ in E. coli, have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamine phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of the YjbQ family enzyme remains unknown [
,
].
The assembly of proteins has been thought to be the sole result of properties inherent in the primary sequence of polypeptides themselves. In some cases, however, structural information from other protein molecules is required for correct folding and subsequent assembly into oligomers [
]. These 'helper' molecules are referred to as molecular chaperones, a subfamily of which are the chaperonins [], which include 10kDa and 60kDa proteins. These are found in abundance in prokaryotes, chloroplasts and mitochondria. They are required for normal cell growth (as demonstrated by the fact that no temperature sensitive mutants for the chaperonin genes can be found in the temperature range 20 to 43 degrees centigrade []), and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions [].The 10kDa chaperonin (Cpn10) and its bacterial homologue groES, exist as a ring-shaped oligomer of between 6 to 8 identical subunits, whereas the 60kDa chaperonin (Cpn60) and its bacterial homologue groEL, form a structure comprising 2 stacked rings, each ring containing 7 identical subunits [
]. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The Cpn10 and Cpn60 oligomers also require Mg2+-ATP in order to interact to form a functional complex, although the mechanism of this interaction is as yet unknown []. This chaperonin complex is essential for the correct folding and assembly of polypeptides into oligomeric structures, of which the chaperonins themselves are not a part []. The binding of Cpn10 to Cpn60 inhibits the weak ATPase activity of Cpn60.TCP-1 (t-complex polypeptide 1) is a subunit of the hetero-oligomeric complex CCT (chaperonin containing TCP- 1) present in the eukaryotic cytosol. It is a member of the chaperonin family which includes GroEL, 60kDa heat shock protein (Hsp60), Rubisco subunit binding protein (RBP) and thermophilic factor 55 (TF55) [
]. This entry represents GroEL, Cpn60, TCP-1 and similar proteins found in bacteria, eukaryots and archaea.
Chaperonins are large cylindrical structures that transiently enclose a partially folded polypeptide and allow it to continue folding in a sequestered environment. Chaperonins are grouped into two families: group I chaperonins, found in eubacteria (e.g. GroEL in Escherichia coli) and eukaryotic organelles
of eubacterial descent (e.g. Cpn60 in mitochondria and chloroplasts), and group II chaperonins, found in archaea and the eukaryotic cytosol (CCT or TCP-1 complex) [,
]. Both groups share a common monomer architecture of three domains: an equatorial domain that carries ATPase activity, an intermediate domain, and an apical domain, involved in substrate binding [,
,
].This superfamily represents the equatorial domain.
Chaperonins are large cylindrical structures that transiently enclose a partially folded polypeptide and allow it to continue folding in a sequestered environment. Chaperonins are grouped into two families: group I chaperonins, found in eubacteria (e.g. GroEL in Escherichia coli) and eukaryotic organelles of eubacterial descent (e.g. Cpn60 in mitochondria and chloroplasts), and group II chaperonins, found in archaea and the eukaryotic cytosol (CCT or TCP-1 complex) [
,
]. Both groups share a common monomer architecture of three domains: an equatorial domain that carries ATPase activity, an intermediate domain, and an apical domain, involved in substrate binding [,
].This superfamily represents the apical domain.
The assembly of proteins has been thought to be the sole result of properties inherent in the primary sequence of polypeptides themselves. In some cases, however, structural information from other protein molecules is required for correct folding and subsequent assembly into oligomers [
]. These `helper' molecules are referred to as molecular chaperones, a subfamily of which are the chaperonins []. They are required for normal cell growth (as demonstrated by the fact that no temperature sensitive mutants for the chaperonin genes can be found in the temperature range 20 to 43 degrees centigrade []), and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions []. This entry represents the 60kDa chaperonin (Cpn60), its bacterial homologue groEL and RuBisCO subunit-binding protein []), which are mainly present in bacteria and eukaryots.The 60kDa form of chaperonin is the immunodominant antigen of patients with Legionnaire's disease [
], and is thought to play a role in the protection of the Legionella spp. bacteria from oxygen radicals within macrophages. This hypothesis is based on the finding that the cpn60 gene is upregulated in response to hydrogen peroxide, a source of oxygen radicals. Cpn60 has also been found to display strong antigenicity in many bacterial species [], and has the potential for inducing immune protection against unrelated bacterial infections. The RuBisCO subunit binding protein (which has been implicated in the assembly of RuBisCO) and cpn60 have been found to be evolutionary homologues, the RuBisCO subunit binding protein having the C-terminal Gly-Gly-Met repeat found in all bacterial cpn60 sequences. Although the precise function of this repeat is unknown, it is thought to be important as it is also found in 70kDa heat-shock proteins []. The crystal structure of Escherichia coli GroEL has been resolved to 2.8A [].
