This entry represents the C-terminal domain found in Sco4008, which is suggested to be a transcriptional repressor of Sco4007 responsible for the multidrug resistance system in S. coelicolor A3 [
].TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [
]. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response []. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis []. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain [].
The histidine phosphatase superfamily is a large and functionally diverse group of proteins. They share a conserved catalytic core centred on a histidine which becomes phosphorylated during the course of the reaction. The superfamily is mainly composed of phosphatases, but the best-studied member is dPGM (cofactor-dependent phosphoglycerate mutase). The superfamily contains two branches sharing very limited sequence similarity: histidine phosphatase clade-1 and clade-2 [
].The larger clade-1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in clade-1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in clade-1 members.The smaller clade-2 is composed mainly of acid phosphatases and phytases. Acid phosphatases are a heterogeneous group of proteins that hydrolyse phosphate esters, optimally at low pH. The catalytic functions of these proteins include phytase, glucose-1-phosphatase and multiple inositol polyphosphate phosphatase. Fungal phytases are histidine acid phosphatases that catalyse the hydrolysis of phytate (myo-inositol hexakisphosphate) to myo-inositol and inorganic phosphate [
,
].
Map (MHC class II analogous protein), also known as eap (extracellular
adherence protein) and p70, is found in Staphylococcus aureus. It is a cell-wall associated protein, which is capable of binding to a number of different extracellular matrix glycoploteins and plasma proteins, and to the cell surface of S. aureus. Besides the broad binding specificity, map has been shown to be important in the adherence to and internalization of S. aureus by eukaryotic cells as well as being capable ofmodulating inflammatory response through its interactions with ICAM-1 (intercellular adhesion molecule-1), although its biological role in vivo remains to date unclear [
].The protein consists of a signal peptide followed by a unique sequence of about 20 amino acids and four to six repeated MAP domains of 110-amino acid residues. Within each repeat there is a subdomain consisting of 31 residues that was found to be highly homologous to the N-terminal beta-chain of many MHC class II molecules [
].This entry represents the MAP domain. The crystal structure of this domain has been solved and shows a core fold that is comprised of an α-helix lying diagonally across a five-stranded, mixed β-sheet. This structure is very similar to the C-terminal domain of bacterial superantigens [
].
Translational GTPases (trGTPases) are a family of proteins in which GTPase activity is stimulated by the large ribosomal subunit. This family includes translation initiation, elongation, and release factors and contains four subfamilies that are widespread, if not ubiquitous, in all three superkingdoms [
]. The trGTPase family members include bacteria elongation factors, EFTu, EFG, and the initiation factor, IF2, and their archaeal homologues, the EF1, EF2, aeIF5b and aeIF2. They all contain two homologous N-terminal domains: a GTPase or G-domain, followed by an OB-domain. These translational proteins' G-domains are both structurally and functionally related to a larger family of GTPase G proteins []. This entry represents the G-domain of the trGTPases.The basic topology of the tr-type G domain consists of a six-stranded central β-sheet surrounded by five α-helices. Helices alpha2, alpha3 and alpha4 are on one side of the sheet, whereas alpha1 and alpha5 are on the other [
]. GTP is bound by the CTF-type G domain in a way common for G domains involving five conserved sequence motifs termed G1-G5. The base is in contact with the NKxD (G4) and SAx (G5) motifs, and the phosphates of the nucleotide are stabilized by main- and side-chain interactions with the P loop GxxxxGKT (G1). The most severe conformational changes are observed for the two switch regions which contain the xT/Sx (G2) and DxxG (G3) motifs that function as sensors for the presence of the gamma-phosphate. A Mg(2+) ion is coordinated by six oxygen ligands with octahedral coordination geometry; two of the ligands are water molecules, two come from the beta- and gamma- phosphates, and two are provided by the side chains of G1 and G2 threonines []. In both prokaryotes and eukaryotes, there are three distinct types of elongation factors, EF-1alpha (EF-Tu), which binds GTP and an aminoacyl-tRNA and delivers the latter to the A site of ribosomes; EF-1beta (EF-Ts), which interacts with EF-1a/EF-Tu to displace GDP and thus allows the
regeneration of GTP-EF-1a; and EF-2 (EF-G), which binds GTP and peptidyl-tRNA and translocates the latter from the A site to the P site. In EF-1-alpha, a specific region has been shown [] to be involved in a conformational change mediated by the hydrolysis of GTP to GDP. This region is conserved in both EF-1alpha/EF-Tu as well as EF-2/EF-G and thus seems typical for GTP-dependent proteins which bind non-initiator tRNAs to the ribosome. The GTP-binding protein synthesis factor family also includes the eukaryotic peptide chain release factor GTP-binding subunits [] and prokaryotic peptide chain release factor 3 (RF-3) []; the prokaryotic GTP-binding protein lepA and its homologue in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1 []; rat statin S1 []; and the prokaryotic selenocysteine-specific elongation factor selB [].
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. This entry represents the zinc fingers identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [
,
]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production [
]. The DksA protein is structurally similar to the transcription factor GreA. Both are comprised of a coiled-coil region and a globular domain. The Dksa zinc finger (C4-type) starts in the coiled-coil and ends in the globular domain. The coiled-coil region binds the RNA polymerase near the ppGpp binding site and could contribute to the stability of the RNA polymerase-ppGpp complex. This entry represents the whole zinc finger.
This domain describes the C-terminal region of RTX toxins, which contains a secretion signal [
]. RTX toxins may interact with lipopolysaccharide (LPS) to functionally impair and eventually kill leukocytes []. This region is found in association with the RTX N-terminal domain () and multiple hemolysin-type calcium-binding repeats (
).
Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior [
,
]. Four principal exotoxin secretion systems have been described. In the type II and IV secretion systems, toxins are first exported to the periplasm by way of a cleaved N-terminal signal sequence; a second set of proteins is used for extracellular transport (type II), or the C terminus of the exotoxin itself is used (type IV). Type III secretion involves at least 20 molecules that assemble into a needle; effector proteins are then translocated through this without need of a signal sequence. In the Type I system, a complete channel is formed through both membranes, and the secretion signal is carried on the C terminus of the exotoxin. The RTX (repeats in toxin) family of cytolytic toxins belong to the Type I secretion system, and are important virulence factors in Gram-negative bacteria, such as Escherichia coli (
), Actinobacillus pleuropneumoniae (
) and Kingella kingae (
). They consist of a hydrophobic pore-forming domain at the N-terminal that harbors four putative transmembrane α-helices, a typical glycine-rich repeats segment and a C-terminal signal sequence [
]. The glycine-rich repeats are essential for binding calcium, and are critical for the biological activity of the secreted toxins []. They can be divided into two different groups, (i) hemolysins, which cause cause the lysis of erythrocytes and exhibit toxicity towards a wide range of cell types from various species; and (ii) leukotoxins, that exhibit narrow cell type and species specificity due to cell-specific binding through the beta2-integrins expressed on the cell surface of leukocytes []. All RTX toxin operons exist in the order rtxCABD, RtxA protein being the structural component of the exotoxin, both RtxB and D being required for its export from the bacterial cell; RtxC is an acyl-carrier-protein-dependent acyl-modification enzyme, required to convert RtxA to its active form [].Escherichia coli haemolysin (HlyA) is often quoted as the model for RTX toxins. Recent work on its relative rtxC gene product HlyC [
] has revealed that it provides the acylation aspect for post-translational modification of two internal lysine residues in the HlyA protein. To cause pathogenicity, the HlyA toxin must first bind Ca2+ ions to the set of glycine-rich repeats and then be activated by HlyC []. This has been demonstrated both in vitroand
in vivo.
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants, and also to animals. Their functions in higher animals likely include the regulation of cell volume, control of electrical excitability and trans-epithelial transport [
].The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata [
], and subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits, and they have varying tissue distributions and functional properties. To date, CLC-0, CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments, rather than of the plasma membrane. However, they are all thought to have a similar transmembrane (TM) topology, initial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains []. Recently, the postulated TM topology has been revised, and it now seems likely that the CLCs have 10 (or possibly 12) TM domains, with both N- and C-termini residing in the cytoplasm [].A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major skeletal muscle Cl- channel, lead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia [
]. Similarly, mutations in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms of inherited kidney stone disease []. These mutations have been demonstrated to reduce or abolish CLC function.In plants, chloride channels contribute to a number of plant-specific
functions, such as regulation of turgor, stomatal movement, nutrienttransport and metal tolerance. By contrast with Cl
-channels in animal cells, they are also responsible for the generation of action potentials.The best documented examples are the chloride channels of guard cells,
which control opening and closing of stomata. Recently, four homologousproteins that belong to the CLC family have been cloned from Arabidopsis thaliana (Mouse-ear cress) [
]. Hydropathy analysis suggests that they havea similar membrane topology to other CLC proteins, with up to 12 TM domains.
Expression in Xenopus oocytes failed to generate measurable Cl-currents,
although protein analysis suggested they had been synthesised and insertedinto cell membranes. However, similar CLC proteins have since been cloned
from other plants, and one, CIC-Nt1 (from tobacco), has been demonstrated toform funtional Cl
-channels, suggesting that at least some of these proteins
do function as Cl-channels in plants [
].
Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [
,
,
]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [,
]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide [].There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The following cytokines can be grouped into a family on the basis of sequence, functional, and structural similarities [
,
,
]: Tumor Necrosis Factor (TNF) (also known as cachectin or TNF-alpha) [
,
] is a cytokine which has a wide variety of functions. It can cause cytolysis of certain tumor cell lines; it is involved in the induction of cachexia; it is a potent pyrogen, causing fever by direct action or by stimulation of interleukin-1 secretion; finally, it can stimulate cell proliferation and induce cell differentiation under certain conditions.Lymphotoxin-alpha (LT-alpha) and lymphotoxin-beta (LT-beta), two related cytokines produced by lymphocytes and which are cytotoxic for a wide range of tumor cells in vitro and in vivo [
]. T cell antigen gp39 (CD40L), a cytokine which seems to be important in B-cell development and activation.CD27L, a cytokine which plays a role in T-cell activation. It induces the proliferation of costimulated T cells and enhances the generation of cytolytic T cells. CD30L, a cytokine which induces proliferation of T cells.FASL, a cytokine involved in cell death [
].4-1BBL, a inducible T cell surface molecule that contributes to T-cell stimulation.OX40L, a cytokine that co-stimulates T cell proliferation and cytokine production [
].TNF-related apoptosis inducing ligand (TRAIL), a cytokine that induces apoptosis [
].TNF-alpha is synthesised as a type II membrane protein which then undergoes post-translational cleavage liberating the extracellular domain. CD27L, CD30L, CD40L, FASL, LT-beta, 4-1BBL and TRAIL also appear to be type II membrane proteins. LT-alpha is a secreted protein. All these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The PROSITE pattern for this family is located in a β-strand in the central section of the protein which is conserved across all members.This entry represents Tumor Necrosis Factor, conserved site.
