The SPX domain is named after SYG1/Pho81/XPR1 proteins. This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal [
] suggesting that all the members of this family are involved in G-protein associated signal transduction. The C-terminal of these proteins often have an EXS domain () [
].The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family [
,
]. NUC-2 contains several ankyrin repeats ().
Several members of this family are the XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with Murine leukemia virus (MLV) [
]. The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae [,
]. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction [,
,
] and may itself function as a phosphate sensor [].
The EXS domain is named after ERD1/XPR1/SYG1 and proteins containing this motif include the C-terminal of the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be Murine leukemia virus (MLV) receptors (XPR1. The N-terminal of these proteins often have an SPX domain (
) [
].While the N-terminal is thought to be involved in signal transduction, the role of the C-terminal is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention defective) S. cerevisiae proteins. ERD1 proteins are involved in the localization of endogenous endoplasmic reticulum (ER) proteins. Erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localization label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via `salvage' vesicles [
].
This domain adopts a multihelical structure, with an irregular array of long and short α-helices. It allows binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex [
].
This family represents Protein FAM136A and similar uncharacterised proteins of unknown function from animals and plants. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation. In humans, FAM136A has been related to Meniere's disease, a complex disorder of the inner ear [
,
].
Rab proteins form a family of signal-transducing GTPases that cycle between
active GTP-bound and inactive GDP-bound forms. The Rab5 GTPase is an essentialregulator of endocytosis and endosome biogenesis. Rab5 is activated by GDP-GTP
exchange factors (GEFs) that contain a VPS9 domain and generate the Rab5-GTPcomplex [
]. The VPS9 domain catalyzes nucleotide exchange on Rab5 or the
yeast homologue VPS21. The domain has a length of ~140 residues and forms thecentral part of the yeast VPS9 (vacuolar protein sorting-associated) protein,
which acts as a GEF for VPS21. Some domains which can occur in combinationwith the VPS9 domain are CUE, A20-type zinc finger, Ras-associating (RA), SH2,
RCC1, DH, PH, rasGAP, MORN and ankyrin repeat.Structurally, the VPS9 domain adopts a layered fold of six alpha helices. Conserved residues from the fourth and sixth helices and the
loops N-terminal to these helices form the surface that interacts with Rab5and Rab21 [
].Some proteins known to contain a VPS9 domain:Fungal Vacuolar Protein Sorting-associated protein VPS9, a guanine
nucleotide exchange factor for the Rab-like GTPase VPS21. VPS9 is neededfor the transport of proteins from biosynthetic and endocytic pathways into
the vacuole.Mammalian Rab5 GDP/GTP exchange factor or Rabex-5 (Rababtin-5 associated
exchange factor for Rab5), catalyzes nucleotide exchange on RAB5A. Rabex-5promotes endocytic membrane fusion and is involved in membrane trafficking
of recycling endosomes.Mammalian Ras and Rab interactor 1 (RIN1), 2 (RIN2) and 3 (RIN3).Mammalian alsin or Amyotrophic Lateral Sclerosis protein 2 (ALS2).
Different juvenile-onset forms of neurodegenerative diseases (ALS2, JPLS,IAHSP) are caused by mutations in the ALS2 gene, which result in truncated
alsin lacking the C-terminal part of the VPS9 domain.Fruit fly protein sprint, which is a RIN homologue.Caenorhabditis elegans RME-6 protein, which is conserved among metazoans.
Peroxisomal proteins catalyse metabolic reactions. The import of proteins from the cytosol into the peroxisomes matrix depends on more than a dozen peroxin (PEX) proteins, among which PEX5 and PEX7 serve as receptors that shuttle proteins bearing one of two peroxisome-targeting signals (PTSs) into the organelle. PEX5 is the PTS1 receptor, while PEX7 is the PTS2 receptor. In plants, PEX7 depends on PEX5 binding to deliver PTS2 cargo into the peroxisome, and PEX7 also facilitates PEX5 accumulation and import of PTS1 cargo into peroxisomes [
,
]. This entry include PEX5 (also known as PTS1R) from animals, fungi and plants. This entry also includes PEX5L from vertebrates. PEX5 binds to the C-terminal PTS1-type tripeptide peroxisomal targeting signal (SKL-type) and plays an essential role in peroxisomal protein import [,
,
]. Based on subcellular localization and binding properties mammalian PEX5 may function as a regulator in an early step of the PTS1 protein import process []. PEX5L acts as an accessory subunit of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, regulating their cell-surface expression and cyclic nucleotide dependence [,
]. Interestingly, although PEX5 and PEX5L have structurally similar binding at their TPR domains, they bind to different substrates in vivo [].
This entry represents the N-terminal domain found in Alfin family members.
The Alfin family includes PHD finger protein Alfin1 and Alfin1-like proteins. They contain a conserved N domain at the N terminus, a PHD finger domain with conserved C4HC3 residues at the C terminus and a variable V region between the two conserved domains [
]. Alfin1 is a histone-binding component that specifically recognises H3 tails trimethylated on 'Lys-4' (H3K4me3), which marks transcription start sites of virtually all active genes [,
]. Alfin1-like proteins have been shown to play roles in root growth and abiotic stress response [].
VAMPs (and its homologue synaptobrevins) define a group of SNARE proteins that contain a C-terminal coiled-coil/SNARE domain, in combination with variable N-terminal domains that are used to classify VAMPs: those containing longin N-terminal domains (~150 aa) are referred to as longins, while those with shorter N-termini are referred to as brevins [
]. Longins are the only type of VAMP protein found in all eukaryotes, suggesting that their longin domain is essential. The longin domain is thought to exert a regulatory function. Longin domains have been shown to share the same structural fold, a profilin-like globular domain consisting of a five-stranded antiparallel β-sheet that is sandwiched by an α-helix on one side, and two α-helices on the other (β(2)-α-β(3)-α(2)).This domain is also found in phytolongins, non-SNARE longin proteins involved in membrane-trafficking machinery.
O-Glycosyl hydrolases (
) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [
,
]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.Glycoside hydrolase family 9
comprises enzymes with several known activities; endoglucanase (
); cellobiohydrolase (
). These enzymes were formerly known as cellulase family E.
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.
This domain superfamily contains up to seven alpha-hairpins arranged in closed circular array.
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates ([intenz:2.4.1.-]) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.The six-hairpin glycoside transferase domain, with an α/α toroid fold, contains six α-hairpins arranged in closed circular array.
The microbial degradation of cellulose and xylans requires several types of
enzymes such as endoglucanases, cellobiohydrolases (exoglucanases), or xylanases [
,
]. Fungi and bacteria producesa spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the
basis of sequence similarities, can be classified into families. One of thesefamilies is known as the cellulase family E [
] or as the glycosyl hydrolases family 9 []. Three conserved regions in these enzymes are centred on conserved residues
which have been shown [,
,
] to be important for the catalytic activity. Thefirst region contains the characteristic DAGD motif, where the C-terminal D
acts as the catalytic base that extracts a proton from the nucleophilic water.The second region contains an active site histidine and the third one contains
two catalytically important residues: an aspartate and a glutamate. The fullyconserved nucleophilic D forms H-bonds with the residues of the active-site
loop, comprising of regions I and II, to bring it in the proper alignement.The fully conserved E acts as an acid that protonates the leaving group and
stabilizes the positively-charged oxocarbonium transition-state.This entry represents the second conserved region containing a histidine.
This entry represents a DNA/RNA binding domain found in the telomere elongation protein EST1 and related sequences, such as the nonsense-mediated mRNA decay pathway proteins SMG5 and SMG7 [
,
,
,
].
Telomerase activating protein Est1-like, N-terminal
Type:
Domain
Description:
Est1 is directly involved in telomere replication. It associates with telomerase and, during its interaction with CDC13, telomerase activity is promoted [
,
]. This entry also includes Est1 homologues, such as human EST1A (also known as SMG6), which is essential for the replication of chromosome termini [] and also plays a role in nonsense-mediated mRNA decay [,
].