Protein folding is thought to be the sole result of properties inherent in polypeptide primary sequences. Sometimes, however, additional proteins are required to mediate correct folding and subsequent oligomer assembly [
]. These `helpers', or chaperones, bind to specific protein surfaces, preventing incorrect folding and formation of non-functional structures [].The tailless complex polypeptide 1 (TCP-1) is a highly structurally conserved molecular chaperone located in the cytosol [
]. The protein has also been shown to bind to Golgi membranes and to microtubules, this latter property suggesting a role in mitotic spindle formation in dividing cells (especially in sperm, where it is highly abundant) []. TCP-1 forms a double ring structure, similar to the 10kDa and 60kDa chaperonins, with 6-8 subunits per ring. The amino acid sequence is significantly similar to the 60kDa chaperonin, and to TF55, a chaperone from the archaebacterium Sulfolobus shibatae [].
Nck-associated protein 1 is part of lamellipodial complex that controls Rac-dependent actin remodeling [
,
]. It associates preferentially with the first SH3 domain of Nck and is a component of the WAVE2 complex composed of ABI1, CYFIP1/SRA1, NCKAP1/NAP1 and WASF2/WAVE2. It is also a component of the WAVE1 complex composed of ABI2, CYFIP2, C3orf10/HSPC300, NCKAP1 and WASF1/WAVE1. CYFIP2 binds to activated RAC1 which causes the complex to dissociate, releasing activated WASF1. The complex can also be activated by NCK1. Expression of this protein was found to be markedly reduced in patients with Alzheimer's disease [].
Alpha-D-phosphohexomutase, alpha/beta/alpha domain I
Type:
Domain
Description:
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) [
]. PGM () converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose [
]. PGM/PMM (;
) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [
,
]. Both PNGM () and PAGM (
) are involved in the biosynthesis of UDP-N-acetylglucosamine [
,
]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme [
].The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate.This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.
Alpha-D-phosphohexomutase, alpha/beta/alpha domain II
Type:
Domain
Description:
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) [
]. PGM () converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose [
]. PGM/PMM (;
) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [
,
]. Both PNGM () and PAGM (
) are involved in the biosynthesis of UDP-N-acetylglucosamine [
,
]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme [
].The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate.This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) [
]. PGM () converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose [
]. PGM/PMM (;
) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [
,
]. Both PNGM () and PAGM (
) are involved in the biosynthesis of UDP-N-acetylglucosamine [
,
]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme [
].The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate.
Alpha-D-phosphohexomutase, alpha/beta/alpha domain III
Type:
Domain
Description:
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) [
]. PGM () converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose [
]. PGM/PMM (;
) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [
,
]. Both PNGM () and PAGM (
) are involved in the biosynthesis of UDP-N-acetylglucosamine [
,
]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme [
].The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate.This entry represents domain III found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer α/β/α topology.
DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases
) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation.
A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. The DNA polymerase structure resembles a right hand with fingers, palm, and thumb, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb [
,
,
]. This superfamily represents the palm domain of DNA polymerase B composed of 6-stranded β-sheet flanked by two long α-helices from one side and a short helix from the other.