The bacterial CyaB like adenylyl cyclase and the mammalian thiamine triphosphatases (ThTPases) define a superfamily of catalytic domains called the CYTH (CyaB, thiamine triphosphatase) domain that is present in all three superkingdoms of life [
]. Proteins containing this domain act on triphosphorylated substrates and require at least one divalent metal cation for catalysis []. The catalytic core of the CYTH domain is predicted to contain an alpha beta scaffold with 6 conserved β-strands and 6 conserved α-helices. The CYTH domains contains several nearly universally conserved charged residues that are likely to form the active site. The most prominent of these are an EXEXK motif associated with strand-1 of the domain, two basic residues in helix-2, a K at the end of strand 3, an E in strand 4, a basic residue in helix-4, a D at the end of strand 5 and two acidic residues (typically glutamates) in strand 6. The presence of around 6 conserved acidic positions in the majority of the CYTH domains suggests that it coordinates two divalent metal ions. Both CyaB and ThTPase have been shown to require Mg(2) ions for their nucleotide cyclase and phosphatase activities. The four conserved basic residues in the CYTH domain are most probably involved in the binding of acidic phosphate moieties of their substrates. The conservation of these two sets of residues in the majority of CYTH domains suggests that most members of this group are likely to possess an activity dependent on two metal ions, with a preference
for nucleotides or related phosphate-moiety -bearing substrates. The proposed biochemical activity, and the arrangement of predicted strands in the primary structure of the CYTH domain imply that they may adopt a barrel or sandwich-like configuration, with metal ions and the substrates bound in the central cavity [].Protein containing a CYTH-like domain include the yeast RNA triphosphatase Cet1, whose active site is located within a topologically closed hydrophilic β-barrel (composed of 8 antiparallel beta strands) known as the "triphosphate tunnel"[
]. The superfamily including Cet-1-like RNA triphosphatases and all other CYTH proteins has been named Triphosphate Tunnel Metalloenzyme (TTM) []. Interestingly, bacterial CYTH-domain containing proteins, such as NeuTTM (
) from Nitrosomonas europaea [
] and CthTTM () from Clostridium thermocellum [
], both have a high PPPase activity (though CthTM was less specific) but neither had any significant adenylyl cyclase activity. However, other bacterial CYTH-domain containing proteins, such as CyaB from A. hydrophyla and ygiF from E. coli, have been shown to have PPPase activity, but this activity is lower than their adenylate cyclase activity []. It has also been suggested that adenylyl cyclase and thiamine triphosphatase are secondary derivatives of proteins that performed an ancient role in polyphosphate and nucleotide metabolism [].
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. This entry represents the zinc fingers identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [
,
]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production [
]. The DksA protein is structurally similar to the transcription factor GreA. Both are comprised of a coiled-coil region and a globular domain. The Dksa zinc finger (C4-type) starts in the coiled-coil and ends in the globular domain. The coiled-coil region binds the RNA polymerase near the ppGpp binding site and could contribute to the stability of the RNA polymerase-ppGpp complex. This entry represents the whole zinc finger.
This entry includes cleft lip and palate transmembrane protein 1 (CLPTM1) and cleft lip and palate transmembrane protein 1-like protein (CLPTM1L, also known as CRR9). This entry also includes uncharacterised proteins from fungi and plants. Clefts of the lip and/or palate (CL/P) are some of the most common birth defects. They may be categorised into syndromic or non-syndromic types, with syndromic defects having an underlying chromosomal or teratogenic cause. Around 70% of clefts are non-syndromic and individuals have no typical physical or developmental abnormalities; these clefts generally show polygenetic behaviour and complex inheritance [
]. Studies have identified regions on chromosomes 19 and 11 which may be involved in non-syndromic cleft lip and palates; this included a novel gene on chromosome 19, cleft lip and palate-associated transmembrane protein 1 (CLPTM1) []. The Poliovirus receptor-related 1 gene (PVRL1), which is located on chromosome 11, has also been shown to associate with non-syndromic cleft lip and palates [,
].Human CLPTM1L is a scramblase that mediates the translocation glucosaminylphosphatidylinositol (alpha-D-GlcN-1-6-(1,2-diacyl-sn-glycero-3-phospho)-1D-myo-inositol, GlcN-PI) across the endoplasmic reticulum (ER) membrane, from the cytosolic leaflet to the luminal leaflet of the ER membrane, where it participates in the biosynthesis of glycosylphosphatidylinositol (GPI) [
]. It protects non-small cell lung cancer tumour cells from genotoxic apoptosis and may contribute to lung cancer risk [,
].
Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified [
]. This sequence motif represents one β-sheet blade, and several of these repeats can associate to form a β-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein (also known as ring canal kelch protein), creating a 6-bladed β-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [,
], and in galactose oxidase from the fungus Dactylium dendroides [,
]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded antiparallel β-sheet motif that forms the repeat unit in a super-barrel structural fold [].The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila [
]. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase [].This entry represents the 6-bladed Kelch β-propeller, which consists of six 4-stranded β-sheet motifs (or six Kelch repeats).
PDZ domains (also known as Discs-large homologous regions (DHR) or GLGF)) are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [
,
]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six β-strands (beta-A to beta-F) and two α-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel β-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands [
].
Cytochrome b5 is a membrane-bound hemoprotein which acts as an electron carrier for several membrane-bound oxygenases [
]. There are two homologous forms of b5, one found in microsomes and one found in the outer membrane of mitochondria. Two conserved histidine residues serve as axial ligands for the heme group. The structure of a number of oxidoreductases consists of the juxtaposition of a heme-binding domain homologous to that of b5 and either a flavodehydrogenase or a molybdopterin domain. These enzymes are:Lactate dehydrogenase (EC 1.1.2.3) [
], an enzyme that consists of a flavodehydrogenase domain and a heme-binding domain called cytochrome b2.Nitrate reductase (EC 1.7.1.-), a key enzyme involved in the first step of nitrate assimilation in plants, fungi and bacteria [
]. Consists of a molybdopterin domain, a heme-binding domain called cytochrome b557, as well as a cytochrome reductase domain.Sulfite oxidase (EC 1.8.3.1) [
], which catalyzes the terminal reaction in the oxidative degradation of sulfur-containing amino acids. Also consists of a molybdopterin domain and a heme-binding domain.Yeast acyl-CoA desaturase 1 (EC 1.14.19.1; gene OLE1). This enzyme contains a C-terminal heme-binding domain.Yeast Scs7 (YMR272c), a sphingolipid alpha-hydroxylase.Proteins containing a cytochrome b5-like domain also include:TU-36B, a Drosophila muscle protein of unknown function [
].Fission yeast hypothetical protein SpAC1F12.10c (C1F12.10c).Yeast Irc21 (YMR073c), a putative protein with unknown function.
The ~75-residue DWNN (Domain With No Name) domain is highly conserved through eukaryotic species but is absent in prokaryotes. The DWNN domain is found only at the N terminus of the RBBP6 family of proteins which includes:Mammalian RBBP6, a splicing-associated protein that plays a role in the induction of apoptosis and regulation of the cell cycle.Drosophila melanogaster (Fruit fly) SNAMA (something that sticks like glue), a protein that appears to play a role in apoptosis.All of the identified RBBP6 homologues include the DWNN domain, a CCHC-type zinc finger (see
) and a RING-type zinc finger (see
). The three domain form is found in plants, protozoa, fungi and microsporidia. The RBBP6 homologues in vertebrates, insects and worms are longer and include additional domains. In addition to forming part of the full-length RBBP6 protein, the DWNN domain is also expressed in vertebrates as a small protein containing a DWNN domain and a short C-terminal tail (RBBP6 variant 3). The DWNN domain adopts a fold similar to the ubiquitin one, characterised by two α-helices and four β-sheets ordered as β-β-α-β-α-β along the sequence. The similarity of DWNN domain to ubiquitin and the presence of the RING finger suggest that the DWNN domain may act as an ubiquitin-like modifier, possibly playing a role in the regulation of the splicing machinery [
,
].
Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase;
) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [
,
]. The PTP superfamily can be divided into four subfamilies []:(1) pTyr-specific phosphatases(2) dual specificity phosphatases (dTyr and dSer/dThr)(3) Cdc25 phosphatases (dTyr and/or dThr)(4) LMW (low molecular weight) phosphatasesBased on their cellular localisation, PTPases are also classified as:Receptor-like, which are transmembrane receptors that contain PTPase domains [
]
Non-receptor (intracellular) PTPases [
]
All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel β-sheet with flanking α-helices containing a β-loop-α-loop that encompasses the PTP signature motif [
]. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents the PTP-signature motif that characterises the catalytic site, and which encompasses only part of the PTPase domain structure.
Papillomaviruses (PPV) are a large family of DNA tumour viruses which give rise to warts in their host species. The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication [
,
]. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins [].The E1 protein is a 70kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase [
]. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity [
].The entry represents the ATPase domain found at the C-terminal of E1.
Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified [
]. This sequence motif represents one β-sheet blade, and several of these repeats can associate to form a β-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein (also known as ring canal kelch protein), creating a 6-bladed β-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [,
], and in galactose oxidase from the fungus Dactylium dendroides [,
]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded antiparallel β-sheet motif that forms the repeat unit in a super-barrel structural fold [].The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila [
]. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase [].This entry represents a type of kelch sequence motif that comprises one β-sheet blade.
This superfamily represents a multi-helical structural domain consisting of two structural repeats (duplication) of a 3-helical motif. This domain can be found in both eukaryotic and prokaryotic haem oxygenases [
,
], in TENA/THI-4 proteins that lack the haem-binding site [], and in coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein C (PqqC) [].Haem oxygenase (
) (HO) is the microsomal enzyme that, in animals, carries out the oxidation of haem, cleaving the haem ring at the alpha-methene bridge to form biliverdin and carbon monoxide. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. In mammals there are three isozymes of haem oxygenase: HO-1 to HO-3. The first two isozymes differ in their tissue expression and their inducibility: HO-1 is highly inducible by its substrate haem and by various non-haem substances, while HO-2 is non-inducible. Haem oxygenase is also present in certain bacteria, where it is involved in the acquisition of iron from the host haem.
The THI-4 protein is involved in thiamine biosynthesis, while TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase.Coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein C (PqqC;
) is required for the synthesis of PQQ, where PQQ is a prosthetic group found in several bacterial enzymes, including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria.
A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [
,
]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar.They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis.There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble [
]. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [
].
The ~250-residue pterin-binding domain has been shown to adopt a (beta/alpha)8 barrel fold, which has the overall shape of a distorted cylinder. It has eight α-helices stacked around the outside of an inner cylinder of parallel β-strands. The pterin ring binds at the bottom of the (beta/alpha;)8 barrel in a polar cup-like region that is relatively solvent exposed and fairly negatively charged. The pterin ring is partially buried within the (beta/alpha)8 barrel. The pterin binding residues are highly conserved and include aspartate and asparagine residues located at the C terminus of the β-strands of the barrel, which are predicted to form hydrogen bonds with the nitrogen and oxygen atoms of the pterin ring [
,
,
].Some proteins known to contain a pterin-binding domain are listed below:
Prokaryotic and eukaryotic B12-dependent methionine synthase (MetH) (
), a large, modular protein that catalyzes the transfer of a methyl group from methyltetrahydrofolate (CH3-H4folate) to Hcy to form methionine, using cobalamin as an intermediate methyl carrier.