Photosystem I (PSI) [
] is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK []. While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna []. This protein family represents Photosystem I reaction center subunit V (PsaG) found in plants, predominantly in Streptophytes. In Arabidopsis thaliana, PsaG is involved in the binding dynamics of plastocyanin to PSI, in the stability of the PSI complex and in light-harvesting [
,
,
]. The crystal structure of the plant PSI complex show this protein is closely related to the similar subunit PsaK [].
Photosystem I reaction center subunit V/PsaK, plant
Type:
Family
Description:
Photosystem I (PSI) [
] is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK []. While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have amembrane-imbedded peripheral antenna [
]. This group represents Photosystem I reaction center subunits V (PsaG) and PsaK from plants.
Photosystem I (PSI) [
] is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK [
]. While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna []. The domain represented by this entry consists of an alpha orthogonal bundle and it is found in photosystem I subunits PsaG and PsaK from chloroplasts.
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.Photosystem I (PSI) [
] is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK []. While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna []. This entry represents Photosystem I reaction centre subunits V (PsaG) and PsaK from Cyanobacteria, Rhodophyta (red algae) and plants.
The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module found in a large number of eukaryotic transcription factors that regulate cell
proliferation, differentiation and development [,
]. The ARID domain appearsas a single-copy motif and can be found in association with other domains,
such as JmjC, JmjN, Tudor and PHD-type zinc finger [].The basic structure of the ARID domain domain appears to be a series of six
α-helices separated by β-strands, loops, or turns, but the structuredregion may extend to an additional helix at either or both ends of the basic
six. Based on primary sequence homology, they can be partitioned into threestructural classes:Minimal ARID proteins that consist of a core domain formed by six alpha-
helices;ARID proteins that supplement the core domain with an N-terminal alpha-
helix;Extended-ARID proteins, which contain the core domain and additional alpha-
helices at their N- and C-termini.Minimal ARIDs are distributed in all eukaryotes, while extended ARIDs are
restricted to metazoans. The ARID domain binds DNA as a monomer, recognizingthe duplex through insertion of a loop and an α-helix into the major
groove, and by extensive non-specific anchoring contacts to the adjacentsugar-phosphate backbone [
,
,
].Some proteins known to contain a ARID domain are listed below:Eukaryotic transcription factors of the jumonji family.Mammalian Bright, a B-cell-specific trans-activator of IgH transcription.Mammalian PLU-1, a protein that is upregulated in breast cancer cells.Mammalian RBP1 and RBP2, retinoblastoma binding factors.Mammalian Mrf-1 and Mrf-2, transcriptional modulators of the
cytomegalovirus major intermediate-early promoter.Drosophila melanogaster Dead ringer protein, a transcriptional regulatory
protein required for early embryonic development.Yeast SWI1 protein, from the SWI/SNF complex involved in chromatin
remodeling and broad aspects of transcription regulation.Drosophila melanogaster Osa. It is structurally related to SWI1 and
associates with the brahma complex, which is the Drosophila equivalent ofthe SWI/SNF complex.
The PB1 (Phox and Bem1) domain, comprising about 80 amino acid residues, is
conserved among animals, fungi, amoebas, and plants. It functions as a proteinbinding module through PB1-mediated heterodimerization or homo-oligomerization
[,
,
,
]. The PB1 domains adopt an ubiquitin-like β-grasp fold, containing two alpha
helices and a mixed five-stranded beta sheet. The β-sheethas a convex surface, and alpha1 fits into the cavity formed by the sheet. PB1
domains may display an acidic surface (type I), a basic surface (tape II), orboth surfaces (type I/II) on opposite faces of the domain structure to allow
for front-to-back orientation of multiple PB1 domains [,
,
,
,
].
This domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [
,
]. Proteins containing this domain include NIN-like proteins (NLPs) and RWP-RK domain proteins (RKDs). RWP-RK domain may serve in dimerisation and DNA binding [].
Presenilin 1 (PSN1) and presenilin 2 (PSN2) are membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. They undergo tightly regulated endolytic processing to generate stable PSN C-terminal and N-terminal fragments that form the catalytic core of the gamma-secretase complex, an endoprotease complex that catalyses the intramembrane cleavage of integral membrane proteins such as Notch receptors [
].Presenelins are related to the signal peptide peptidase (SPP) family of aspartic proteases that promote intramembrane proteolysis to release biologically important peptides. However, the SPPs work as single polypeptides. SPP catalyses intramembrane proteolysis of some signal peptides after they have been cleaved from a preprotein. In humans, SPP activity is required to generate signal sequence-derived human lymphocyte antigen-E epitopes that are recognised by the immune system, and are required in the processing of the hepatitis C virus core protein [
,
].This group of aspartic peptidases belong to MEROPS peptidase family A22 (presenilin family, clan AD).
This group of sequences contain aspartic endopeptidases that belong to MEROPS peptidase family A22 (presenilin family), subfamily A22B. These are intramembrane cleaving proteases (I-CLiPs). They are also known as signal peptide peptidases (SPPs) [
]. SPP cleaves remnant signal peptides left behind in the membrane by the action of signal peptidase and also plays key roles in immune surveillance and the maturation of certain viral proteins [].The tertiary structure of a homologue from the archaean
Methanoculleus marisnigrihas been solved and shows a unique fold which includes nine transmembrane segments that form a horseshoe shape [
]. SPPs do not require cofactors as demonstrated by expression in bacteria and purification of a proteolytically active form. The C-terminal region defines the functional domain, which is in itself sufficient for proteolytic activity [].Aspartic peptidases, also known as aspartyl proteases ([intenz:3.4.23.-]), are widely distributed proteolytic enzymes [,
,
] known to exist in vertebrates, fungi, plants, protozoa, bacteria, archaea, retroviruses and some plant viruses. All known aspartic peptidases are endopeptidases. A water molecule, activated by two aspartic acid residues, acts as the nucleophile in catalysis. Aspartic peptidases can be grouped into five clans, each of which shows a unique structural fold [].Peptidases in clan AA are either bilobed (family A1 or the pepsin family) or are a homodimer (all other families in the clan, including retropepsin from HIV-1/AIDS) [
]. Each lobe consists of a single domain with a closed β-barrel and each lobe contributes one Asp to form the active site. Most peptidases in the clan are inhibited by the naturally occurring small-molecule inhibitor pepstatin [].Clan AC contains the single family A8: the signal peptidase 2 family. Members of the family are found in all bacteria. Signal peptidase 2 processes the premurein precursor, removing the signal peptide. The peptidase has four transmembrane domains and the active site is on the periplasmic side of the cell membrane. Cleavage occurs on the amino side of a cysteine where the thiol group has been substituted by a diacylglyceryl group. Site-directed mutagenesis has identified two essential aspartic acid residues which occur in the motifs GNXXDRX and FNXAD (where X is a hydrophobic residue) [
]. No tertiary structures have been solved for any member of the family, but because of the intramembrane location, the structure is assumed not to be pepsin-like.Clan AD contains two families of transmembrane endopeptidases: A22 and A24. These are also known as "GXGD peptidases"because of a common GXGD motif which includes one of the pair of catalytic aspartic acid residues. Structures are known for members of both families and show a unique, common fold with up to nine transmembrane regions [
]. The active site aspartic acids are located within a large cavity in the membrane into which water can gain access [].Clan AE contains two families, A25 and A31. Tertiary structures have been solved for members of both families and show a common fold consisting of an α-β-alpha sandwich, in which the beta sheet is five stranded [
,
].Clan AF contains the single family A26. Members of the clan are membrane-proteins with a unique fold. Homologues are known only from bacteria. The structure of omptin (also known as OmpT) shows a cylindrical barrel containing ten beta strands inserted in the membrane with the active site residues on the outer surface [
].There are two families of aspartic peptidases for which neither structure nor active site residues are known and these are not assigned to clans. Family A5 includes thermopsin, an endopeptidase found only in thermophilic archaea. Family A36 contains sporulation factor SpoIIGA, which is known to process and activate sigma factor E, one of the transcription factors that controls sporulation in bacteria [
].