This entry includes a group of DNA helicases, including Pif1 and Rrm3 from budding yeasts and Pfh1 from fusion yeast. This entry also includes Pif1 like proteins from prokaryotes and eukaryotes including plants. Pif1 is a DNA helicase conserved from bacteria to humans [
,
]. It suppresses both G-quadruplex-associated DNA damage and telomere lengthening. In budding yeast, it exists in two forms, nuclear form and mitochondrial form. Its nuclear form inhibits telomerase, while its mitochondrial form is involved in repair and recombination of mitochondrial DNA [,
]. In budding yeasts, another DNA replicative helicase, Rrm3 is recruited to paused replisomes to promote fork progression throughout nonhistone protein-DNA complexes, naturally occurring impediments that are encountered in each S phase where replication forks pauses [
]. It shares protein sequence similarities with another DNA helicase, Pif1. However, their functions are different. Rrm3 promotes telomere replication, while Pif1 inhibits telomere replication []. They also have opposite effects on replication fork progression in ribosomal DNA [].In fission yeasts, Pfh1 is required for the maintenance of both mitochondrial and nuclear genome stability [
,
].
This domain is found in Helitrons, recently recognised eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism [
]. In many instances a protein-coding gene is disrupted by their insertion.
This domain is found in proteins that are related to
and are probably endonucleases of the DDE superfamily. Proteins containing this domain include the putative nuclease HARBI1. HARBI1 is a transposase-derived protein that may have nuclease activity potential. It does not have transposase activity [
,
].
This domain is found in a variety of carbohydrate and pyrimidine kinases. It is found in phosphomethylpyrimidine kinase (
), which is part of the thiamine pyrophosphate (TPP) synthesis pathway - TPP being an essential cofactor for many enzymes [
]. It is also found in 2-keto-3-deoxygluconate kinase, which is a component of the Entner-Doudoroff pathway in hyperthermophilic archaea [].
It has been shown [
,
,
] that the following carbohydrate and purine kinases are evolutionary related and can be grouped into a single family, which is known [] as the 'pfkB family':Fructokinase (
) (gene scrK).
6-phosphofructokinase isozyme 2 (
) (phosphofructokinase-2) (gene pfkB). pfkB is a minor phosphofructokinase isozyme in Escherichia coli and is not evolutionary related to the major isozyme (gene pfkA). Plant 6-phosphofructokinase also belong to this family.
Ribokinase (
) (gene rbsK).
Adenosine kinase (
) (gene ADK).
2-dehydro-3-deoxygluconokinase (
) (gene: kdgK).
1-phosphofructokinase (
) (fructose 1-phosphate kinase) (gene fruK).
Inosine-guanosine kinase (
) (gene gsk).
Tagatose-6-phosphate kinase (
) (phosphotagatokinase) (gene lacC).
E. coli hypothetical protein yeiC.E. coli hypothetical protein yeiI.E. coli hypothetical protein yhfQ.E. coli hypothetical protein yihV.Yeast hypothetical protein YJR105w.All the above kinases are proteins of from 280 to 430 amino acid residues that share a few region of sequence similarity.Note: some bacterial fructokinases belong to the ROK family (see
).
This entry represents those sugar-binding regions of glycosyltransferases that contain a DXD motif. The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases [
].
The glycosphingolipids (GSL) form part of eukaryotic cell membranes. They consist of a hydrophilic carbohydrate moiety linked to a hydrophobic ceramide tail embedded within the lipid bilayer of the membrane. Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common synthetic precursor to the majority of GSL found in vertebrates. Alpha 1.4-glycosyltransferases utilise UDP donors and transfer the sugar to a beta-linked acceptor [
].No function has been yet assigned to this domain
The N-terminal domain of PEX1 adopts a double psi β-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation [
]. This domain can be subdivided in N- and C-lobes. This entry represents the C-lobe.