Prokaryotic and eukaryotic dihydropteroate synthase (DHPS) (
). It catalyzes the condensation of para-aminobenzoic acid (pABA) with 7,8- dihydropterin-pyrophosphate (DHPPP), eliminating pyrophosphate to form 7,8- dihydropteroate which is subsequently converted to tetrahydrofolate.
Moorella thermoacetica 5-methyltetrahydrofolate corrinoid/iron sulphur protein methyltransferase (MeTr). It transfers the N5-methyl group from CH3-H4folate to a cob(I)amide centre in another protein, the corrinoid iron sulphur protein.
The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many
transcription factors. HD-containing proteins are found indiverse organisms such as humans, Drosophila, nematode worms, and plants,
where they play important roles in development. Zinc-finger-homeodomain (ZF-HD) subfamily proteins have only been identified in plants, and likely play
plant specific roles. ZF-HD proteins are expressed predominantly orexclusively in floral tissue, indicating a likely regulatory role during
floral development []. The ZF-HD class of homeodomain proteins may also beinvolved in the photosynthesis-related mesophyll-specific gene expression of
phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signalingand plant defense mechanisms [
]. These proteins share three domains of high sequence similarity: the
homeodomain (II) located at the carboxy-terminus, and two other segments (Iaand Ib) located in the amino-terminal part. These N-terminal domains contain
five conserved cysteine residues and at least three conserved histidineresidues whose spacing ressembles zinc-binding domains involved in
dimerization of transcription factors. Although the two domains contain atleast eight potential zinc-binding amino-acids, the unique spacing of the
conserved cysteine and histidine residues within domain Ib suggests that bothdomains form one rather than two zinc finger structures. The two conserved
motifs Ia and Ib constitute a dimerization domain which is sufficient for theformation of homo- and heterodimers [
]. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in
.
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].There are two conserved cysteine residues important for thiolase activity. The signature pattern for this entry contains the first conserved cysteine located in the N-terminal section of the enzymes, which is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction [
].
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction.Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction.Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second, which is found in the signature pattern in this entry, is located at the C-terminal extremity and is the active site base involved in deprotonation in the condensation reaction [].
Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified [
]. This sequence motif represents one β-sheet blade, and several of these repeats can associate to form a β-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein (also known as ring canal kelch protein), creating a 6-bladed β-propeller. The motif is also found in mouse protein MIPP [] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [,
], and in galactose oxidase from the fungus Dactylium dendroides [,
]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded antiparallel β-sheet motif that forms the repeat unit in a super-barrel structural fold [].The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila [
]. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase [].This entry represents a type of kelch sequence motif that comprises one β-sheet blade.
The C-CAP/cofactor C-like domain is present in several cytoskeleton-related proteins, which also contain a number of additional domains [
,
,
,
]:Eukaryotic cyclase-associated protein (CAP or SRV2), a modular actin monomer binding that directly regulates filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity.Vertebrate retinitis pigmentosa 2 (XRP2). In Homo sapiens (Human), it is the protein responsible for X-linked forms of retinitis pigmentosa, a disease characterised by severe retinal degeneration.Eukaryotic tubulin-specific chaperone cofactor C (TBCC), a GTPase- activating component of the tubulin-folding supercomplex, which directs the assembly of the alpha- and beta-tubulin heterodimer.The cyclase-associated protein C-CAP/cofactor C-like domain binds G-actin and is responsible for oligomerisation of the entire CAP molecule [
], whereas the XRP2 C-CAP/cofactor C-like domain is required for binding of ADP ribosylation factor-like protein 3 (Arl3) [].The central core of the C-CAP/cofactor C-like domain is composed of six coils of right-handed parallel β-helices, termed coils 1-6, which form an elliptical barrel with a tightly packed interior. Each β-helical coil is composed of three relatively short β-strands, designated a-c, separated by sharp turns. Flanking the central β-helical core is an N-terminal β-strand, β0, that packs antiparallel to the core, and strand β7 packs antiparallel to the core near the C-terminal end of the parallel β-helix [,
].
Dynamin superfamily members are large GTPases, conserved through evolution, mainly described as mechanochemical enzymes involved in membrane scission events. The dynamin superfamily has been subdivided into several subgroups based on domain organisation: classical dynamin, dynamin-like proteins (Dlps), Mc proteins, optic atrophy 1 protein (OPA1), Mitofusins, guanylate-binding proteins (GBP) and alastatins. All members display a common architecture: a large GTPase (see
) domain followed by a 'middle domain' of ill-defined function and a downstream coiled-coil GTPase effector domain (GED) that functions in higher order assembly and as a GTPase activating protein (GAP) for dynamin's GTPase activity. Most members contain additional domains that characterise the different subgroups. For example, classical dynamins contain a lipid binding Pleckstrin-homology (PH) (see
) domain between the middle domain and the GED domain as well as a C-terminal proline-arginine rich domain (PRD) that interacts with numerous SH3 domain-containing binding partners while Dlps lack the PRD but have a PH domain, which may, however, be highly divergent. These various domains confer a variety of biochemical properties and cellular localisations to dynamin, that may explain the diversity of their biological implications in endocytosis, intracellular traffic, organelle fission and fusion, cytokinesis and pathogen resistance [
,
,
,
].The GED is seen to be largely helical in nature, and its oligomerisation occurs via intermolecular packing of the helices [
].
The PFU (for PLAA family ubiquitin binding domain) is an ubiquitin binding domain with no homology to several known ubiquitin binding domains (e.g., UIM, NZF, UBA, UEV, UBP, or CUE domains). The PFU domain appears to be unique to the PLAA family of proteins. A single member of this family of proteins exists in every eukaryotic species examined. Each of these homologues possesses identical domain structure: an N-terminal domain containing seven WD40 repeats, a central PFU domain, and a C-terminal PUL domain, which directly binds to Cdc48, a member of the AAA-ATPase family of molecular chaperone [
]. In addition to ubiquitin, the PFU domain of DOA1 has been shown to bind to the SH3 domain [].Secondary structure predictions of the PFU domain suggest the presence of an extensive length of β-sheet, N-terminal to an α-helical region [
].Some proteins known to contain a PFU domain include:
Saccharomyces cerevisiae DOA1 (UFD3, ZZZ4), involved in the ubiquitin conjugation pathway. DOA1 participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone.Schizosaccharomyces pombe ubiquitin homeostasis protein Lub1, acts as a negative regulator of vacuole-dependent ubiquitin degradation.Mammalian phospholipase A-2-activating protein (PLA2P, PLAA), the homologue of DOA1. PLA2P plays an important role in the regulation of specific inflammatory disease processes.This superfamily represents the central PFU domain.
This entry represents the C-terminal domain present the transcriptional regulator KstR that regulates a large set of genes responsible for cholesterol catabolism. This is important for Mycobacterium tuberculosis during infection, both at an early stage in the macrophage phagosome and later within the necrotic granuloma [
].TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [
]. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response []. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis []. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain [].
PDZ domains (also known as Discs-large homologous regions (DHR) or GLGF)) are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [
,
]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six β-strands (beta-A to beta-F) and two α-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel β-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands [
].
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions (including various autocrine, para-crine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices [,
,
]. A cluster of four intronless GPCR genes, sharing significant sequence similarity with one another, have been identified on human chromosome 19q13.1, downstream from the CD22 gene []. The receptors have been named GPR40, GPR41, GPR42 and GPR43. The GPR42 protein sequence shares more than 98% amino acid identity with GPR41 and is located on a possible polymorphic insert [].
This entry represents the RNA recognition motif 1 (RRM1) of p54nrb. p54nrb (also known as NONO) belongs to the DBHS (Drosophila behavior human splicing) family. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcription, splicing, and RNA export [
]. p54nrb binds both, single- and double-stranded RNA and DNA []. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner as well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF) []. p54nrb contains two conserved RNA recognition motifs (RRMs) at the N terminus [,
].DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain, and a ~100 amino acid coiled-coil domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein [
,
].
This entry represents the RNA recognition motif 2 (RRM2) of p54nrb.p54nrb (also known as NONO) belongs to the DBHS (Drosophila behavior human splicing) family. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcription, splicing, and RNA export [
]. p54nrb binds both, single- and double-stranded RNA and DNA []. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner as well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF) []. p54nrb contains two conserved RNA recognition motifs (RRMs) at the N terminus [,
].DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain, and a ~100 amino acid coiled-coil domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein [
,
].
Telomeres function to shield chromosome ends from degradation and end-to-end fusions, as well as preventing the activation of DNA damage checkpoints. Telomeric repeat binding factor (TRF) proteins TRF1 and TRF2 are major components of vertebrate telomeres required for regulation of telomere stability. TRF1 and TRF2 bind to telomeric DNA as homodimers. Dimerisation involves the TRF homology (TRFH) subdomain contained within the dimerisation domain. The TRFH subdomain is important not only for dimerisation, but for DNA binding, telomere localisation, and interactions with other telomeric proteins. The dimerisation domains of TRF1 and TRF2 show the same multi-helical structure, arranged in a solenoid conformation similar to TPR repeats, which can be divided into an α-α superhelix and a long alpha hairpin [
].The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain
at the carboxy terminus [
]. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection []. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe (Fission yeast) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres []. This entry represents the dimerisation domain.
The Groucho (Gro)/transducin-like enhancers (TLE) are a family of
evolutionarily conserved corepressor proteins that play a critical role indiverse developmental and cellular pathways, including lateral inhibition,
segmentation, sex determination, dorsal/ventral pattern formation, terminalpattern formation, and eye development [
]. The Gro/TLE family contain two highly conserved domains, a C-terminal
WD-repeat domain and an N-terminal glutamine rich (Q) domain, in additionto a variable central region. The highly conserved Q domains are unique to
the Gro/TLE family and are not found in other WD-repeat proteins. Thevariable region contains a loosely conserved CcN motif, consisting of
putative cdc2 kinase (cdc2) and casein kinase II (CKII) phosphorylation sites, as well as a nuclear localisation signal [
]. The CcN motif is flanked by two poorly conserved regions, which are characteristically rich
in either glycine and proline or serine and proline residues, GP and SP domains respectively.
Gro/TLE family proteins do not bind to DNA directly as they lack any
DNA-binding domain. However, they are recruited to the template by DNA-boundrepressor proteins. Gro/TLE Co-repressors assemble into high order oligomeric
structures [] through their conserved Q domain - the Q domains are able tomediate both homo- and hetero-oligomerisation. The GP domain is able to
recruit histone deacetylase to the template; this, together with otherfindings, shows that Gro/TLE proteins specifically associate with histones,
and suggests that Gro/TLE Co-repressors negatively regulate transcription byinducing a silenced chromatin structure.