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 ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [
].
This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved [
]. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants.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.
In eukaryotes, glutathione S-transferases (GSTs) participate in the detoxification of reactive electrophillic compounds by catalysing their conjugation to glutathione. GST is found as a domain in S-crystallins from squid, and proteins with no known GST activity, such as eukaryotic elongation factors 1-gamma and the HSP26 family of stress-related proteins, which include auxin-regulated proteins in plants and stringent starvation proteins in Escherichia coli. The major lens polypeptide of cephalopods is also a GST [
]. Bacterial GSTs of known function often have a specific, growth-supporting role in biodegradative metabolism: epoxide ring opening and tetrachlorohydroquinone reductive dehalogenation are two examples of the reactions catalysed by these bacterial GSTs. Some regulatory proteins, like the stringent starvation proteins, also belong to the GST family []. GST seems to be absent from Archaea in which gamma-glutamylcysteine substitute to glutathione as major thiol.Glutathione S-transferases form homodimers, but in eukaryotes can also form heterodimers of the A1 and A2 or YC1 and YC2 subunits. The homodimeric enzymes display a conserved structural fold. Each monomer is composed of a distinct N-terminal sub-domain, which adopts the thioredoxin fold, and a C-terminal all-helical sub-domain, which adopts a 4-helical bundle fold. This entry is the C-terminal domain.Glutaredoxin 2 (Grx2), glutathione-dependent disulphide oxidoreductases, is structurally similar to GSTs, even though they lack any sequence similarity. Grx2 is also composed of N and C-terminal subdomains. It is thought that the primary function of Grx2 is to catalyse reversible glutathionylation of proteins with glutathione in cellular redox regulation including the response to oxidative stress. Grx2 is dissimilar to other glutaredoxins apart from containing the conserved active site residues [
].
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [
,
,
]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) [
].This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma).
Translation elongation factor EF1B, beta/delta chains, conserved site
Type:
Conserved_site
Description:
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [
,
,
]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) [
].This entry represents the C-terminal region of the beta (EF-1beta or EF1B-alpha) and delta (EF-1delta or EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous C-terminal regions. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma).
Translation elongation factor EF1B/ribosomal protein S6
Type:
Homologous_superfamily
Description:
An alpha+beta sandwich domain with a Ferredoxin-like fold can be found in the beta chain of the translation elongation factor EF1B [
], and in the ribosomal protein S6 from the small subunit [].Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) [
].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. The best conserved region is located in the C-terminal section of these proteins. In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups:Eubacterial L2.Algal and plant chloroplast L2.Cyanelle L2.Archaebacterial L2.Plant L2.Slime mold L2.Marchantia polymorpha mitochondrial L2.Paramecium tetraurelia mitochondrial L2.Fission yeast K5, K37 and KD4.Yeast YL6.Vertebrate L8.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [,
].Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. The best conserved region is located in the C-terminal section of these proteins. In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [
], groups:Eubacterial L2.Algal and plant chloroplast L2.Cyanelle L2.Archaebacterial L2.Plant L2.Slime mold L2.Marchantia polymorpha mitochondrial L2.Paramecium tetraurelia mitochondrial L2.Fission yeast K5, K37 and KD4.Yeast YL6.Vertebrate L8.
This entry includes RINT-1 from animals, Tip20 from yeasts and MAIGO2 (Mag2) from plants. They play a role in anterograde transport from the endoplasmic reticulum (ER) to the Golgi and/or retrograde transport from the Golgi to the ER share sequence similarity [
]. They are part of the CATCHR (complexes associated with tethering containing helical rods) family which comprises the exocyst, COG, GARP, and DSL1 complexes and share a similar structure organisation with an N-terminal coiled-coil and a C-terminal α-helical bundle, which might be a protein-protein interaction module necessary for the formation of functional complexes.RINT-1 interacts with Rad50 only during late S and G2/M phases and participates in radiation induced checkpoint control [
]. RINT-1 also functions in membrane trafficking from the endoplasmic reticulum (ER) to the Golgi complex in interphase cells [,
,
].Tip20 is involved in the retrograde transport from the Golgi to the ER [
,
].Arabidopsis Mag2 functions in the transport of storage protein precursors between the ER and Golgi complex in plants [
,
].
This entry represents Ecd (ecdysoneless) family. Drosophila ecd mutants display reduced steroid titers during larval development [
]. Mammalian Ecd (also known as SGT1 and hEcd in humans) has been shown to stimulate cell proliferation by interacting with the Retinoblastoma (Rb) proteins []. Ecd proteins may be involved in pre-mRNA splicing []. Overexpression of Ecd has been linked to cancer progression [
,
].
Subtilases [
] are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.This entry represents the conserved sequence around the His active site.
This entry represents the second Ig-like domain found in the central region of tripeptidyl peptidase II (TPPII, MEROPS peptidase family S8A). TPPII is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides [
,
]. It consists of three main parts: the N-terminal subtilisin-like domain (), a central domain and a C-terminal domain [
]. According to the structures, the central domain can be subdivided into Ig-like and galactose-binding domain-like (GBD).
These proteins contain a domain found in serine peptidases belonging to the MEROPS peptidase families S8 (subfamilies S8A (subtilisin) and S8B (kexin) and S53 (sedolisin), both of which are members of clan SB [
].The subtilisin family is one of the largest serine peptidase families characterised to date. Over 200 subtilises are presently known, more than 170 of which with their complete amino acid sequence [
]. It is widespread, being found in eubacteria, archaebacteria, eukaryotes and viruses []. The vast majority of the family are endopeptidases, although there is an exopeptidase, tripeptidyl peptidase [,
]. Structures have been determined for several members of the subtilisin family: they exploit the same catalytic triad as the chymotrypsins, although the residues occur in a different order (HDS in chymotrypsin and DHS in subtilisin), but the structures show no other similarity [,
]. Some subtilisins are mosaic proteins, while others contain N- and C-terminal extensions that show no sequence similarity to any other known protein [].The proprotein-processing endopeptidases kexin, furin and related enzymes
form a distinct subfamily known as the kexin subfamily (S8B). These preferentially cleave C-terminally to paired basic amino acids. Members of this subfamily can be identified by subtly different motifs around the active site [,
]. Members of the kexin subfamily, along with endopeptidases R, T and K from the yeast Tritirachium and cuticle-degrading peptidase from Metarhizium, require thiol activation. This can be attributed to the presence of a cysteine near to the active site histidine []. Only one viral member of the subtilisin family is known, a 56kDa protease from herpes virus 1, which infects the channel catfish []. Sedolisins (serine-carboxyl peptidases) are proteolytic enzymes whose fold resembles that of subtilisin; however, they are considerably larger, with the mature catalytic domains containing approximately 375 amino acids. The defining features of these enzymes are a unique catalytic triad, Ser-Glu-Asp, as well as the presence of an aspartic acid residue in the oxyanion hole. High-resolution crystal structures have now been solved for sedolisin from Pseudomonas sp. 101, as well as for kumamolisin from a thermophilic bacterium, Bacillus sp. MN-32. Mutations in the human gene leads to a fatal neurodegenerative disease [
]. This domain is also found in Neisserial autotransporter lipoprotein NalP from Neisseria meningitidis, a major human immunogenic protein that cleaves human (host) complement factor C3, generating a shorter alpha chain and a longer beta chain than normal [
].
Subtilases [
] are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.This entry represents the conserved sequence around the Ser active site.