β-barrels are commonly observed in protein structures. They are classified in terms of two integral parameters: the number of strands in the sheet, n, and the shear number, S, a measure of the stagger of the strands in the β-sheet. These two parameters have been shown to determine the major geometrical features of β-barrels. Six-stranded β-barrels with a pseudo-twofold axis are found in several proteins. One involving parallel strands forming two psi structures is known as the double-psi barrel. The first psi structure consists of the loop connecting strands β1 and β2 (a 'psi loop') and the strand β5, whereas the second psi structure consists of the loop connecting strands β4 and β5 and the strand β2. All the psi structures in double-psi barrels have a unique handedness, in that β1 (β4), β2 (β5) and the loop following β5 (β2) form a right-handed helix. The unique handedness may be related to the fact that the twisting angle between the parallel pair of strands is always larger than that between the antiparallel pair [
].In many cases, including aspartate decarboxylase and aspartic proteinases, strands 1 and 4 are each bent and consist of two sections. The two sections normally make a right angle; sometimes their hydrogen-bond patterns are disrupted at the corner by a bulge or even by a large insertion. In these cases, the barrel can also be viewed as a pair of orthogonally packed sheets, each with four strands.
Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [
]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [].These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:Uroporphyrinogen III methyltransferase (
) (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [
].Precorrin-2 C20-methyltransferase CobI/CbiL (
), which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [
]. In some species, this enzyme is part of a bifunctional protein.Precorrin-4 C11-methyltransferase CobM/CbiF (
), which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [
].Sirohaem synthase CysG (
), domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [
].Diphthine synthase (
), which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.
This entry represents a tetrapyrrole methylase domain, which consist of two non-similar subdomains [
].
Diphthine synthase (
), also known as diphthamide biosynthesis S-adenosylmethionine-dependent methyltransferase, participates in the modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. It is required for the methylation step in dipthamide biosynthesis.
This entry also includes diphthine methyl ester synthase (
) from Saccharomyces cerevisiae (a product of the DPH5 gene), which is an S-adenosyl-L-methionine-dependent methyltransferase that catalyzes methylations of a modified histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine methyl ester: the second step of diphthamide biosynthesis [
].
Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [
]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [].This entry represents the N-terminal subdomain 1 from several tetrapyrrole methylases, which consist of two non-similar domains. These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:Uroporphyrinogen III methyltransferase (
) (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [
].Precorrin-2 C20-methyltransferase CobI/CbiL (
), which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [
]. In some species, this enzyme is part of a bifunctional protein.Precorrin-4 C11-methyltransferase CobM/CbiF (
), which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [
].Sirohaem synthase CysG (
), domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [
].Diphthine synthase (
), which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.
The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to dnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of dnaK, which interacts stably with the polypeptide substrate [
,
]. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues.Such a structure is shown in the following schematic representation:
+------------+-+-------+-----+-----------+--------------------------------+
| J-domain | | Gly-R | | CXXCXGXG | C-terminal |+------------+-+-------+-----+-----------+--------------------------------+
The structure of the J-domain has been solved [
]. The J domain consists of four helices, the second of which has a charged surface that includes basic residues that are essential for interaction with the ATPase domain of hsp70 []. J-domains are found in many prokaryotic and eukaryotic proteins [
]. In yeast, three J-like proteins have been identified containing regions closely resembling a J-domain, but lacking the conserved HPD motif - these proteins do not appear to act as molecular chaperones [
]. This entry represents a conserved site found within the J-domain.
This entry represents a conserved region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in [
]. This region is found in I, II and III phosphatidylinositol-4-phosphate 5-kinases (PIP5K enzymes). PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphoinositide signalling pathway.
This superfamily represents the N-terminal domain of the phosphatidylinositol-4-phosphate 5-kinase (PIP5K). It has a 2-layer sandwich structure [
]. PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate, a precursor in the phosphinositide signalling 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 [
,
].L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homologue of bacterial L16. L16 and L10e exhibit structural differences at the N terminus [
,
,
,
,
,
,
,
].This entry represents a structural domain with an alpha/β-hammerhead fold, where the β-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16.
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.
COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex [
]. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger, an α/β trunk domain (
), an all-helical region (
), and a C-terminal gelsolin-like domain (
). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the β-barrel at the periphery of the complex.
COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex [
]. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger (
), an α/β trunk domain, an all-helical region (
), and a C-terminal gelsolin-like domain (
). This entry describes the Sec23/24 α/β trunk domain, which is formed from a single, approximately 250-residue segment plugged into the β-barrel between strands β-1 and β-19. The trunk has an α/β fold with a vWA topology, and it forms the dimer interface, primarily involving strand β-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.
COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex [
]. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger (
), an α/β trunk domain (
), an all-helical region, and a C-terminal gelsolin-like domain (
). This entry describes the all-helical domain, which forms an approximately 105-residue segment with the C-terminal 30 residues. The linker between alpha-M and alpha-N contacts Sar1.
COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex [
]. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger (
), an α/β trunk domain (
), an all-helical region (
), and a C-terminal gelsolin-like domain (
). This entry describes part of the Sec23/24 β-barrel domain, which is formed from approximately 180 residues from three segments of the polypeptide. The strands of the barrel are oriented roughly parallel to the membrane such that one end of the barrel forms part of the inner surface of the coat and the other end part of the membrane-distal surface. The barrel is constructed from two opposed sheets: a six-stranded β-sheet facing partly towards the zinc finger domain and partly towards the solvent, and a five-stranded β-sheet facing the helical domain.
Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) [
]. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing.Sequence comparisons indicate an evolutionary relationship between gelsolin,
villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].This gelsolin-like domain can also be found in the C-terminal of the members of Sec23/Sec24 family. They are components of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).
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 and archaebacterial ribosomal proteins have been grouped on the basis of sequence similarities. Ribosomal protein S6 is the major substrate of protein kinases in eukaryotic ribosomes [
] and may play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.
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 and archaeal ribosomal proteins have been grouped on the basis of sequence similarities. Ribosomal protein S6 is the major substrate of protein kinases in eukaryotic ribosomes [
] and may play an important role in controlling cell growth and proliferationthrough the selective translation of particular classes of mRNA.
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 and archaeal ribosomal proteins have been grouped on the basis of sequence similarities. Ribosomal protein S6 is the major substrate of protein kinases in eukaryotic ribosomes [
] and may play an important role in controlling cell growth and proliferationthrough the selective translation of particular classes of mRNA.
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.This group of endo-beta-N-acetylglucosaminidases belong to the glycoside hydrolase family 85 (
). These enzymes work on a broad spectrum of substrates.
This entry represents a conserved domain found in a group of sulphate transporters, known as the SLC26A/SulP family [
,
]. These proteins contain an N-terminal membrane domain and a C-terminal cytoplasmic STAS domain a STAS (sulfate transporter and anti-sigma factor antagonist) domain []. This central domain is usually found next to the STAS domain (). Proteins containing this domain include:
Neurospora crassa sulphate permease II (gene cys-14).Yeast sulphate permeases (genes SUL1 and SUL2).Rat sulphate anion transporter 1 (SAT-1).Mammalian DTDST, a probable sulphate transporter which, in human, is involved in the genetic disease, diastrophic dysplasia (DTD).Sulphate transporters 1, 2 and 3 from the legume Stylosanthes hamata.Human pendrin (gene PDS), which is involved in a number of hearing loss genetic diseases.Human protein DRA (Down-Regulated in Adenoma).Soybean early nodulin 70.Escherichia coli hypothetical protein ychM.Caenorhabditis elegans hypothetical protein F41D9.5.