This superfamily represents the interlocking domain of various eukaryotic nuclear receptor coactivators, including CREBP, P300, Ncoa1, Ncoa2 and Ncoa3. The interlocking domain forms a 3-helical non-globular array that forms interlocked heterodimers with its target.Nuclear receptors are ligand-activated transcription factors involved in the regulation of many processes, including development, reproduction and homeostasis. Nuclear receptor coactivators act to modulate the function of nuclear receptors. Coactivators associate with promoters and enhancers primarily through protein-protein contacts to facilitate the interaction between DNA-bound transcription factors and the transcription machinery. Many of these coactivators are structurally related, including CBP (CREB-binding protein), P300 and ACTR (activator for thyroid and retinoid receptors) [
]. CBP and P300 both have histone acetyltransferase activity (). CBP/P300 proteins function synergistically to activate transcription, acting to remodel chromatin and to recruit RNA polymerase II and the basal transcription machinery. CBP is required for proper cell cycle control, differentiation and apoptosis. The interaction of CBP/P300 with transcription factors involves several small domains. The IBiD domain in the C-terminal of CBP is responsible for CBP interaction with IRF-3, as well as with the adenoviral oncoprotein E1A, TIF-2 coactivator, and the IRF homologue KSHV IRF-1 [
].Ncoa1, Ncoa2 and Ncoa3 are all coactivators of various nuclear receptors. In addition, Ncoa1 and Ncoa3 both have histone acetyltransferase activity, but Ncoa2 does not [
,
].
Bestrophin is a 68kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterised by a depressed light peak in the electrooculogram [
]. VMD2 encodes a 585-amino acid protein with an approximate mass of 68kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif. Bestrophin is a plasma membrane protein, localised to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of calcium-activated chloride channels (CaCC) [], indicating a direct role for bestrophin in generating the light peak [,
,
]. Bestrophins are also permeable to other monovalent anions including bicarbonate, bromine, iodine, thiocyanate an nitrate [,
]. Structural analysis revealed that N-terminal region of the proteins is highly conserved and sufficient for its CaCC activity. The C-terminal region has low sequence identity. The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal domain altering the electrophysiological properties of the channel [,
].
This entry represents the SH2 domain of STAT5b.STAT5 is a member of the STAT family of transcription factors. Two highly related proteins, STAT5a and STAT5b are encoded by separate genes, but are 90% identical at the amino acid level. Both STAT5a and STAT5b are ubiquitously expressed and functionally interchangeable. They regulate B and T cell development [
,
]. These proteins are central signalling molecules in leukaemias driven by Abelson fusion tyrosine kinases, having a key role in resistance of leukaemic cells against treatment with tyrosine kinase inhibitors (TKI) []. They differentially regulate cellular behaviour in human mammary carcinoma []. STAT proteins have a dual function: signal transduction and activation of transcription. When cytokines are bound to cell surface receptors, the associated Janus kinases (JAKs) are activated, leading to tyrosine phosphorylation of the given STAT proteins [
]. Phosphorylated STATs form dimers, translocate to the nucleus, and bind specific response elements to activate transcription of target genes []. STAT proteins contain an N-terminal domain (NTD), a coiled-coil domain (CCD), a DNA-binding domain (DBD), an α-helical linker domain (LD), an SH2 domain, and a transactivation domain (TAD). The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6 [].
The archease superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing and therefore have been predicted to be modulators or chaperones involved in DNA or RNA metabolism. Many of the roles of archeases remain to be established experimentally. The function of one of the archeases from the hyperthermophile Pyrococcus abyssi has been determined. The gene encoding the archease (PAB1946) is located in a bicistronic operon immediately upstream from a second open reading frame (PAB1947), which encodes a tRNA m5C methyltransferase. The methyl transferase catalyses m5C formation at several cytosine's within tRNAs with preference for C49; the specificity of the methyltransferase reaction being increased by the archease. The archease protects the tRNA (cytosine-5-)-methyltransferase PAB1947 against aggregation and increases its specificity. The archease exists in monomeric and oligomeric states, with only the oligomeric forms able to bind the methyltransferase [
].The function of this family of archeases as chaperones is supported by structural analysis of
from Methanobacterium thermoautotrophicum, which shows homology to heat shock protein 33, which is a chaperone protein that inhibits the aggregation of partially denatured proteins [
].Structurally, the archeases are composed of a single three layer beta-α-β sandwich domain similar to those found in other chaperones.
Nucleoside diphosphate kinases (
) (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerisation.
NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP.NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown [
] that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23. The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism [].The enzyme is a hexamer composed by identical subunits with a novel mononucleotide binding fold. Each subunit contains an alpha/beta domain with a four stranded, anti-parallel β-sheet [
].This alpha/beta domain is also found at the C terminus of retinitis pigmentosa 2 protein (XRP2/RP2) [
]. XRP2, a GTPase-activating protein, is required for maintenance of rod and cone photoreceptor cells in the retina [].
Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin [
] (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) []; retinoic acid-induced heparin-binding protein (RIHB) []; and pleiotrophic factors alpha-1 and -2 and beta-1 and -2 from Xenopus laevis, the homologues of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.
Pleiotrophin is structurally divided into two domains, both domains consisting of three antiparallel β-strands, but the C-terminal domain has a long flexible hairpin loop where a heparin-binding consensus sequence is located [
]. This superfamily represents the all-beta 3 antiparallel strands disulfide-rich fold found both in the N-terminal and C-terminal domains of pleiotrophin and midkine.
STAT proteins have a dual function: signal transduction and activation of transcription. When cytokines are bound to cell surface receptors, the associated Janus kinases (JAKs) are activated, leading to tyrosine phosphorylation of the given STAT proteins [
]. Phosphorylated STATs form dimers, translocate to the nucleus, and bind specific response elements to activate transcription of target genes []. STAT proteins contain an N-terminal domain (NTD), a coiled-coil domain (CCD), a DNA-binding domain (DBD), an α-helical linker domain (LD), an SH2 domain, and a transactivation domain (TAD). The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6 []. STAT5 is a member of the STAT family of transcription factors. Two highly related proteins, STAT5a and STAT5b are encoded by separate genes, but are 90% identical at the amino acid level. Both STAT5a and STAT5b are ubiquitously expressed and functionally interchangeable. They regulate B and T cell development [
,
]. These proteins are central signalling molecules in leukaemias driven by Abelson fusion tyrosine kinases, having a key role in resistance of leukaemic cells against treatment with tyrosine kinase inhibitors (TKI) []. They differentially regulate cellular behaviour in human mammary carcinoma []. This entry represents the coiled--coil domain (CCD) of STAT5.
Nucleoside diphosphate kinases (
) (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerisation.
NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP.NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown [
] that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23. The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism [].The enzyme is a hexamer composed by identical subunits with a novel mononucleotide binding fold. Each subunit contains an alpha/beta domain with a four stranded, anti-parallel β-sheet [
].This alpha/beta domain is also found at the C terminus of retinitis pigmentosa 2 protein (XRP2/RP2) [
]. XRP2, a GTPase-activating protein, is required for maintenance of rod and cone photoreceptor cells in the retina [].
Glycosyl transferase, family 2, hopene-associated, HpnB
Type:
Family
Description:
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'.Proteins in this entry contain glycosyl transferase family 2 domains which are responsible, generally, for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. These proteins are often encoded in the same genetic locus as squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. Indeed, proteins in this entry appear to never be encoded in a genome lacking squalene-hopene cyclase (SHC), although not all genomes encoding SHC have this glycosyl transferase. In the organism Zymomonas mobilis the linkage of this protein to hopanoid biosynthesis has been noted and it was named HpnB [
]. Hopanoids are known to feature polar glycosyl head groups in many organisms.
Eosinophil major basic protein, C-type lectin-like domain
Type:
Domain
Description:
This is a C-type lectin-like domain (CTLD) of the type found in the human proteins eosinophil major basic protein (EMBP) and prepro major basic protein homologue (MBPH) [
]. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins []. Eosinophils and basophils carry out various functions in allergic, parasitic, and inflammatory diseases. EMBP is stored in eosinophil crystalloid granules and is released upon degranulation. EMBP is also expressed in basophils. The proform of EMBP is expressed in placental X cells and breast tissue and increases significantly during human pregnancy. The proform inhibits the metallopeptidase pregnancy-associated plasma protein A [
,
] and is considered to be a peptidase inhibitor (MEROPS identifier I63.001). EMBP has cytotoxic properties and damages bacteria and mammalian cells, in vitro, as well as, helminth parasites []. EMBP deposition has been observed in the inflamed tissue of allergy patients in a variety of diseases including asthma, atopic dermatitis, and rhinitis. In addition to its cytotoxic functions, EMBP activates cells and stimulates cytokine production []. EMBP has been shown to bind the proteoglycan heparin. The binding site is similar to the carbohydrate binding site of other classical CTLD, such as mannose-binding protein (MBP1), however, heparin binding to EMBP is calcium ion independent []. MBPH has reduced potency in cytotoxic and cytostimulatory assays compared with EMBP [,
].
The paired domain is a ~126 amino acid DNA-binding domain, which is found in eukaryotic transcription regulatory proteins involved in embryogenesis. The domain was originally described as the 'paired box' in the Drosophila protein paired (prd) [
,
]. The paired DNA-binding domain is generally located in the N-terminal part. An octapeptide [] and/or a homeodomain can occur C-terminal to the paired DNA-binding domain, as well as a Pro-Ser-Thr-rich C-terminal. Paired DNA-binding domain proteins can function as transcription repressors or activators. The paired DNA-binding domain contains three subdomains, which show functional differences in DNA-binding.The crystal structures of prd and Pax proteins show that the DNA-bound paired domain is bipartite, consisting of an N-terminal subdomain (PAI or NTD) and a C-terminal subdomain (RED or CTD), connected by a linker. PAI and RED each form a three-helical fold, with the most C-terminal helices
comprising a helix-turn-helix (HTH) motif that binds the DNA major groove. In addition, the PAI subdomain encompasses an N-terminal β-turn andβ-hairpin, also named 'wing', participating in DNA-binding. The linker can bind into the DNA minor groove. Different Pax proteins and their alternatively spliced isoforms use different (sub)domains for DNA-binding to mediate the specificity of sequence recognition [
,
].This entry represents the paired DNA-binding domain. This conserved region spans the DNA-binding HTH located in the N-terminal subdomain.
This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C terminus of TRIM27, also known as RING finger protein 76 (RNF76) or RET finger protein (RFP). TRIM proteins are defined by the presence of the tripartite motif RING/B-box/coiled-coil region and are also known as RBCC proteins [
]. TRIM27 exhibits either nuclear or cytosolic localization depending on the cell type. TRIM27 negatively regulates nucleotide-binding oligomerization domain containing 2 (NOD2)-mediated signaling by proteasomal degradation of NOD2, suggesting that TRIM27 could be a new target for therapeutic intervention in NOD2-associated diseases such as Crohn's []. High expression of TRIM27 is observed in several human cancers, including breast and endometrial cancer, where elevated TRIM27 expression predicts poor prognosis []. Also, TRIM27 forms an oncogenic fusion protein with Ret proto-oncogene. It is involved in different stages of spermatogenesis and its significant expression in male germ cells and seminomas, suggests that TRIM27 may be associated with the regulation of testicular germ cell proliferation and histological-type of germ cell tumors [
,
]. TRIM27 could also be a predictive marker for chemoresistance in ovarian cancer patients []. In the neurotoxin model of Parkinson's disease (PD), deficiency of TRIM27 decreases apoptosis and protects dopaminergic neurons, making TRIM27 an effective potential target during the treatment of PD [].