Arsenic is a toxic metalloid whose trivalent and pentavalent ions inhibit
a variety of biochemical processes. Operons that encode arsenic resistancehave been found in multicopy plasmids from both Gram-positive and
Gram-negative bacteria []. The resistance mechanism is encoded from a singleoperon, which houses an anion pump. The pump has two polypeptide components:a catalytic subunit (the ArsA protein), which functions as an
oxyanion-stimulated ATPase; and an arsenite export component (the ArsB protein),which is associated with the inner membrane [
]. The ArsA and ArsB proteinsare thought to form a membrane complex that functions as an
anion-translocating ATPase.The ArsB protein is distinguished by its overall hydrophobic character,
in keeping with its role as a membrane-associated channel. Sequenceanalysis reveals the presence of 13 putative transmembrane (TM) regions.
This domain is found in proteins belonging to the CitM transporter, NhaD Na+/H+ antiporter and Na+/sulfate symporter families, such as CitM from Bacillus subtilis [
], NhaD from Halomonas elongata [] and SLT1 from Chlamydomonas reinhardtii [].
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein S4 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S4 is known to bind directly to 16S ribosomal RNA. Mutations in S4 have been shown to increase translational error frequencies [
].S4 is a protein of 171 to 205 amino-acid residues (except for NAM9, which is much larger). The crystal structure of a bacterial S4 protein revealed a two domain molecule. The first domain is composed of four helices in the known structure. The second domain is in the middle of the first one and displays some structural homology with the ETS DNA binding domain [
].This family includes the small ribosomal subunits S4 and S9.
The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation [
]. The S4 domain probably mediates binding to RNA [].
This domain is found as part of an RNase-H fold section in a number of hAT-like transposases, such as protein DAYSLEEPER (At3g42170) from Arabidopsis [
]. Protein DAYSLEEPER is essential for plant development and can also regulate global gene expression []. This entry also includes some uncharacterised fungal proteins.
This entry includes membrane insertase YidC from bacteria, ALBINO3-like proteins from plants, and mitochondrial membrane insertase OXA1 and cytochrome c oxidase assembly protein COX18 from eukaryotes. They are a group of evolutionarily conserved proteins that function in membrane protein integration and protein complex stabilization. They share a conserved region composed of five transmembrane regions [
]. YidC is required for the insertion of integral membrane proteins into the membrane. It may also be involved in protein secretion processes [
]. YidC from Gram-negative bacteria contains an extra transmembrane segment (TM1) at the N-terminal and a large periplasmic domain, located between TM1 and TM2, that adopts a β-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase [
,
]. The well-characterised YidC protein from Escherichia coli and its close homologues contain a large N-terminal periplasmic domain (). This protein interacts with SecYEG protein-conducting channel and the accessory proteins SecDF-YajC to form the bacterial holo-translocon (HTL) [
].COX18 is a mitochondrial membrane insertase required for the translocation of the C-terminal of cytochrome c oxidase subunit II (MT-CO2/COX2) across the mitochondrial inner membrane. It plays a role in MT-CO2/COX2 maturation following the COX20-mediated stabilization of newly synthesized MT-CO2/COX2 protein and before the action of the metallochaperones SCO1/2 [
].OXA1 is a mitochondrial inner membrane insertase that mediates the insertion of both mitochondrion-encoded precursors and nuclear-encoded proteins from the matrix into the inner membrane. It links mitoribosomes with the inner membrane [
].Plant ALBINO3-like proteins are required for the insertion of some light harvesting chlorophyll-binding proteins (LHCP) into the chloroplast thylakoid membrane [
,
].
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 superfamily represents domains I, II and III found in alpha-D-phosphohexomutase enzymes. All three domains share a 3-layer alpha/beta/alpha topology.
This family is composed of root UVB sensitive proteins and their homologues. In Arabidopsis thaliana, proteins in this family are involved in UVB-sensing and in early seedling morphogenesis and development [
].
This entry represents the U-box domain.The molecular mechanism underlying the transfer of ubiquitin (Ub) to a substrate consists of three key enzymatic steps. First, ubiquitin itself is adenylated at its C-terminal glycine residue by an activating enzyme (E1). Second, the adenylated Ub forms a covalent linkage to a conjugating enzyme (E2). Finally, a ligating enzyme (E3) recruits both the Ub-charged E2 species and the target protein. There are three classes of E3 enzymes- HECT, RING, and U-box, which are distinguished on the basis of their E2-recruiting domains. The U-box and RING classes of E3 ligases act as scaffolding molecules that recruit and colocalize both a Ub-charged E2 and the substrate concomitantly. The recruitement of substrate in these proteins involves protein interaction modules such as a WD-40 repeat, TPR, and armadillo repeat domains. In addition to a common organisation, the architecture of U-box and RING domains are similar. Both contain a central α-helix flanked by two surface-exposed loops arranged in a cross-brace formation. the structure of RING domains is built around two zinc binding sites that are critical to its stability. In contrast, U-boxes do not bind zinc but have evolved instead networks of hydrogen bonds and salt bridges in corresponding location in the structure. Other similarities between these two domains include an antiparallel β-sheet type arrangement involving the first surface exposed loop and the central alpha helix. The β-sheet is stabilised by highly conserved hydrophobic residues responsible for the core packing and stability of the molecule. Most U-box and RING domain structures also contain an elongated C-terminal helix. The physical basis and physiological rationale for evolving distinct U-box and RING E3 ligases are not yet known [
,
,
].The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the β-β-α-β-alpha-fold typical of U-box and RING domains (see PDB:2QIZ). The central alpha helix is flanked by two prominent surface-exposed loop regions. The characteristic network of hydrogen bonds within each loop stabilises the overall structure. The U-box protein appear to catalyze their own ubiquitination as well as that of heterologous substrate [
,
,
].
The C2 domain is one of the most prevalent eukaryotic lipid-binding domains
deployed in diverse functional contexts. Many C2 domainsbind directly to membrane lipids and display a wide range of lipid
selectivity, with preference for anionic phosphatidylserine (PS) andphosphatidylinositol-phosphates (PIPs).Despite their limited sequence similarity, all C2 domains contain at their
core a compact β-sandwich composed of two four-stranded beta sheets withhighly variable inter-strand regions that might contain one or more alpha-
helices.The NT-type C2 domain shows a diverse range of domain architectures but it is
nearly always found at the N-termini of proteins that contain it. Hence, ithas been named the N-terminal C2 (NT-C2) family. It is typically coupled with
a coiled-coil domain, that could mediate di/oligo-merization and the DIL(Dilute) domain. It is also coupled with the Calponin
homology (CH) domain in EHBP1 proteins, Filamin/ABP280repeats and Mg2+ transporter MgtE N-terminal domain in
proteins from chlorophyte algae such as Micromonas and Ostreococcus tauri.Thus, a common theme across the NT-type C2 domain proteins is the combination
to several different domains with microfilament-binding or actin-related roles(i.e. such as CH, DIL, and Filamin). Other conserved groups of the NT-type C2
proteins prototyped by EEIG1, PMI1, and SYNC1 have their own distinct C-terminal conserved extensions that are restricted to these groups and might
mediate specific interactions. The primary function of the NT-type C2 domainappears to be the linking of actin/microfilament-binding adaptors to the
membrane and to act as a link that tethers endosomal vesicles to thecytoskeleton in course of their intracellular trafficking [
,
].
This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this entry (such as
), which may indicate that these domains are able to interact with one another, raising the possibility that it mediates heterodimerisation.
Mitochondrial intermembrane space import and assembly protein 40 (MIA40) from the yeast Ashbya gossypii also belongs to this entry. Experimental data showed that its cysteine residues have an structural role while the disulfide bond formed by the third and sixth cysteine residues seem to support a conformation essencial for the function of this protein [
].