The STAS (Sulphate Transporter and AntiSigma factor antagonist) domain is found in the bacterial anti-sigma factor antagonists (ASA) and the C-terminal region of SLC26 (SulP) anion transporters. The activity of bacterial sigma transcription factors is controlled by a regulatory cascade involving an antisigma-factor, the antisigma-factor antagonist (ASA) and a phosphatase. The antisigma-factor binds to sigma and holds it in an inactive complex. The ASA can also interact with the anti-sigma-factor, allowing the release of the active sigma factor. As the antisigma-factor is a protein kinase, it can phosphorylate the antisigma antagonist on a conserved serine residue of the STAS domain. This phosphorylation inactivates the ASA that can be reactivated through dephosphorylation by a phosphatase [
,
]. The STAS domain of the ASA SpoIIAA binds GTP and ATP and possesses a weak NTPase activity. Strong sequence conservation suggests that the STAS domain could possess general NTP-binding activity, and it has been proposed that the NTPs are likely to elicit specific conformational changes in the STAS domain through binding and/or hydrolysis []. Resolution of the solution structure of the ASA SpoIIAA from Bacillus subtilis has shown that the STAS domain consists of a four-stranded β-sheet and four α-helices. The STAS domain forms a characteristic α-helical handle-like structure [,
]. The STAS domain of E. coli YchM protein, a SLC26 (SulP) family member, has been shown to interact with acyl carrier protein (ACP), which is an activated thiol ester carrier of acyl intermediates during fatty acid biosynthesis (FAB) and other acylation reactions [
]. Malfunctions in members of the SLC26A family of anion transporters are involved in three human diseases: diastrophic dysplasia/achondrogenesis type 1B (DTDST), Pendred's syndrome (PDS) and congenital chloride diarrhea (CLD). These proteins contain 12 transmembrane helices followed by a cytoplasmic STAS domain at the C terminus. The importance of the STAS domain in these transporters is illustrated by the fact that a number of mutations in PDS and DTDST map to it [
,
].
The SLC26A/SulP family is a large and ubiquitous family with members derived from archaea, bacteria, fungi, plants and animals. Many organisms including Bacillus subtilis, Synechocystis sp, Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans possess multiple SulP family paralogues. Many of these proteins are functionally characterised, and most are inorganic anion uptake transporters or anion:anion exchange transporters. Some transport their substrate(s) with high affinities, while others transport it or them with relatively low affinities [
,
,
].SLC26A/SulP family proteins consist of N- and C- termini flanking a transmembrane domain thought to span the lipid bilayer 10-14 times. In most cases, the C-terminal cytoplasmic region includes a STAS (sulfate transporter and anti-sigma factor antagonist) domain [
].Malfunctions in members of the SLC26A family of anion transporters are involved in three human diseases: diastrophic dysplasia/achondrogenesis type 1B (DTDST), Pendred's syndrome (PDS) and congenital chloride diarrhoea (CLD). These proteins contain 12 transmembrane helices followed by a cytoplasmic STAS domain at the C terminus. The importance of the STAS domain in these transporters is illustrated by the fact that a number of mutations in PDS and DTDST map to it [
].Proteins in this family include:Neurospora crassa sulphate permease II (gene cys-14).Yeast sulphate permeases (SUL1 and SUL2).Rat sulphate anion transporter 1 (SAT-1).Mammalian DTDST, a probable sulphate transporter which, in human, is involved in the genetic disease, diastrophic dysplasia (DTD).Sulphate transporters 1, 2 and 3 from the legume Stylosanthes hamata.Human pendrin (gene PDS), which is involved in a number of hearing loss genetic diseases.Human protein DRA (Down-Regulated in Adenoma).Soybean early nodulin 70.Escherichia coli hypothetical protein YchM.Caenorhabditis elegans hypothetical protein F41D9.5.
A number of proteins involved in the transport of sulphate across a membrane
as well as some yet uncharacterised proteins have been shown [,
] to be evolutionary related.These proteins are:
Neurospora crassa sulphate permease II (gene cys-14).Yeast sulphate permeases (genes SUL1 and SUL2).Rat sulphate anion transporter 1 (SAT-1).Mammalian DTDST, a probable sulphate transporter which, in human, is involved in the genetic disease, diastrophic dysplasia (DTD).Sulphate transporters 1, 2 and 3 from the legume Stylosanthes hamata.Human pendrin (gene PDS), which is involved in a number of hearing loss genetic diseases.Human protein DRA (Down-Regulated in Adenoma).Soybean early nodulin 70.Escherichia coli hypothetical protein ychM.Caenorhabditis elegans hypothetical protein F41D9.5.These proteins are highly hydrophobic and seem to contain about 12 transmembrane domains.