Telomeres function to shield chromosome ends from degradation and end-to-end fusions, as well as preventing the activation of DNA damage checkpoints. Telomeric repeat binding factor (TRF) proteins TRF1 and TRF2 are major components of vertebrate telomeres required for regulation of telomere stability. TRF1 and TRF2 bind to telomeric DNA as homodimers. Dimerisation involves the TRF homology (TRFH) subdomain contained within the dimerisation domain. The TRFH subdomain is important not only for dimerisation, but for DNA binding, telomere localisation, and interactions with other telomeric proteins. The dimerisation domains of TRF1 and TRF2 show the same multi-helical structure, arranged in a solenoid conformation similar to TPR repeats, which can be divided into an α-α superhelix and a long alpha hairpin [
].The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain
at the carboxy terminus [
]. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection []. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe (Fission yeast) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres []. This entry represents the dimerisation domain.
The archease superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing and therefore have been predicted to be modulators or chaperones involved in DNA or RNA metabolism. Many of the roles of archeases remain to be established experimentally. The function of one of the archeases from the hyperthermophile Pyrococcus abyssi has been determined. The gene encoding the archease (PAB1946) is located in a bicistronic operon immediately upstream from a second open reading frame (PAB1947), which encodes a tRNA m5C methyltransferase. The methyl transferase catalyses m5C formation at several cytosine's within tRNAs with preference for C49; the specificity of the methyltransferase reaction being increased by the archease. The archease protects the tRNA (cytosine-5-)-methyltransferase PAB1947 against aggregation and increases its specificity. The archease exists in monomeric and oligomeric states, with only the oligomeric forms able to bind the methyltransferase [
].The function of this family of archeases as chaperones is supported by structural analysis of
from Methanobacterium thermoautotrophicum, which shows homology to heat shock protein 33, which is a chaperone protein that inhibits the aggregation of partially denatured proteins [
].Structurally, the archeases are composed of a single three layer beta-α-β sandwich domain similar to those found in other chaperones.
STAT proteins have a dual function: signal transduction and activation of transcription. When cytokines are bound to cell surface receptors, the associated Janus kinases (JAKs) are activated, leading to tyrosine phosphorylation of the given STAT proteins [
]. Phosphorylated STATs form dimers, translocate to the nucleus, and bind specific response elements to activate transcription of target genes []. STAT proteins contain an N-terminal domain (NTD), a coiled-coil domain (CCD), a DNA-binding domain (DBD), an α-helical linker domain (LD), an SH2 domain, and a transactivation domain (TAD). The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6 []. STAT5 is a member of the STAT family of transcription factors. Two highly related proteins, STAT5a and STAT5b are encoded by separate genes, but are 90% identical at the amino acid level. Both STAT5a and STAT5b are ubiquitously expressed and functionally interchangeable. They regulate B and T cell development [
,
]. These proteins are central signalling molecules in leukaemias driven by Abelson fusion tyrosine kinases, having a key role in resistance of leukaemic cells against treatment with tyrosine kinase inhibitors (TKI) []. They differentially regulate cellular behaviour in human mammary carcinoma []. This entry represents the DNA-binding domain (DBD) of STAT5, which has an Ig-like fold.
The secretion of protein products occurs by a number of different pathways in bacteria and several secretion mechanisms have been described for Gram-negative bacteria [
], an increasing number employ a highly efficient but simple mechanism first described for the immunoglobulin A1 (IgA1) proteases [,
]. The autotransporter secretion pathway [
] is a distinct secretion mechanism, in which the protein moiety mediating export through the outer membrane is contained within the precursor of the secreted protein itself. Autotransporters have been implicated as important or putative virulence factors [] such as mediating adhesion to host cells or by mediating actin-promoted bacterial mobility [].The key feature of an autotransporter is that it contains all the information for secretion in the precursor of the secreted protein itself [
]. Autotransporters comprise three functional domains: 1) an N-terminal targeting domain (amino-terminal leader sequence) that functions as a signal peptide to mediate targeting to and translocation across the inner membrane 2) a C-terminal translocation domain (carboxy-terminal) that forms a β-barrel pore to allow the secretion [] of 3) the passenger domain, the secreted mature protein [].This entry shows the C-terminal autotransporter domain, it is about 400 amino acids in length and includes the aromatic amino acid-rich OMP signal, typically ending with a Phe or Trp residue, at the extreme C terminus.
The tumour necrosis factor (TNF)-like domains are found in both TNF and C1q protein families. Structurally these domains self-associate to make a compact bell-shaped homotrimer, each monomer being composed of an anti-parallel β-sheet sandwich with a jellyroll topology. Both TNF and C1q family members can be expressed as soluble plasma proteins or as type II membrane-bound proteins.TNF family members bind extracellularly to cysteine-rich receptors, thereby inducing a clustering of the receptors, which subsequently triggers the intracellular apoptotic cascade. The TNF proteins are important mediators in inflammation, immune responses and cytotoxicity through their interaction with the TNF-R55 and the TNF-R75 cell-surface receptors [
]. Other TNF family members include the CD40 ligand (C-terminal TNF-like domain) which is involved in the immune response via the CD40 receptor []; TRAIL, which selectively induces apoptosis in tumour cells via DR4 and DR5 receptors []; the RANK ligand (TNFSF11), which triggers osteoclastogenesis via the RANK receptor []; and TALL-1 (soluble domain), which is involved in the immune response via the TACI, BCMA, and BAFF-R receptors [].C1q proteins also contain TNF-like domains. C1q family members include the Adiponectin/ACRP30 (C-terminal TNF-like domain), which regulates metabolism and energy homeostasis [
], and NC1 (non-collagenous domain 1), the C-terminal TNF-like domain of collagen X, which is crucial for collagen X assembly in bone tissue [].
Cytochromes c (cytC) can be defined as electron-transfer proteins having
one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes.Ambler [
] recognised four classes of cytC. Class 1 cytochromes have the haem-attachment site towards the N terminus, and can be further subdivided into five groups (1A to 1E) based on sequence similarity. Cytochrome C550 (CytC550) is a class 1A cytochrome. CytC550 (also known as PsbV) is an extrinsic membrane protein that forms part of the oxygen-evolving complex in photosystem II, this complex being responsible for the splitting of water into O(2) and 4H+, the latter being used to reduce CO2 to glucose. CytC550 is only found in cyanobacteria and red algae [], this protein having been lost during the evolution of green plants []. Other Class 1A cytochrome C proteins include mitochondrial cytochrome C, which acts as an electron carrier between cytochrome reductase and the cytochrome oxidase complex, the final electron carrier in the mitochondrial electron transport chain; and cytochrome C6, which acts as an electron carrier between cytochrome b6f and photosystem I in cyanobacteria [].
Cytochromes c (cytC) can be defined as electron-transfer proteins having
one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes.Ambler [
] recognised four classes of cytC. Class 1 cytochromes have the haem-attachment site towards the N terminus, and can be further subdivided into five groups (1A to 1E) based on sequence similarity. Cytochrome C550 (CytC550) is a class 1A cytochrome. CytC550 (also known as PsbV) is an extrinsic membrane protein that forms part of the oxygen-evolving complex in photosystem II, this complex being responsible for the splitting of water into O(2) and 4H+, the latter being used to reduce CO2 to glucose. CytC550 is only found in cyanobacteria and red algae [], this protein having been lost during the evolution of green plants []. Other Class 1A cytochrome C proteins include mitochondrial cytochrome C, which acts as an electron carrier between cytochrome reductase and the cytochrome oxidase complex, the final electron carrier in the mitochondrial electron transport chain; and cytochrome C6, which acts as an electron carrier between cytochrome b6f and photosystem I in cyanobacteria [].
Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related strains. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, e.g.
. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein [
]. The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter []. It seems likely that the whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins, and the same bacteriocins can be produced by different species.The proteins in this entry include amylovorin-L, lactacin-F and salivaricin CRL 1328, all of them class IIb two-peptide bacteriocins.
This entry represents budding yeast Zip3 (also known as Cst9) and its homologues including Vilya/Nenya/narya from Drosophila melanogaster, RNF212/RNF212B from animals and Zip homologous proteins 1, 2, 3 and 4 from Caenorhabditis elegans. In budding yeasts, Zip3 is a SUMO E3 ligase and a component of the synapsis initiation complex (SIC) required for synaptonemal complex formation. Zip3 possesses a C3H2C3 RING finger motif, which is required for its E3 SUMO ligase activity in vitro [
].The synaptonemal complex (SC) is a proteinaceous complex that apparently mediates synapsis between homologous chromosomes during meiotic prophase [
]. A number of chromosomal crossover factors and DNA damage repair components have been found to associate with both synaptonemal complexes and multiple synaptonemal complexes (polycomplexes). These include Zip3 (Cst9) from budding yeast, which localizes throughout the body of polycomplexes []. The presence of several Zip3-related proteins within the same organism, for instance the mammalian RNF212 ortholog (RNF212B), expands recombination control by E3-ligase activities [
]. Mouse RNF212 acts as a regulator of crossing-over during meiosis [].The Caenorhabditis elegans genome encodes at least four RING finger E3 ligase proteins, ZHP-1, ZHP-2, ZHP-3 and ZHP-4 that act together to promote a spatio-temporal accumulation of pro-crossover factors [
].Drosophila melanogaster contain three Zip3-related proteins Vilya, Nenya and Narya which function in the formation of meiotic DNA DSBs and in the process of crossing over [
].
Lysosomes are membrane-bound organelles found in animals that are involved in degradation of endogenous and exogenous macromolecules [
]. Lysosome-related organelles occur in specific cell types and fulfil specialised functions e.g. melanosomes which synthesise and store pigments in higher eukaryotes. Lysosome biogenesis is linked to the to the secretory and endocytic pathways for protein and lipid trafficking.One of the protein complexes involved in this process is biogenesis of lysosome-related organelles complex 1 (BLOC-1). This complex consists of seven distinct subunits: dysbindin, pallidin, muted, snapin, cappuccino, and BLOS1-3 subunits [
]. Apart from BLOCS3 all of these subunits are predicted to form coiled-coil structures. BLOC-1 can be found in the cytosol and also associated with membranes. Protein interaction studies suggest that this complex interacts with a number of proteins including syntaxin, filametous actin, dystrobrevin and mysopryn, though the molecluar function of this complex is not yet known. Mutations in BLOC-1 subunits are associated with Hermansky-Pudlak syndrome - a disorder characterised by deficiencies in melanosomes, platelet-dense granules and other lysosome-related organelles. Cells that lack lysosome-related organelles express BLOC-1 but do not appear to need it for lysosome biosynthesis. In concert with the AP-3 complex, the BLOC-1 complex is required to target membrane protein cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals [].This group represents subunit 3 of the BLOC-1 complex, also known as BLOS3 [
].
This entry represents the pleckstrin homology (PH) domain found in Sip3 and its paralogue, Lam1 (also known as Ysp1), from budding yeasts. They have an N-terminal Bin/Amphiphysin/Rvs (BAR) domain followed by a PH domain, and a C-terminal StART-like domain. They may be involved in sterol transfer between intracellular membranes [
]. This domain can also be found in uncharacterized protein C19A8.02 from fission yeasts. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner [
]. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity []. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane []. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes [].