In eukaryotes, glutathione S-transferases (GSTs) participate in the detoxification of reactive electrophilic compounds by catalysing their
conjugation to glutathione. The GST domain is also found in S-crystallins from squid, and proteins with no known GST activity, such as eukaryotic elongation factors 1-gamma and the HSP26 family of stress-related proteins, which include auxin-regulated proteins in plants and stringent starvation proteins in Escherichia coli. The major lens polypeptide of Cephalopoda is also a GST [,
,
,
].Bacterial GSTs of known function often have a specific, growth-supporting role in biodegradative metabolism: epoxide ring opening and tetrachlorohydroquinone reductive dehalogenation are two examples of the reactions catalysed by these bacterial GSTs. Some regulatory proteins, like the stringent starvation proteins, also belong to the GST family [
,
]. GST seems to be absent from Archaea in which gamma-glutamylcysteine substitute to glutathione as major thiol.Soluble GSTs activate glutathione (GSH) to GS-. In many GSTs, this is accomplished by a Tyr at H-bonding distance from the sulphur of GSH. These enzymes catalyse nucleophilic attack by reduced glutathione (GSH) on nonpolar compounds that contain an electrophilic carbon, nitrogen, or sulphur atom [
].Glutathione S-transferases form homodimers, but in eukaryotes can also form heterodimers of the A1 and A2 or YC1 and YC2 subunits. The homodimeric enzymes display a conserved structural fold, with each monomer composed of two distinct domains [
]. The N-terminal domain forms a thioredoxin-like fold that binds the glutathione moiety, while the C-terminal domain contains several hydrophobic α-helices that specifically bind hydrophobic substrates.This entry represents the N-terminal domain of GST.
Glutaredoxins [
,
,
], also known as thioltransferases (disulphide reductases), are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system [].Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin (TRX), which functions in a similar way, glutaredoxin possesses an active centre disulphide bond [
]. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH ->GSH reductase ->GSH ->GRX ->protein substrates [
,
,
,
]. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress.Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [
] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.This entry represents Glutaredoxin.
The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [
,
,
]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding [].The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that
TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallelfashion, resulting in a spiral of repeating anti-parallel α-helices [
]. The two helices are denotedhelix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a
single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B andwith helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is
contributed to mainly by residue on helices A, and the other surface presents residues from bothhelices A and B.
Carbonic anhydrases (CA:
) are zinc metalloenzymes which catalyse the reversible hydration of carbon dioxide to bicarbonate [
,
]. The alpha-CAs are found predominantly in animals but also in bacteria and green algae. There are at least 15 isoforms found in mammals, which can be subdivided into cytosolic CAs (CA-I, CA-II, CA-III, CA-VII and CA XIII), mitochondrial CAs (CA-VA and CA-VB), secreted CAs (CA-VI), membrane-associated (CA-IV, CA-IX, CA-XII and CA-XIV) and those without CA activity, the CA-related proteins (CA-RP VIII, X and XI).
This entry represents a domain characteristic of alpha class carbonic anhydrases. The dominating secondary structure is a 10-stranded, twisted β-sheet, which divides the molecules into two halves [
]. Alpha-CAs contain a single zinc atom bound to three conserved histidine residues. The catalytically active group is the zinc-bound water which ionizes to a hydroxide group. In the mechanism of catalysis, nucleophilic attack of CO2 by a zinc-bound hydroxide ion is followed by displacement of the resulting zinc-bound bicarbonate ion by water; subsequent deprotonation regenerates the nucleophilic zinc-bound hydroxide ion [,
].A carbonic anhydrase-like domain with striking homology to that of the alpha class carbonic anhydrases is also found in receptor-type tyrosine-protein phosphatase gamma and zeta. In this case it may have a different function, as only one of the three His residues that ligate the zinc atom and are required for catalytic activity is conserved [
].Carbonic anhydrases (CA:
) are zinc metalloenzymes which catalyse the reversible hydration of carbon dioxide to bicarbonate [
,
]. The alpha-CAs are found predominantly in animals but also in bacteria and green algae. There are at least 15 isoforms found in mammals, which can be subdivided into cytosolic CAs (CA-I, CA-II, CA-III, CA-VII and CA XIII), mitochondrial CAs (CA-VA and CA-VB), secreted CAs (CA-VI), membrane-associated (CA-IV, CA-IX, CA-XII and CA-XIV) and those without CA activity, the CA-related proteins (CA-RP VIII, X and XI).
This superfamily represents an actin-crosslinking domain with a β-trefoil structure, consisting of a triplet of β-hairpins packed against a six-stranded antiparallel β-barrel. Proteins containing this domain include fascin, which carries a tandem repeat of four copies of this domain, and the histidine-rich actin-binding protein hisactophilin. Actin-crosslinking proteins organise actin filaments into dynamic and complex subcellular scaffolds that orchestrate important mechanical functions, including cell motility and adhesion [
].The fascins are a structurally unique and evolutionarily conserved group of actin cross-linking proteins. Fascins function in the organisation of two major forms of actin-based structures: dynamic, cortical cell protrusions and cytoplasmic microfilament bundles [
].A related protein, hisactophilin, is an essential protein for the osmoprotection of dictyostelium cells [
,
].
The actin-depolymerising factor homology (ADF-H) domain is an ~150-amino acid motif that is present in three phylogenetically distinct classes of eukaryotic actin-binding proteins [,
,
]:ADF/cofilins, which include ADF, cofilin, destrin, actophorin, coactosin, depactin and glia maturation factors (GMFs) beta and gamma. ADF/cofilins are small actin-binding proteins composed of a single ADF-H domain. They bind both actin-monomers and filaments and promote rapid filament turnover in cells by depolymerising/fragmenting actin filaments. ADF/cofilins bind ADP-actin with higher affinity than ATP-actin and inhibit the spontaneous nucleotide exchange on actin monomersTwinfilins, which are actin monomer-binding proteins that are composed of two ADF-H domainsAbp1/Drebrins, which are relatively large proteins composed of an N-terminal ADF-H domain followed by a variable region and a C-terminal SH3 domain. Abp1/Drebrins interact only with actin filaments and do not promote filament depolymerisation or fragmentationAlthough these proteins are biochemically distinct and play different roles in actin dynamics, they all appear to use the ADF-H domain for their interactions with actin.The ADF-H domain consists of a six-stranded mixed β-sheet in which the four central strands (β2-β5) are antiparallel and the two edge strands (β1 and β6) run parallel with the neighbouring strands. The sheet is surrounded by two α-helices on each side [
,
,
].
Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. These proteins enhance the turnover rate of actin, and interact with actin monomers (G-actin) as well as actin filaments (F-actin), typically with a preference for ADP-G-actin subunits [
,
,
]. The basic function of cofilin is to promote disassembly of aged actin filaments. Vertebrates have three isoforms of cofilin: cofilin-1 (Cfl1, non-muscle cofilin), cofilin-2 (muscle cofilin), and ADF (destrin) [,
]. The modes of action of ADF/cofilins highly depend on their concentration. When ADF/cofilins are present in low concentrations they prefer to sever the actin filaments and promote the depolymerization of the pointed end of the filament. At high concentrations they can increase the polymerization by nucleating new actin filaments [].
Lectins are carbohydrate-binding proteins. Leguminous lectins form one of the largest lectin families and resemble each other in their physicochemical properties, though they differ in their carbohydrate specificities. They bind either glucose/mannose or galactose [
]. Carbohydrate-binding activity depends on the simultaneous presence of both acalcium and a transition metal ion [
]. The exact function of legume lectins is not known, but they may be involved in the attachment of nitrogen-fixing bacteria to legumes and in the protection against pathogens [,
].Some legume lectins are proteolytically processed to produce two chains, beta (which corresponds to the N-terminal) and alpha (C-terminal) [
]. The lectin concanavalin A (conA) from jack bean is exceptional in that the two chains are transposed and ligated (by formation of a new peptide bond). The N terminus of mature conA thus corresponds to that of the alpha chain and the C terminus to the beta chain []. Though the legume lectins monomer is structurally well conserved, their quaternary structures vary widely [].The signature pattern for this entry is located in the C-terminal section of the beta chain and contains a conserved aspartic acid residue important for the binding of calcium and manganese.
RNA polymerase III subunit RPC82-related, helix-turn-helix
Type:
Domain
Description:
DNA-directed RNA polymerases
(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric
enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [
]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.
Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10kDa to about 160kDa [
]. This region is probably a DNA-binding helix-turn-helix.
This family consists of several plant specific PAR1 proteins from Nicotiana tabacum (Common tobacco) and Arabidopsis thaliana (Mouse-ear cress). The function of this family is unknown.
This is a small domain that is found C-terminal to
in ATP-dependent AMP-binding enzymes from eukaryotes, bacteria and archaea, including Acetyl-coenzyme A synthetase (Acs). In Acs, this domain undergoes a large rotation to allow for both half-reaction to occur. It shows a central β-sheet core that is flanked by α-helices [].
The stability of beta-tubulin mRNAs are autoregulated by their own translation product [
]. Unpolymerised tubulin subunits bind directly (or activate a factor(s) which binds co-translationally) to the nascent N terminus of beta-tubulin. This binding is transduced through the adjacent ribosomes to activate an RNAse that degrades the polysome-bound mRNA. The recognition element has been shown to be the first four amino acids of beta-tubulin: Met-Arg-Glu-Ile. Mutations to this sequence abolish the autoregulation effect (except for the replacement of Glu by Asp); transposition of this sequence to an internal region of a polypeptide also suppresses the autoregulatory effect.
Glyceraldehyde/Erythrose phosphate dehydrogenase family
Type:
Family
Description:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [
] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme [].GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis [
]. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself.GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins [
].This entry contains a small clade of dehydrogenases in gamma-proteobacteria which utilise NAD+ to oxidize erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose [
]. This enzyme activity appears to have evolved from glyceraldehyde-3-phosphate dehydrogenase, whose substrate differs only in the lack of one carbon relative to E4P. It is possible that some of the GAPDH enzymes may prove to be bifunctional in certain species.
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [
] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme [].GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis [
]. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself.GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins [
].This entry represents the C-terminal domain which is a mixed alpha/antiparallel beta fold.
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [
] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain []. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme [].GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis [
]. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself.GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins [
].This entry represents the N-terminal domain which is a Rossmann NAD(P) binding fold.
This family represents plant AT-rich sequence and zinc-binding proteins (PLATZ), which are zinc dependent DNA binding proteins. They bind to AT rich sequences and functions in transcriptional repression [
]. Included in this family is the protein RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), a transcription factor that plays a central role in mediating RGF1 hormone peptide signalling, leading to the production of reactive oxygen species (ROS) in roots to modulate meristem size and root growth, probably via oxidative post-translational modification of the transcription factor PLETHORA [].
The C-terminal catalytic domains of glutamine synthetase and the guanido kinase family (which includes creatine kinase and arginine kinase) share a common structural fold, namely a common core consisting of two beta-alpha-beta2-alpha repeats [
].Glutamine synthetase (
) (GS) [
] plays an essential role in the metabolism of nitrogen by catalysing the condensation of glutamate and ammonia to form glutamine. There seem to be three different classes of GS [,
,
]. Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits; the activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. Class II enzymes (GSII) are found in eukaryotes and in bacteria, and are oligomers of 8 identical subunits. Class III enzymes (GSIII) have been found in Bacteroides fragilis in Butyrivibrio fibrisolvens, and are oligomers of six identical subunits. While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.ATP:guanido phosphotransferases are a family of structurally and functionally related enzymes [
,
] that reversibly catalyse the transfer of phosphate between ATP and various phosphogens. The enzymes belonging to this family include:Glycocyamine kinase (
), which catalyses the transfer of phosphate from ATP to guanidoacetate.
Arginine kinase (
), which catalyses the transfer of phosphate from ATP to arginine.
Taurocyamine kinase (
), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to taurocyamine.
Lombricine kinase (
), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to lombricine.
Smc74, a cercaria-specific enzyme from Schistosoma mansoni [
].Creatine kinase (
) (CK) [
,
], which plays an important role in energy metabolism of vertebrates.
Expansins are unusual proteins that mediate cell wall extension in plants. They are believed to act as a sort of chemical grease, allowing
polymers to slide past one another by disrupting non-covalent hydrogenbonds that hold many wall polymers to one another. This process is not
degradative and hence does not weaken the wall, which could otherwiserupture under internal pressure during growth.
Sequence comparisons indicate at least four distinct expansin cDNAs inrice and at least six in Arabidopsis thaliana. The proteins are highly conserved in
size and sequence (75-95% amino acid sequence similarity between any pairwise comparison), and phylogenetic trees indicate that this multigene
family formed before the evolutionary divergence of monocotyledons and dicotyledons. Sequence and motif analyses show no similarities to known
functional domains that might account for expansin action on wall extension[
]. It is thought that several highly-conserved tryptophans may function in expansin binding to cellulose, or other glycans. The high conservation
of the family indicates that the mechanism by which expansins promote wallextensin tolerates little variation in protein structure.
The PapD-like superfamily of periplasmic chaperones directs the assembly of over 30 diverse adhesive surface organelles that mediate the attachment of many different pathogenic bacteria to host tissues, a critical early step in the development of disease. PapD, the prototypical chaperone, is necessary for the assembly of P pili. P pili contain the adhesin PapG, which mediates the attachment of uropathogenic Escherichia coli to Gal(alpha) Gal receptors present on kidney cells and are critical for the initiation of pyelonephritis. The PapD-like chaperones consist of two Ig-like domains oriented toward each other, forming L-shaped molecules. In the chaperone-subunit complex, the G1beta strand of the chaperone completes an atypical Ig fold in the subunit by occupying the groove and running parallel to the subunit C-terminal F strand. This donor strand complementation interaction simultaneously stabilises pilus subunits and caps their interactive surfaces, preventing their premature oligomerisation in the periplasm. During pilus biogenesis, the highly conserved N-terminal extension of one subunit has been proposed to displace the chaperone G1beta strand from its neighbouring subunit in a mechanism termed donor strand exchange [
].This entry represents the immunoglobulin (Ig)-like β-sandwich domain found in PapD, as well as in other periplasmic chaperone proteins that include FimC and SfaE from E. coli, and Caf1m from Yersinia pestis [
]. In addition, major sperm proteins (MSP) and other related sperm proteins (such as WR4 and SSP-19) contain an Ig-like domain with a similar structural fold to PapD [,
]. Major sperm proteins are central components in molecular interactions underlying sperm motility, with many isoforms existing in Caenorhabditis elegans.
Nematode sperm are unusual amoeboid cells in which motility is not based on actin, but instead on the major sperm protein (MSP). MSP is a dimeric molecule that polymerises to form non-polar filaments constructed from two helical subfilaments that wind round one another. The filaments then assemble into larger macromolecular assemblies called fibre complexes. MSP is a small (~14kDa) basic protein typically encoded by a multigene family of up to 28 members [
,
,
,
]. An about 120-amino acid domain similar to MSP has been found in other proteins, including:Animal Vesicle-Associated Membrane Protein-associated (VAMP-associated) protein family of 33kDa (VAP33). VAP33 is required for neurotransmitter release. It binds to the v-SNARE synaptobrevin/VAMP which is associated with vesicle fusion. VAP33 has a two-domain structure with its N terminus being highly homologous to MSP, whereas its C terminus is based on a putative α-helical coiled-coil combined with an extremely hydrophobic membrane-attachment region [
].Nicotiana plumbaginifolia VAP27, a VAP33 homologue. It interacts with the resistance protein Cf9 [
].Yeast inositol regulator SCS2, a VAP33 homologue. It is C-terminally anchored to the endoplasmic reticulum [
].The MSP polypeptide chain has an immunoglobulin-like fold based on a seven-stranded beta sandwich measuring approximately 15 A x 20 A x 45 A and having opposing three-stranded and four-stranded beta sheets [].This entry represents the MSP domain.