This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [
].The bacterial deoxygenase 2-aminoethylphosphonate dioxygenase (PhnY) hydroxyles 2-aminoethylphosphonic acid to form (2-amino-1-hydroxyethyl)phosphonic acid, which is then oxidatively converted to inorganic phosphate and glycine by 2-amino-1-hydroxyethylphosphonate dioxygenase (PhnZ) [
].Ectoine dioxygenase from Streptomyces coelicolor (EctD) is involved in the biosynthesis of 5-hydroxyectoine, called compatible solute, which helps organisms to survive extreme osmotic stress by acting as a highly soluble organic osmolyte [
].
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 includes the asparagine, aspartic acid and lysine tRNA synthetases.
Asparagine tRNA ligase (
) is an alpha2 dimer that belongs to class IIb.
There is a striking similarity between asparagine-tRNA ligases and archaeal/eukaryotic type aspartyl-tRNA ligases () and a striking divergence of bacterial type aspartyl-tRNA ligases (
). This family, AsnS, represents asparagine-tRNA ligases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
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 [].
Sec15 is a component of the exocyst complex involved in the the tethering of post-Golgi Golgi secretory vesicles to the plasma membrane during exocytosis and plays a role in several cellular functions such as cell polarisation, cytokinesis, ciliogenesis and tumour invasion. The exocyst is one of the members of the complexes associated with tethering containing helical rods (CATCHR), together with COG, GARP, and Dsl1 complexes, which share a fold consisting of α-helical bundles forming a rod structure [
,
]. Its C-terminal domain mediates Rab GTPases binding which occurs in a GTP-dependent manner [].
Most of the hereditary idiopathic epilepsies are due to mutation in ion
channels expressed in brain. Recently two non-ion channel genes LGI1 andVGLR1 have emerged as important causes of specific epilepsy syndromes. The
product of these two genes share a conserved repeated region of about 44 aminoacid residues, the EAR domain (for epilepsy-associated repeat) [
].The predicted secondary structure (four β-strands) and the numbers of
repeated copies (seven) suggest that the EAR domain belongs to theβ-propeller fold. A common functional feature found in all characterised
domains of this class is a participation in protein-protein interactions.Since the EAR repeat is found in the ectodomain of VLGR1, it is most probably
involved in ligand recognition by the receptor [
].Proteins known to contain EAR repeats are listed below:Mammalian LGI1 to LGI4. LGI1 is mutated in autosomal dominant partial
epilepsy with auditory features (ADPEAF). The F348C missense mutation islocated in the third EAR repeat (7 copies).Mammalian thrombo-spondin N-terminal domain and EAR repeats containg
protein (TSPEAR) (7 copies).Mammalian very large G protein-coupled receptor 1 (VGLR1) or monogenic
audiogenic seizure-susceptible (MASS1) protein. In mouse, mutations inMASS1 gene are associated with generalized epilepsy and seizures in
response to loud noises (7 copies) [].
This domain is found in a group of prokaryotic proteins which includes Escherichia coli MazG, which hydrolyses all canonical nucleoside triphosphates but it also might have a 'housecleaning' function by hydrolysing noncanonical NTPs, whose incorporation into the nascent DNA leads to the increased mutagenesis and DNA damage [
,
, ]. Phylogenetic distribution studies of this domain revealed that it commonly appears as two domains in tandem, although there are single-domain analogs. In E. coli there are two tandem globular domains, in which the NTPase activity was observed only at the C-terminal domain [].
The microtubule organizing centres (MTOCs) of eukaryotic cells are the sites of nucleation of microtubules, and are known as the centrosome in animal cells and the spindle pole body in yeast. Gamma-tubulin, which is 30% identical to alpha and beta tubulins that form microtubules, appears to be a key protein involved in nucleation of microtubules.Gamma tubulin can assemble into complexes of various sizes with members of the GCP family. In budding yeast, the gamma tubulin-containing small complex (gammaTuSC) contains gamma tubulin, GCP2 and GCP3 (also known as Spc97 and Spc98). In Drosophila and vertebrates, gamma tubulin forms much larger assemblies, termed gamma-tubulin ring complexes (gammaTuRCs), with gamma tubulin, GCP2, GCP3, GCP4, GCP5 and GCP6. The purified gammaTuSC and gammaTuRC complexes exhibit a 'lock washer' shape [
]. However, the purified gammaTuSC has been shown to have a much lower microtubule-nucleating activity than intact gammaTuRC []. Several models have been proposed to explain their assembly and nucleation mechanism []. This entry represents the GCP family, whose members include GCP2/3/4/5/6 and Spc97/98 [
]. They contain the GRIP1 and GRIP2 motifs, which are predicted to participate in protein-protein interactions []. They are gamma tubulin binding proteins that have similar protein structures [].