This group represents telomeric repeat-binding factors 1 (TERF1, also known as TRF1).Telomeres function to shield chromosome ends from degradation and end-to-end fusions, as well as preventing the activation of DNA damage checkpoints. Telomeric repeat binding factor (TRF) proteins TRF1 and TRF2 are major components of vertebrate telomeres required for regulation of telomere stability. TRF1 and TRF2 bind to telomeric DNA as homodimers. Dimerisation involves the TRF homology (TRFH) subdomain contained within the dimerisation domain. The TRFH subdomain is important not only for dimerisation, but for DNA binding, telomere localisation, and interactions with other telomeric proteins. The dimerisation domains of TRF1 and TRF2 show the same multi-helical structure, arranged in a solenoid conformation similar to TPR repeats, which can be divided into an α-α superhelix and a long alpha hairpin [
].The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain
at the carboxy terminus [
]. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection []. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe (Fission yeast) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres [].
This entry represents telomeric repeat-binding factor 2 (TERF2, also known as TRF2).Telomeres function to shield chromosome ends from degradation and end-to-end fusions, as well as preventing the activation of DNA damage checkpoints. Telomeric repeat binding factor (TRF) proteins TRF1 and TRF2 are major components of vertebrate telomeres required for regulation of telomere stability. TRF1 and TRF2 bind to telomeric DNA as homodimers. Dimerisation involves the TRF homology (TRFH) subdomain contained within the dimerisation domain. The TRFH subdomain is important not only for dimerisation, but for DNA binding, telomere localisation, and interactions with other telomeric proteins. The dimerisation domains of TRF1 and TRF2 show the same multi-helical structure, arranged in a solenoid conformation similar to TPR repeats, which can be divided into an α-α superhelix and a long alpha hairpin [
].The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain
at the carboxy terminus [
]. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection []. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe (Fission yeast) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres [].
Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. This N-terminal domain is not required for transcriptional activity, and while a similar sequence has been identified in other transcription factors, and proteins that are predominantly nuclear localized [
,
], the domain is also found in proteins not directly involved in transcription. This domain is found in (amongst others):MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved [
].
The sterile alpha motif (SAM) domain is a protein interaction module present in a wide variety of proteins [
,
] involved in many biological processes. The SAM domain that spreads over around 70 residues and one of the most common protein modules found in eukaryotic genomes []. SAM domains have been shown to form homo- and hetero-oligomers, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant [
]. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologues. These results suggest that the SAM domain might have a primary role in RNA binding.Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces [
]. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures [].
The stress-response A/B barrel domain is found in a class of stress-response
proteins in plants. It is also found in some bacterial fructose-bisphosphate aldolase such as at the C terminus of a fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus () [
]. is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine.
The stress-response A/B barrel domain forms a very stable dimer. This dimer
belongs to the superfamily of dimeric alpha+beta barrels in which the twoβ-sheets form a β-barrel. The two molecules in the dimer are related by
a 2-fold axis parallel to helix H1 and β-strands B3 and B4. C-terminal residues extending from the beta4 strand of each monomer wrap around and connect with the beta2 strand and alpha1 helix of the opposing monomer to form the dimer interface [,
,
].The outer surface of the β-sheets of the two molecules forms a β-barrel-like structure defining a central pore.The function of the stress-response A/B barrel domain is unknown [
,
,
], but it is upregulated in response to salt stress in Populus balsamifera (balsam poplar) [].Some proteins known to contain a stress response A/B barrel domain are listedbelow:
- Arabidopsis thaliana At3g17210- Arabidopsis thaliana At5g22580-Populus tremula stable protein 1 (SP-1)(Populus species), a thermostable stress-responsive protein.- Pseudomonas hydrogenothermophila fructose 1,6-bisphosphate aldolase (cbbA).The structure of one of these proteins has been solved (
) and the domain forms an α-β barrel dimer [
].
Sphingolipids are bioactive compounds found in lower and higher eukaryotes.
They are involved in the regulation of various cellular functions, such asgrowth, differentiation and apoptosis, and are believed to be essential in
a healthy diet. Sphigolipids are degraded in the lysosome, and theproducts from their hydrolysis are used in other biosynthetic and regulatory
pathways in the host.There are a number of lysosomal enzymes involved in the breakdown ofsphinogolipids, and these act in sequence to degrade the moieties [
]. These enzymes require co-proteins called sphingolipid activator proteins, (SAPs or saposins), to stabilise and activate them as necessary. SAPs are non-enzymatic and usually have a low molecular weight. They are conserved across a wide range of eukaryotes and contain specific saposin domains that aid in the activation of hydrolase enzymes. There have been four human saposins described so far, sharing significant similarity with each otherand with other eukaryotic SAP proteins.
Mutations in SAP genes have been linked to a number of conditions. A defectin the saposin B region leads to metachromatic leucodystrophy (MLD), while
a single nucleotide polymorphism in the SAP-C region may give rise toGaucher disease [
]. More recently, an opportunistic protozoan parasite protein has shown similarity both to the higher and lower eukaryotic saposins. The pore-forming protein isolated from virulent Naegleria fowleri (Brain eating amoeba) has been dubbed Naegleriapore A. It also shares structural similarity with cytolytic bacterial peptides, although this similarity does not extend to the sequence level.
Dihydroorotase belongs to MEROPS peptidase family M38 (clan MJ), where it is classified as a non-peptidase homologue. DHOase catalyses the third step in the
de novobiosynthesis of pyrimidine, the conversion of ureidosuccinic acid (N-carbamoyl-L-aspartate) into dihydroorotate. Dihydroorotase binds a zinc ion which is required for its catalytic activity [
].In bacteria, DHOase is a dimer of identical chains of about 400 amino-acid residues (gene pyrC). In the metazoa, DHOase is part of a large multi-functional protein known as 'rudimentary' in Drosophila melanogaster and CAD in mammals and which catalyzes the first three steps of pyrimidine biosynthesis [
]. The DHOase domain is located in the central part of this polyprotein. In yeast, DHOase is encoded by a monofunctional protein (gene URA4). However, a defective DHOase domain [] is found in a multifunctional protein (gene URA2) that catalyzes the first two steps of pyrimidine biosynthesis.The comparison of DHOase sequences from various sources shows [
] that there are two highly conserved regions. The first located in the N-terminal extremity contains two histidine residues suggested [] to be involved in binding the zinc ion. The second is found in the C-terminal part. Members of this family of proteins are predicted to adopt a TIM barrel fold [].This family represents the homodimeric form of dihydroorotase
. It is found in bacteria, plants and fungi; URA4 of yeast is a member of this group of sequences.
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. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C.
Ubiquitin-conjugating enzymes (UBC or E2 enzymes) (
) [
,
,
]
catalyse the covalent attachment of ubiquitin to target proteins. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, ), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3,
,
), which work sequentially in a cascade [
]. The E1 enzyme mediates an ATP-dependent transfer of a thioester-linked ubiquitin molecule to a cysteine residue on the E2 enzyme. The E2 enzyme then either transfers the ubiquitin moiety directly to a substrate, or to an E3 ligase, which can also ubiquitinylate a substrate.There are several different E2 enzymes (over 30 in humans), which are broadly grouped into four classes, all of which have a core catalytic domain (containing the active site cysteine), and some of which have short N- and C-terminal amino acid extensions: class I enzymes consist of just the catalytic core domain (UBC), class II possess a UBC and a C-terminal extension, class III possess a UBC and an N-terminal extension, and class IV possess a UBC and both N- and C-terminal extensions. These extensions appear to be important for some subfamily function, including E2 localisation and protein-protein interactions [
]. In addition, there are proteins with an E2-like fold that are devoid of catalytic activity (such as protein crossbronx from flies), but which appear to assist in poly-ubiquitin chain formation.
Two different types of thiolase [
,
,
] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase () and 3-ketoacyl-CoA thiolase (
). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.
In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction [
].Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [
].The signature pattern for this entry is a conserved sequence located towards the C-terminal end.
Cytochromes b561 constitute a class of intrinsic membrane proteins containing two haem molecules that are involved in ascorbate (vitamin C) regeneration. They have been suggested to function as electron transporters, shuttling electrons across membranes from ascorbate to an acceptor molecule. The one-electron oxidation product of ascorbate, monodehydro-ascorbate (MDHA) has been shown to function as an electon acceptor for mammalian and plant cytochromes b561. The cytochrome b561-catalysed reduction of MDHA results in the regeneration of the fully reduced ascorbate molecule. Cytochromes b561 have been identified in a large number of phylogenetically distant species, but are absent in prokaryotes. Most species contain three or four cytochrome b561 paralogous proteins [
].Members of the cytochrome b561 protein family are characterised by a number of structural features, likely to play an essential part in their function. They are highly hydrophobic proteins with six transmembrane helices (named TMH1 through TMH6), four conserved histidine residues, probably coordinating the two haem molecules, and predicted substrate-binding sites for ascorbate and MDHA [
]. The functionally relevant and structurally most conserved region in the cytochrome b561 family is the TMH2 to -5 4-helix core with an amino acid composition that is very well conserved in the inner surface and somewhat less conserved in the outer surface of the core. The two terminal helices (TMH1 and TMH6) are less conserved [,
].The entry represents a conserved region containing six transmembrane helices, found in cytochrome b651 and homologous proteins including some ferric reductases.
The B30.2 domain was first identified as a protein domain encoded by an exon (named B30-2) in the Homo sapiens class I major histocompatibility complex region [], whereas the SPRY domain was first identified in a Dictyostelium discoideum kinase splA and mammalian calcium-release channels ryanodine receptors []. B30.2 domain consists of PRY and SPRY subdomains. The SPRY domains (after SPla and the RYanodine Receptor) are shorter at the N terminus than the B30.2 domains. The ~200-residue B30.2/SPRY (for B30.2 and/or SPRY) domain is present in a large number of proteins with diverse individual functions in different biological processes. The B30.2/SPRY domain in these proteins is likely to function through protein-protein interaction [].The N-terminal ~60 residues of B30.2/SPRY domains are poorly conserved and, as a consequence, a new domain name PRY was coined for a group of similar sequence segments N-terminal to the SPRY domains [
]. The B30.2/SPRY domain contains three highly conserved motifs (LDP, WEVE and LDYE) []. The B30.2/SPRY domain adopts a highly distorted, compact β-sandwich fold with two additional short β-helices at the N terminus. The β-sandwich of the B30.2/SPRY domain consists of two layers of β-sheets: sheet A composed of eight strands and sheet B composed of seven strands. All the β-strands are in antiparallel arrangement []. The 5th β-strand corresponding to WEVE motif []. Both the N- and C-terminal ends of the B30.2/SPRY domains in general are close to each other [].
Papillomaviruses (PPV) are a large family of DNA tumour viruses which give rise to warts in their host species. The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication [
,
]. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins [].The E1 protein is a 70kDa polypeptide with a centrally-located DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase [
]. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity [].This entry represents the N-terminal region of E1, which contains the nuclear localisation signal.
This zinc-finger containing domain is found in eukaryotes.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.
Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans [
]. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death.Ced-4 is a family of apoptosis proteins. Caenorhabditis elegans has three genes, ced-3, ced-4 and ced-9, which code for the components of an induction pathway of apoptosis that is conserved in the nematode and mammals. Homologues in have also been found in Drosophila [
]. Egl-1 binds to and directly inhibits the activity of ced-9, releasing the cell death activator ced-4 from a ced-9/ced-4 containing protein complex. This allows ced-4 to activate the cell-killing caspase ced-3. Apoptotic protease-activating factor-1 (Apaf-1) is a key regulator of the mitochondrial apoptosis pathway. It consists of three functional regions: an N-terminal caspase recruitment domain (CARD) that can bind to procaspase-9, a CED-4-like region enabling self-oligomerization, and a regulatory C terminus with WD-40 repeats masking the CARD and CED-4 region [
].DEFCAP a novel member of Ced-4 family of apoptosis proteins. It is similar to the other mammalian Ced-4 proteins (Apaf-1 and Nod1) in that it contains a caspase recruitment domain (CARD) and a putative nucleotide binding domain signified by a P-loop and magnesium binding site [
].
This entry represents the redox inactive TRX-like domain b' found at the C terminus of vertebrate nucleoredoxins (NRX). Despite its name, nucleoredoxins is localized in both the cytosol and the nucleus [
]. It interacts with phosphofructokinase 1 and protein phosphatase 2A [,
]. It may be involved in transcriptional regulation [] and has been shown to negatively regulate Wnt-beta-catenin signalling and binds to Dvl (Dishevelled) in a redox-dependent manner []. The mouse NRX gene is implicated in streptozotocin-induced diabetes []. The NRX protein contains three TRX domains organized in a structure similar to those of PDIs that contain three to four TRX domains. The N- and C-terminal domains of NRX share a high similarity to the b' domains of PDIs and lack a redox active centre. The central domain, however, contains the dithiol active site motif Cys-Pro-Pro-Cys and was shown to be active in the insulin reduction assay. The function of the PDI-like domains in NRX is unclear; they may be important for substrate recognition [].Thioredoxin family members are evolutionary conserved proteins that possess catalytically active cysteine residues that can reduce the disulphide bonds of target proteins. Thioredoxin family members include nucleoredoxins (NRX), Trxs, glutaredoxins (Grxs), peroxiredoxins (Prxs), and protein disulfide isomerases (PDIs) that catalyze cellular redox signaling [
]. Thioredoxin possesses a conserved WCGPC (Trp-Cys-Gly-Pro-Cys) motif, and the two cysteine residues (Cys32 and Cys35 in human TRX1) are directly involved in oxidoreductase reactivity [].
FRS2 (also called Suc1-associated neurotrophic factor (SNT)-induced tyrosine-phosphorylated target) proteins are membrane-anchored adaptor proteins. They are composed of an N-terminal myristoylation site followed by a phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a C-terminal effector domain containing multiple tyrosine and serine/threonine phosphorylation site. The FRS2/SNT proteins show increased tyrosine phosphorylation by activated receptors, such as fibroblast growth factor receptor (FGFR) and TrkA, recruit SH2 domain containing proteins such as Grb2, and mediate signals from activated receptors to a variety of downstream pathways. The PTB domains of the SNT proteins directly interact with the canonical NPXpY motif of TrkA in a phosphorylation dependent manner, they directly bind to the juxtamembrane region of FGFR in a phosphorylation-independent manner [
,
]. This domain can also be found in FRS3 []. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lacking tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This domain is part of the IRS-like subgroup [
,
].
C2cd3 is a novel C2 domain-containing protein specific to vertebrates. C2cd3 functions in regulator of cilia formation, Hedgehog signaling, and mouse embryonic development [
]. Mutations in C2cd3 mice resulted in lethality in some cases and exencephaly, a twisted body axis, and pericardial edema in others []. It is required for centriole elongation []. Mutations in the human C2cd3 gene cause Orofaciodigital syndrome 14, which is characterised by malformations of the face, oral cavity, and digits []. It plays an important part in centriolar distal appendage assembly and ciliary vesicle docking in mammals []. C2 domains fold into an 8-standed β-sandwich that can adopt 2 structural arrangements: type I and type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions [
,
,
,
].
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. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses.
This entry represents the RNA recognition motif 1 (RRM1) of paraspeckle component 1 (PSP1). PSP1 (also known as PSPC1) is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm [
]. PSP1 belongs to the DBHS (Drosophila behavior human splicing) family. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently; however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner []. PSPC1 contains two conserved RNA recognition motifs (RRMs) at the N terminus.DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a ~100 amino acid coiled-coil domain, and a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein [
,
].
This entry represents the RNA recognition motif 2 (RRM2) of paraspeckle component 1 (PSP1).PSP1 (also known as PSPC1) is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm [
]. PSP1 belongs to the DBHS (Drosophila behavior human splicing) family. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently; however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner []. PSPC1 contains two conserved RNA recognition motifs (RRMs) at the N terminus.DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a ~100 amino acid coiled-coil domain, and a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein [
,
].
PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [
,
,
]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This superfamily represents PsbZ (Ycf9), which is a core low molecular weight transmembrane protein of photosystem II in thylakoid-containing chloroplasts of cyanobacteria and plants. It is thought to be located at the interface of PSII and LHCII (light-harvesting complex II) complexes, the latter containing the light-harvesting antenna. PsbZ appears to act as a structural factor, or linker, that stabilises the PSII-LHCII supercomplexes, which fail to form in PsbZ-deficient mutants. This may in part be due to the marked decrease in two LHCII antenna proteins, CP26 and CP29, found in PsbZ-deficient mutants, which result in structural changes, as well as functional modifications in PSII [
]. PsbZ may also be involved in photo-protective processes under sub-optimal growth conditions.Structurally, PsbZ has two antiparallel transmembrane helices.
This group of cysteine peptidases belong to the MEROPS peptidase family C12 (ubiquitin C-terminal hydrolase family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. The type example is the human ubiquitin C-terminal hydrolase UCH-L1.Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly [
]. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [,
], and inhibited by thiol-blocking agents and ubiquitin aldehyde [,
], and as such have the properties of cysteine proteases [].The deubiquitinsing proteases can be split into 2 size ranges: 20-30kDa (this entry) and 100-200kDa (
) [
]. The 20-30kDa group includes the yeast yuh1, which is known to be active only against small ubiquitin conjugates, being inactive against conjugated beta-galactosidase []. A mammalian homologue, UCH (ubiquitin conjugate hydrolase), is one of the most abundant proteins in the brain []. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative ofthe cysteine/histidine spacing of a cysteine protease catalytic dyad [
].
Frk (RAK) is a member of the Src non-receptor type tyrosine kinase family of proteins. The Frk subfamily is composed of Frk/Rak and Iyk/Bsk/Gst. It is expressed primarily epithelial cells. Frk is a nuclear protein and may function during G1 and S phase of the cell cycle and suppress growth [
]. Unlike the other Src members it lacks a glycine at position 2 of SH4 which is important for addition of a myristic acid moiety that is involved in targeting Src PTKs to cellular membranes []. FRK and SHB exert similar effects when overexpressed in rat phaeochromocytoma (PC12) and beta-cells, where both induce PC12 cell differentiation and beta-cell proliferation. Under conditions that cause beta-cell degeneration these proteins augment beta-cell apoptosis. The FRK-SHB responses involve FAK and insulin receptor substrates (IRS) -1 and -2 []. Frk has been demonstrated to interact with retinoblastoma protein []. Frk regulates PTEN protein stability by phosphorylating PTEN, which in turn prevents PTEN degradation []. Frk also plays a role in regulation of embryonal pancreatic beta cell formation [].The Src non-receptor type tyrosine kinase (SFK) family members have an unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail. The SH2 domain of SFKs is involved in kinase autoinhibition and T-cell receptor signaling. The binding SH2 domains to phosphotyrosine (pY) sites is critical for the autoinhibition and substrate recognition of the SFKs [
].
ESX-1 to ESX-5 gene clusters encode proteins that are either secreted or building blocks of the actinobacterial Type 7 secretion system (T7SS) [
]. In Mycobacterium tuberculosis ESX-1 is responsible for secretion of important virulence factors such as EsxA and EsxB as well as other virulence-associated proteins, ESX-3 is involved in metal acquisition being critical for mycobacterial survival. ESX-5 is also important for the secretion of members of the PE/PPE family of proteins that play a role in virulence and cell wall integrity. The function of ESX-2 and ESX-4 is still unknown although ESX-4 seems to be the ancestral system from which ESX systems have evolved. All ESX gene clusters contain three or four ESX conserved components (Ecc), named EccB, EccC, and EccD, with EccE being present in all ESX systems, except of ESX-4. EccC is a member of the FtsK/SpoIIIE-like ATPase family and provides the energy to transport proteins across the mycobacterial membrane; EccB and EccE have N-terminal transmembrane elements and large C-terminal regions predicted to be localised in the periplasm, but their function, molecular function or interacting partners remain unknown. EccD contains an N-terminal cytoplasmic domain followed by 11 predicted transmembrane helices, which is thought to form a cytoplasmic membrane channel through which the proteins are secreted [].This domain is found in EccD members from the Type VII secretion system such as EccD2, EccD4 and EccD5, which includes 11 predicted transmembrane α-helices.
DOCK family members are evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases [
]. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis. The N-terminal SH3 domain of the DOCK proteins functions as an inhibitor of GEF, which can be relieved upon its binding to the ELMO1-3 adaptor proteins, after their binding to active RhoG at the plasma membrane [,
]. DOCK family proteins are categorised into four subfamilies based on their sequence homology: DOCK-A subfamily (DOCK1/180, 2, 5), DOCK-B subfamily (DOCK3, 4), DOCK-C subfamily (DOCK6, 7, 8), DOCK-D subfamily (DOCK9, 10, 11) []. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). This entry represents the C2 domain of the Dock-B members. Most of these members have been shown to be GEFs specific for Rac, although Dock4 has also been shown to interact indirectly with the Ras family GTPase Rap1, probably through Rap regulatory proteins. In addition to the C2 domain (also known as DHR-1 domain) and the DHR-2 domain, Dock-B members contain a SH3 domain upstream of the C2 domain and a proline-rich region downstream. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock1 (also known as Dock180) and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3)[
,
,
].
Herpesviruses are large and complex DNA viruses, widely found in nature. Human cytomegalovirus (HCMV), an important human pathogen, defines the betaherpesvirus family. Mouse cytomegalovirus (MCMV) and rat cytomegalovirus serve as biological model systems for HCMV. HCMV, MCMV, and rat CMV display the largest genomes among the herpesviruses and are essentially co-linear over the central 180 kb of the 230-kb genomes. Betaherpesviruses, which include the CMVs as well as human herpesviruses 6 and 7, differ from alpha- and gammaherpesviruses by the presence of additional gene families such as the US22 gene family, which are mainly clustered at the ends of the genome. The US22 family was first described in HCMV. This gene family comprises 12 members in both HCMV and MCMV and 11 in rat CMV [
].US22 proteins have been found across many animal DNA viruses and some vertebrates [
]. The name sake of this family US22 () is an early nuclear protein that is secreted from cells [
]. The US22 family may have a role in virus replication and pathogenesis []. Domain analysis showed that US22 proteins usually contain two copies of conserved modules which is homologous to several other families like SMI1 and SYD (commonly called SUKH superfamily). Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins [].