This entry includes folate-biopterin transporters (FBTs) from blue-green algae and plants, including Slr0642 protein from Synechocystis and its plastidial orthologue At2g32040 from Arabidopsis [
]. Both Slr0642 protein and At2g32040 mediate folate monoglutamate transport involved in tetrahydrofolate biosynthesis. However, this entry also includes 7 other
Arabidopsis FBT proteins that lack conserved critical residues and may not have folate or pterin transport activity [].
Trehalose-phosphatases
catalyse the de-phosphorylation of
trehalose-6-phosphate to trehalose and orthophosphate. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance. A pathway for trehalose biosynthesis may also exist in plants []. The trehalose-phosphatase signature is found in the C terminus oftrehalose-6-phosphate synthase
adjacent to the trehalose-6-phosphate synthase domain (see
). It would appear that the two equivalent genes in the Escherichia coli otsBA operon: otsA, the
trehalose-6-phosphate synthase and otsB, trehalose-phosphatase (this family) have undergone gene fusion inmost eukaryotes [
].
This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class II subfamilies are characterised by a domain that is located between the second and third conserved catalytic motifs of the superfamily domain. The IIB subfamily is distinguished from the IIA subfamily (
) by homology and the predicted secondary structure of this domain by PSI-PRED. The IIB subfamilys Class II domain has the following predicted structure: Helix-Sheet-Sheet-(Helix or Sheet)-Helix-Sheet-(variable)-Helix-Sheet-Sheet. The IIB subfamily consists of trehalose-6-phosphatase, plant and cyanobacterial sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase, a large subfamily of Cof-like hydrolases, containing many closely related bacterial sequences, a hypothetical equivalog containing the Escherichia coli YedP protein, as well as two other small clusters whose relationship to the other groups is unclear.
O-Glycosyl hydrolases (
) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [
,
]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.Glycoside hydrolase family 32
comprises enzymes with several known activities; invertase/fructofuranosidase (
); inulinase (
); levanase (
); exo-inulinase (
); sucrose:sucrose 1-fructosyltransferase (
); fructan:fructan 1-fructosyltransferase (
).
This entry represents the N-terminal domain of beta-fructofuranosidase (also known as vacuolar invertase) (
), which is involved in the hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides [
].
This is a five-bladed β-propeller fold catalytic domain where each blade has four twisted antiparallel β-strands radially orientated around a pseudo-5-fold axis [
]. It can be found in the glycosyl hydrolase family 43 (GH43) members, including beta-xylosidases, alpha-L-arabinanases and bifunctional beta-xylosidases/alpha-L-arabinofuranosidases [,
,
]. This domain can also be found in other GH families, such as GH32, GH62 and GH68 [].
This ammonium transporter domain consists of a duplication of 2 structural repeats of five helices each plus one extra C-terminal helix. It has been described as a channel that spans the membrane 11 times [
].
All functionally characterised members of the ammonium transporter family are ammonia or ammonium uptake transporters. Some, but not others, also transport methylammonium. Uptake of ammonium/ammonia by AtmB protein from E. coli is electrogenic. Following sequestration of NH4+ at the periplasmic face, NH4+ is deprotonated and neutral NH3 is transported into the cytoplasm. Neutral NH3 and charged H+ are carried separately across the membrane on a unique two-lane pathway, before recombining to NH4+ inside the cell. It also acts as a sensor of the extracellular ammonium concentration [
,
].This entry represents ammonium transporters belonging to the Amt family, but it does not include the Rhesus (Rh) subgroup.
The plant augmin complex is involved in assembly of microtubules (MT) arrays during mitosis and contains eight subunits (AUG1 -AUG8). Among them, AUG1 to AUG6 share similarity with their animal counterparts, but AUG7 and AUG8 share homology only with proteins of plant origin [
]. AUG8 belongs to the plant QWRF motif-containing protein family, which also includes microtubule-associated protein ENDOSPERM DEFECTIVE 1 [,
] and SNOWY COTYLEDON 3 []. AUG8 binds the microtubule and participates in the reorientation of microtubules in hypocotyls (the stem of a germinating seedling) [].
The IQ motif is an extremely basic unit of about 23 amino acids, whose conserved core usually fits the consensus A-x(3)-I-Q-x(2)-F-R-x(4)-K-K. The IQ motif, which can be present in one or more copies, serves as a binding site for different EF-hand proteins including the essential and regulatory myosin light chains, calmodulin (CaM), and CaM-like proteins [
,
].Many IQ motifs are protein kinase C (PKC) phosphorylation sites [,
].Resolution of the 3D structure of scallop myosin has shown that the IQ motif forms a basic amphipathic helix [
].Some proteins known to contain an IQ motif are listed below:
A number of conventional and unconventional myosins.Neuromodulin (GAP-43). This protein is associated with nerve growth. It is a major component of the motile "growth cones"that form the tips of elongating axons.Neurogranin (NG/p17). Acts as a "third messenger"substrate of protein kinase C-mediated molecular cascades during synaptic development and remodeling.Sperm surface protein Sp17.Ras GTPase-activating-like protein IQGAP1. IQGAP1 contains 4 IQ motifs.This entry covers the entire IQ motif.
Conserved oligomeric Golgi complex subunit 8 acts as component of the peripheral membrane COG complex that is involved in intra-Golgi protein trafficking [
].
This entry represents the bacterial ornithine cyclodeaminase enzyme family, which catalyse the deamination of ornithine to proline [
]. The family also includes archaeal alanine dehydrogenase [] and mu-crystallin, a mammalian homologue of bacterial ornithine cyclodeaminase [], which is the major component of the eye lens in several Australian marsupials. mRNA for mu-crystallin has also been found in human retina [].This entry also includes protein SAR DEFICIENT 4 (SARD4) from Arabidopsis. SARD4 is involved in the biosynthesis of pipecolate (Pip), a metabolite that orchestrates defense amplification, positive regulation of salicylic acid (SA) biosynthesis, and priming to guarantee effective local resistance induction and the establishment of systemic acquired resistance (SAR) [
]. It does not possess ornithine cyclodeaminase activity in vitro [].
This entry represents the N-terminal domain of the ornithine cyclodeanimase family. This is an alpha/beta two layer sandwich domain. Members of this family includes ornithine cyclodeanimase [
], alanine dehydrogenase from Archaeoglobus [] and human cytosolic 3,5,39-triiodo-L-thyronine-binding protein, also called mu-crystallin or CRYM []. The function of this domain in ornithine cyclodeaminases, in combination with the C terminus, is responsible for substrate binding. This is a dimerisation domain of alanine dehydrogenase and CRYM.
Aspartate racemase (
) and glutamate racemase (
) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity [
]. Glutamate racemase catalyses the interconversion of d- and l-glutamic acid and is the source of d-glutamate in most bacterial strains. d-Glutamic acid is an important biosynthetic building block since it is required in the formation of peptidoglycan that protects bacteria from osmotic lysis. Two conserved cysteines are present in the sequence of these enzymes. They are expected to play a role in catalytic activity by acting as bases in proton abstraction from the substrate [,
].Glutamate racemase forms a dimer and each monomer consists of two α/β fold domains [
].
This entry represents a group of related proteins that includes aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase. Two conserved cysteines are present in the sequence of these enzymes. They play a role in catalytic activity by acting as bases in proton abstraction from the substrate [,
,
].Aspartate racemase (
) and glutamate racemase (
) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity [
]. Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan and some peptide-based antibiotics such as gramicidin S. The E.coli L-aspartate/glutamate specific racemase Ygea, which was previously an hypothetical protein, has been shown to have racemase activity for both L-glutamate and L-aspartate with higher preference for L-glutamate [].Hydantoin racemases catalyse the racemization of various 5-substituted hydantoins. The structure of the allantoin racemase from Klebsiella pneumoniae has been solved [
].