The homocysteine (Hcy) binding domain is an ~300-residue module which is found in a set of enzymes involved in alkyl transfer to thiols:Prokaryotic and eukaryotic B12-dependent methionine synthase (MetH) (EC 2.1.1.13), a large, modular protein that catalyses the transfer of a methyl group from methyltetrahydrofolate (CH3-H4folate) to Hcy to form methionine, using cobalamin as an intermediate methyl carrier.Mammalian betaine-homocysteine S-methyltransferase (BHMT) (EC 2.1.1.5). It catalyzes the transfer of a methyl group from glycine betaine to Hcy, forming methionine and dimethylglycine.Plant selenocysteine methyltransferase (EC 2.1.1.-).Plant and fungal AdoMet homocysteine S-methyltransferases (EC 2.1.1.10).The Hcy-binding domain utilises a Zn(Cys)3 cluster to bind and activate Hcy. It has been shown to form a (beta/alpha)8 barrel. The Hcy binding domain barrel is distorted to form the metal- and substrate-binding sites. To accommodate the substrate, strands 1 and 2 of the barrel are loosely joined by nonclassic hydrogen bonds; to accommodate the metal, strands 6 and 8 are drawn together and strand 7 is extruded from the end of the barrel. The cysteines ligating the catalytic zinc atom are located at the C-terminal ends of strands 6 and 8 [
,
].
3-hydroxyacyl-CoA dehydrogenase (
) (HCDH) [
] is an enzyme involved in fatty acid metabolism, it catalyses 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 [
].There are two major regions of similarity 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 represents the N-terminal domain (although in some proteins is central) which is also found in lambda crystallin. Some proteins include two copies of this domain.
6-phosphogluconate dehydrogenase (
) catalyses the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate with the concomitant reduction of NADP to NADPH. The metazoan 6PGDHs have a well-conserved glycine-serine rich sequence at the C terminus, which is lacking from bacterial enzymes and from those of the parasitic protozoan Trypanosoma brucei. The active dimer of the mammalian enzyme assembles with the C-terminal tail of one subunit threaded through the other, forming part of the substrate-binding site. The tail of T. brucei 6PGDH is shorter than that of the mammalian enzyme and its terminal residues associate tightly with the second monomer. The three-dimensional structure shows this generates additional interactions between the subunits close to the active site; the coenzyme-binding domain is thereby associated more tightly with the helical domain. Three residues, conserved in all other known sequences, are important in creating a salt bridge between monomers close to the substrate-binding site [
].This domain is structurally similar to domains found in several different families, including those represented by mannitol 2-dehydrogenase, acetohydroxy acid isomeroreductase, short chain L-3-hydroxyacyl CoA dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase (dimerisation domain), N-(1-D-carboxylethyl)-L-norvaline dehydrogenase, glycerol-3-phosphate dehydrogenase, and ketopantoate reductase (PanE).
This superfamily represents a multi-helical domain found in several NAD or NADP-utilizing dehydrogenases, including 6-phosphogluconate dehydrogenase [
], classes I and II ketol-acid reductoisomerases [], L-3-hydroxyacyl CoA dehydrogenase [], UDP-glucose dehydrogenase [], glycerol-3-phosphate dehydrogenase [], ketopantoate reductase [], N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [], and mannitol 2-dehydrogenase []. This domain is often found in the C-terminal region of the protein.
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 [
].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 represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.
The members of this family are hypothetical eukaryotic proteins of unknown function. The region in question is approximately 100 amino acid residues long.