The HD domain, named after the conserved doublet of predicted catalytic residues, is found in a wide range of bacterial, archaeal and eukaryotic proteins. It defines a superfamily of phosphohydrolases that can catalyze both metal-dependent and -independent phosphomonoesterase and phosphodiesterase reactions for a broad range of substrates [
,
].The HD-domain proteins appear to be involved in nucleic acid and nucleotide metabolism, signal transduction and possibly other functions. They are diverse in terms of both domain architecture and phylogenetic distribution; each of the completely sequenced genomes encodes more than one version of this domain. The HD domain is composed of a bundle of alpha helices with a 5-helix core. Although all HD domains share key design features, a striking diversity of catalytic centres have been identified, containing no metal, mono-, bi- or trinuclear metal binding sites [
,
].A distinct version of this domain, HD-GYP, contains a number of additional highly conserved residues. The spectrum of the domains that are associated with HD-GYP in multidomain proteins suggests that it is probably involved in signal transduction. The HD-GYP domain is likely to be a conserved scaffold whose main role is to allow protein-protein interactions with partner GGDEF domains while achieving (a) different function(s) through diversification of the active-site cavity and the N-terminal regulatory domains [
,
,
]. In addition to the HD domain 5-helix core, the HD-GYP domain contains two extra C-terminal helices [,
,
,
].
The putative band 4.1 homologues' binding motif is found in neurexins,
syndecans and glycophorin C intracellular C-termini. Syndecans are cell surface proteoglycans and glycophorin C is a minor sialoglycoprotein in human erythrocyte membranes, which play an important role in regulating the stability of red cells.Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [
,
].Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin C (PAS-2') belongs to the Gerbich blood group system and is associated with An(a), Dh(A), Ls(a) and Wb antigens.
This group of sequences represent the p20 subunit found in caspases. Caspases are composed of an N-terminal pro-domain that is cleaved during activation, and C-terminal catalytic and interaction domains [
]. All caspases contain two essential caspase catalytic domains: the p20 subunit (20kDa) and the p10 subunit (10kDa) (), which are derived from the p45 (45kDa) precursor. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases are cysteine proteases (MEROPS clan CD, family C14) that use the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The key catalytic residues, a cysteine and a histidine, are on the p20 subunit.
Caspases are mainly involved in mediating cell death (apoptosis), either as initiators that trigger the cell death process, or as effectors of the process itself [
,
]. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [
].
Transglutaminases (EC 2.3.2.13) (TGase) [
,
] are calcium-dependent enzymes that catalyze the cross-linking of proteins by promoting the formation of isopeptide bonds between the γ-carboxyl group of a glutamine in one polypeptide chain and the ε-amino group of a lysine in a second polypeptide chain. TGases also catalyze the conjugation of polyamines to proteins.The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilizing the fibrin clot.Other forms of transglutaminases are widely distributed in various organs, tissues and body fluids. Sequence data is available for the following forms of TGase:Transglutaminase K (Tgase K), a membrane-bound enzyme found in mammalian epidermis and important for the formation of the cornified cell envelopε (gene TGM1).Tissue transglutaminase (TGase C), a monomeric ubiquitous enzyme located in the cytoplasm (gene TGM2).Transglutaminase 3, responsible for the later stages of cell envelope formation in the epidermis and the hair follicle (gene TGM3).Transglutaminase 4 (gene TGM4).Transglutaminase X (Tgase X) (gene TGM5).Transglutaminase Z (Tgase Z) (gene TGM7).A conserved cysteine is known to be involved in the catalytic mechanism of TGases.The erythrocyte membrane band 4.2 protein, which probably plays an important role in regulating the shape of erythrocytes and their mechanical properties, is evolutionary related to TGases. However the active site cysteine is substituted by an alanine and the 4.2 protein does not show TGase activity [
].
ARHGEF18 is a guanine nucleotide exchange factor that activates RhoA, a small GTPase protein that is a key component of tight junctions and adherens junctions [
]. It is crucial for maintenance of polarity in the vertebrate retinal epithelium, and consequently is essential for cellular differentiation, morphology and eventually organ function []. ARHGEF18 contains Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA. This entry represents the PH domain of ARHGEF18.PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner [
]. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity [
]. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane []. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes [].
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. This entry describes a plant mutator transposase zinc finger.
This superfamily represents a structural domain with a complex fold consisting of several coiled β-sheets. This domain exists as a duplication, consisting of a tandem repeat of two similar structural motifs. These domains can be found in:Mss4, which contains a zinc-binding site.Translationally controlled tumour-associated protein TCTP, which contains an insertion of an α-helix hairpin, and which lacks a zinc-binding site.The C-terminal MsrB domain of peptide methionine sulphoxide reductase.Mss4 is a conserved accessory factor for Rab GTPases, which function as ubiquitous regulators of intracellular membrane trafficking [
]. Mss4 acts to promote nucleotide release from exocytic but not endocytic Rab GTPases. Mss4 has a complex fold made of several coiled β-sheets, and consists of a duplication of tandem repeats of two similar structural motifs. It contains a zinc-binding site.Other proteins that show structure similarity to Mss4 include the translationally controlled tumour-associated proteins TCTPs, which contains an insertion of an alpha helical hairpin, and lacks the zinc-binding site. TCTPs are a highly conserved and abundantly expressed family of eukaryotic proteins that are implicated in both cell growth and the human acute allergic response [
].The C-terminal MsrB domain of peptide methionine sulphoxide reductase PilB is structurally similar to Mss4. Methionine sulphoxide reductases protect against oxidative damage that can contribute to cell death. The tandem Msr domains (MsrA and MsrB) of the pilB protein from Neisseria gonorrhoeae each reduce different epimeric forms of methionine sulphoxide [
].
PLEKHG1 (also called ARHGEF41), PLEKHG2 (also called ARHGEF42 or CLG/common-site lymphoma/leukemia guanine nucleotide exchange factor2), and PLEKHG3 (also called ARHGEF43) have RhoGEF DH/double-homology domains in tandem with a PH domain which is involved in phospholipid binding. They function as a guanine nucleotide exchange factor (GEF) and are involved in the regulation of Rho protein signal transduction [
]. Mutations in PLEKHG1 have been associated panic disorder (PD), an anxiety disorder characterized by panic attacks and anticipatory anxiety [].PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane [
]. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Lysosomes are membrane-bound organelles found in animals that are involved in degradation of endogenous and exogenous macromolecules [
]. Lysosome-related organelles occur in specific cell types and fulfil specialised functions e.g. melanosomes which synthesise and store pigments in higher eukaryotes. Lysosome biogenesis is linked to the to the secretory and endocytic pathways for protein and lipid trafficking.One of the protein complexes involved in this process is biogenesis of lysosome-related organelles complex 1 (BLOC-1). This complex consists of seven distinct subunits: dysbindin, pallidin, muted, snapin, cappuccino, and BLOS1-3 subunits []. Apart from BLOCS3 all of these subunits are predicted to form coiled-coil structures. BLOC-1 can be found in the cytosol and also associated with membranes. Protein interaction studies suggest that this complex interacts with a number of proteins including syntaxin, filametous actin, dystrobrevin and mysopryn, though the molecluar function of this complex is not yet known. Mutations in BLOC-1 subunits are associated with Hermansky-Pudlak syndrome - a disorder characterised by deficiencies in melanosomes, platelet-dense granules and other lysosome-related organelles. Cells that lack lysosome-related organelles express BLOC-1 but do not appear to need it for lysosome biosynthesis. In concert with the AP-3 complex, the BLOC-1 complex is required to target membrane protein cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals [].This group represents the pallidin subunit (or subunit 6) of BLOC-1 [
]. BLOC-1 is composed in higher eukaryotes of blos1, blos2, blos3, blos4, dysb, muted, pallidin and snapin.
Growth factor receptor-bound protein 2 (Grb2) is an SH2 and SH3 domain-containing adaptor protein that links receptor tyrosine kinases to Ras signalling [
]. Grb2 interacts with the cytoplasmic tyrosine kinase ACK1 (activated Cdc42-associated kinase 1) and mediates its interaction with other receptor tyrosine kinases []. ACK1 is implicated in metastatic behaviour, cell spreading and migration, and epidermal growth factor receptor (EGFR) signalling [].Human GRAP and its Drosophila homologue, downstream of receptor kinase (drk), have been shown to have a function in hearing [
].Src-like adapter proteins (SLAP and SLAP2) are involved in the regulation of immune cell surface expression and signaling. They negatively regulate T cell receptor signaling [
] and act as critical inhibitors of platelet (hem)ITAM signaling in the setting of arterial thrombosis and ischemic stroke []. They contain adjacent Src homology 3 (SH3) and Src homology 2 (SH2) domains. SLAP has been shown to regulate receptor tyrosine kinase (RTK) signaling []. It also binds to the receptor tyrosine kinase Flt3 and plays a role in signal transduction downstream of Flt3 []. SLAP2 acts as a negative regulator of FLT3 signaling []. This entry includes a group of adapter proteins including Grb2, GRAP, GRAPL and SLAP/SLAP2 from humans. This entry also includes Sem-5 from Caenorhabditis elegans. Sem-5 is an adapter protein which modulates signaling mediated by several receptor tyrosine kinases such as egl-15 and let-23 probably acting upstream of let-60/ras [,
].
MYLIP/IDOL is a regulator of the LDL receptor (LDLR) pathway via the nuclear receptor liver X receptor (LXR). In response to cellular cholesterol loading, the activation of LXR leads to the induction of MYLIP expression. MYLIP stimulates ubiquitination of the LDLR on its cytoplasmic tail, directing its degradation. The LXR-MYLIP-LDLR pathway provides a complementary pathway to sterol regulatory element-binding proteins for the feedback inhibition of cholesterol uptake. MYLIP has an N-terminal FERM domain and in some cases a C-terminal RING domain [
,
].The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. Like most other ERM members they have a phosphoinositide-binding site in their FERM domain. The FERM C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites [
,
].
The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses [
]. Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see ,
), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see
,
) [
].This group represents a large T antigen, Polyomaviridae type.The oncogenic large tumour antigen (LTag) is a protein found in polyomaviruses which is essential for viral DNA replication [
]. LTag contains three domains, an N-terminal DnaJ domain which mediates protein interactions (), a domain which binds the origin of DNA replication (
), and a C-terminal helicase domain. Replication is intitated by LTag assembling at the origin as a double hexamer that distorts and melts the origin DNA [
,
]. During elongation LTag acts as a helicase that unwinds duplex DNA at the replication forks [].
This entry represents the C-terminal domain present in the Pseudomonas aeruginosa PsrA which regulates the fadBA5 beta-oxidation operon. Functional analysis of PsrA indicated its importance in regulating b-oxidative enzymes [
]. It has also been suggested that PsrA, a member of the TetR family of repressors, could affect global gene expression including activation of rpoS [].TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [
]. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response []. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis []. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain [].