Flavoprotein pyridine nucleotide cytochrome reductases [
] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [
], plant and fungal NAD(P)H:nitrate reductases [,
], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.Despite functional similarities, FPNCRs show no sequence similarity to NADPH:adrenodoxin reductases [
], nor to bacterial ferredoxin:NAD
+reductases and their homologues [
]. To date, 3D-structures of 4 members of the family have been solved: Spinacia oleracea (Spinach) ferredoxin:NADP+reductase [
]; Burkholderia cepacia (Pseudomonas cepacia)phthalate dioxygenase reductase [
]; the flavoprotein domain of Zea mays (Maize) nitrate reductase []; and Sus scrofa (Pig) NADH:cytochrome b5 reductase []. In all of them, the FAD-binding domain (N-terminal) has the topology of an anti-parallel β-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel β-sheet with 2 helices on each side) []. In spite of such structural similarities, the level of amino acid identity between family members is at or below the limit of significance (e.g., nitrate reductase is only 15% identical to FNR) [].
Bacterial ferredoxin-NADP
+reductase may be bound to the thylakoid membrane or anchored to the thylakoid-bound phycobilisomes.
Chloroplast ferredoxin-NADP+reductase (
) may play a key role in regulating the relative amounts of cyclic and non-cyclic electron flow to meet the demands of the plant for ATP and reducing power. It is involved in the final step in the linear photosynthetic electron transport chain and has also been implicated in cyclic electron flow around photosystem I where its role would be to return electrons from ferredoxin to the cytochrome B-F complex.
This domain is present in a variety of proteins that include, bacterial flavohemoprotein, mammalian NADH-cytochrome b5 reductase, eukaryotic NADPH-cytochrome P450 reductase, nitrate reductase from plants, nitric-oxide synthase, bacterial vanillate demethylase, as well as others.
Flavoprotein pyridine nucleotide cytochrome reductases [
] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes includeferredoxin:NADP
+reductases (FNR) [
].plant and fungal NAD(P)H:nitrate reductases [
,
].NADH:cytochrome b5 reductases [
].NADPH:P450 reductases.NADPH:sulphite reductases.nitric oxide synthases.phthalate dioxygenase reductase.and various other flavoproteins.NADH:cytochrome b5 reductase (CBR) serves as electron donor for cytochrome b5, a ubiquitous electron carrier (see
), thus participating in a variety of metabolic pathways (including steroid biosynthesis, desaturation and elongation of fatty acids, P450-dependent reactions, methaemoglobin reduction, etc.). A membrane-bound form of CBR is located on the cytosolic side of the endoplasmic reticulum, while a soluble form is found in erythrocytes [
]. In the membrane-bound form, the N-terminal residue is myristoylated []. Deficiency of the erythrocyte form causes hereditary methaemoglobinemia [].In biological nitrate assimilation, reduction of nitrate to nitrite is catalysed by the multidomain redox enzyme NAD(P)H:nitrate reductase (NR). Three forms of NR are known: an NADH-specific enzyme found in higher plants and algae (
); an NAD(P)H-bispecific enzyme found in higher plants, algae and fungi (
); and an NADPH-specific enzyme found only in fungi (
) [
]. NR can be divided into 3 structure/function domains: the molybdopterin cofactor binds in the N-terminal domain; the central region is the cytochrome b domain, which is similar to animal cytochrome b5 (see ); and the C-terminal portion of the protein is occupied by the FAD/NAD(P)H binding domain, which is similar to CBR [
]. The catalytic reduction of nitrate to nitrite can be viewed as a single polypeptide electron transport chain with electron flow from NAD(P)H ->FAD ->cytochrome b5 ->molybdopterin ->NO(3). Thus, the flavin domain of NR is functionally identical to CBR.
To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [
] and of Sus scrofa (Pig) NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+reductase [
]: the FAD-binding domain (N-terminal) has the topology of an anti-parallel β-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel β-sheet flanked by 2 helices on each side).
These sequences represent the FAD-binding domain found in NADH:cytochrome b5 reductases and nitrate reductases. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [
] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+reductase [
]: the FAD-binding domain (N-terminal) has the topology of an anti-parallel β-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel β-sheet flanked by 2 helices on each side).
This superfamily represents a structural domain with a closed β-barrel fold with greek-key topology. Domains with this structure can be found in the following proteins:Riboflavin synthase, which contains two homologous domains of this structure [
].The FAD-binding (N-terminal) domain of ferredoxin reductase (flavodoxin reductase), where the FAD-binding domain is coupled with a NADP-binding domain of the alpha/beta class [
].The FAD-binding domain of NADPH-cytochrome p450 reductase; however, this domain has an additional α-helical domain inserted into it [
].Riboflavin synthase (
) catalyses the final step in the biosynthesis of vitamin B2, namely the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine to yield riboflavin and 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine (which is recycled) [
].Flavins can act as primary and secondary emitters in bacterial luminescence. Lumazine proteins are involved in the bioluminescence of certain marine bacteria. These proteins are catalytically inactive, but they resemble riboflavin synthase [
]. Lumazine is non-covalently bound to the fluorophore 6,7-dimethyl-8-ribityllumazine, which is the substrate of riboflavin synthase.Ferredoxin reductase is a FAD-containing oxidoreductase that transports electrons between flavodoxin or ferredoxin and NADPH. In Escherichia coli, ferredoxin reductase together with flavodoxin is involved in the reductive activation of three enzymes: cobalamin-dependent methionine synthase, pyruvate formate lyase and anaerobic ribonucleotide reductase [
]. An additional function for the oxidoreductase appears to be to protect the bacteria against oxygen radicals. The β-barrel domain found in ferredoxin reductase is similar to that found in: NAD(P)H:flavin oxidoreductase [], the core domain of nitrate reductase [], cytochrome b5 reductase [], phthalate dioxygenase reductase (which contains an additional 2Fe-2S ferredoxin domain) [], benzoate dioxygenase reductase [], the PyrK subunit of dihydroorotate dehydrogenase B [], the central domain of flavohaemoglobin (which contains an additional globin domain) [], and methane monooxygenase component C (MmoC) []. Microsomal NADPH-cytochrome P450 reductase (
) (CPR) (NADPH-haemoprotein reductase) is a membrane-bound protein that contains both FAD and FMN. CPR catalyses electron transfer from NADPH to all known microsomal cytochromes P450. The β-barrel domain found in NADPH-cytochrome p450 reductase is similar to that found in: sulphite reductase flavoprotein [], and the FAD/NADP+ domain of neuronal nitric-oxide synthase [].
Modular polyketide synthases are giant multifunctional enzymes that biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains [
]. This entry represents the enoylreductase domain from a number of polyketide synthases.
GroES (chaperonin 10) is an oligomeric molecular chaperone, which functions in protein folding and possibly in intercellular signalling, being found on the surface of various prokaryotic and eukaryotic cells, as well as being released from cells. Secreted chaperonins are thought to act as intercellular signals, interacting with a variety of cell types, including leukocytes, vascular endothelial cells and epithelial cells, as well as activating key cellular activities such as the synthesis of cytokines and adhesion proteins [
]. GroES works as a co-chaperone with GroEL (chaperonin 60) during protein folding. The polypeptide substrate is captured by GroEL, which bind the co-chaperone GroES and ATP, and discharges the substrate into a unique microenvironment inside of the chaperone, which promotes productive folding. After hydrolysis of ATP, the polypeptide is released into solution []. GP31 from Bacteriophage T4 is functionally equivalent to GroES. GroES folds as a partly opened β-barrel.
The N-terminal domain of alcohol dehydrogenase-like proteins have a GroES-like fold, the C-terminal domain having a classical Rossman-fold [
]. These proteins include, alcohol dehydrogenase, which contains a zinc-finger subdomain within the GroES-like domain, ketose reductase (sorbitol dehydrogenase), formaldehyde dehydrogenase, quinone oxidoreductase and 2,4-dienoyl-CoA reductase.
This is the catalytic domain of alcohol dehydrogenases (
). Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; a name derived from the superfamily of proteins with a GroES fold. Proteins with a GroES fold structure have a highly conserved hydrophobic core and a glycyl-aspartate dipeptide which is thought to maintain the fold [
,
].
