HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella []. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria []. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain α-helical []protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain. This entry represents acid stress chaperone HdeA.
HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella []. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotypeessential for the pathogenesis of enteric bacteria []. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain α-helical []protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain. This entry represents the acid stress chaperone HdeA superfamily.
Formylmethanofuran dehydrogenase () is found in methanogenic and sulphate-reducing archaea. The enzyme contains molybdenum or tungsten, a molybdopterin guanine dinuceotide cofactor (MGD) and iron-sulphur clusters []. It catalyses the reversible reduction of CO2and methanofuran via N-carboxymethanofuran (carbamate) to N-formylmethanofuran, the first and second steps in methanogenesis from CO2[, ]. This reaction is important for the reduction of CO2to methane, in autotrophic CO2fixation, and in CO2formation from reduced C1units []. The synthesis of formylmethanofuran is crucial for the energy metabolism of archaea. Methanogenic archaea derives the energy for autrophic growth from the reduction of CO2with molecular hydrogen as the electron donor []. The process of methanogenesis consists of a series of reduction reactions at which the one-carbon unit derived from CO2is bound to C1carriers.There are two isoenzymes of formylmethanofuran dehydrogenase: a tungsten-containing isoenzyme (Fwd) and a molybdenum-containing isoenzyme (Fmd). The tungsten isoenzyme is constitutively transcribed, whereas transcription of the molybdenum operon is induced by molybdate []. The archaean Methanobacterium thermoautotrophicum contains a 4-subunit (FwdA, FwdB, FwdC, FwdD) tungsten formylmethanofuran dehydrogenase and a 3-subunit (FmdA, FmdB, FmdC) molybdenum formylmethanofuran dehydrogenase [].This entry represents subunit A (FmdA and FwdA) of formylmethanofuran dehydrogenases. The other subunits are subunit B (), subunit C (), subunit D (), subunit E (), and subunit F. Some organisms also encode a fusion of the C and D subunits(). Members of this entry share sequence similarity with the two highly conserved regions of dihydroorotase () (an amidohydrolase): the first is located at the N-terminal end and contains two histidine residues suggested to be involved in binding a zinc ion []; the second conserved region is at the C terminus [].In Methylobacterium extorquens, homologues of FmdA, FmdB and FmdC subunits were found and shown to copurify with a functional formyltransferase complex. However, there is no evidence that the complex catalyses the oxidation of formylmethanofuran [].Methanogenic bacteria and archea derive the energy for autotrophic growth from methanogenesis, the reduction of CO2 with molecular hydrogen as the electron donor. FMDH catalyzes the first step in methanogenesis, the formyl-methanofuran synthesis. In this step, CO2 is bound to methanofuran and subsequently reduced to the formyl state with electrons derived from hydrogen [, ].
This group of metallopeptidases belong to the MEROPS peptidase family M2 (clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The catalytic residues and zinc ligands have been identified, the zinc ion being ligated to two His residues within the motif HEXXH, showing that the enzyme belongs to the glu-zincin sub-group of metalloproteases [].Peptidyl-dipeptidase A (angiotensin-converting enzyme or ACE, ) is a mammalian enzyme responsible for cleavage of dipeptides from the C-termini of proteins, notably converting decapeptide angiotensin I to the octapeptide angiotensin II []. The enzyme exists in two differentially transcribed forms, the most common of which is from lung endothelium; this contains two homologous domains that have arisen by gene duplication []. The testis-specific form contains only the C-terminal domain, arising from a duplicated promoter region present in intron 12 of the gene []. Both enzymatic forms are membrane proteins that are anchored by means of a C-terminal transmembrane domain. Both domains of the endothelial enzyme are active, but have differing kinetic constants [, ]. ACE is well-known as a key part of the renin-angiotensin system that regulates blood pressure and ACE inhibitors are important for the treatment of hypertension [, ].An ACE homologue, ACE2 (MEROPS identifier M02.006), has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function [, ]. ACE3 is a non-peptidase homologue included in this entry which lacks Glu378 in the HEXXH motif.A number of insect enzymes have been shown to be similar to peptidyl-dipeptidase A, these containing a single catalytic domain [, ].
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.
In Eubacteria and some Archaea, the first steps in nucleotide excision repair are carried out by the coordinated action of the UvrA, UvrB, and UvrC proteins. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB β-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage [].This entry represents the UvrA subunit. UvrA is an ATPase and a DNA-binding protein [].
This entry contains signal peptide peptidase A (SppA; protease IV; MEROPS identifier S49.001). SppA is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown SppA to be a serine protease. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic centre comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in many serine proteases []. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain, similar to Arabidopsis thaliana SppA1 peptidase. Others, including sohB peptidase, protein C and archaeal signal peptide peptidase, do not contain the amino-terminal domain. Unusually, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain [, , ].
Hydroxymethylglutaryl-CoA synthase () catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA [].HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria []. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [, ].This entry represents the N-terminal domain of HMG-CoA synthase enzymes from both eukaryotes and prokaryotes.
Neurotransmitter ligand-gatedion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. GABAA receptors can be characterised by their sensitivitytowards a selective antagonist, bicuculline. A GABA receptor has been identified that is insensitive to bicuculline and classical GABAA modulators but has an enhanced affinity for GABA. This receptor, unlike most GABAA receptors, is composed principally of rho subunits and was initially termed 'GABAC' in recognition of its altered pharmacology []. Despite these differences, rho subunits are generally considered to be part of the GABAAfamily of receptor proteins due to similarities in sequence and topology.Whilst early studies supported the view that rho subunits assembled to forma homopentamer, it has been shown that a mutant rho 1 protein is able tocoassemble with GABAA gamma 2 subunits as well as the glycine receptor alphasubunit. Rho subunit mRNA occurs prominently in both human and ratretina [], each subunit showing a characteristic pattern of spatial expression. In rat retina, rho 1 mRNA has been detected only in bipolarcells, whereas rho 2 transcripts have been detected in both bipolar andganglion cells. In retinal tissues, expression of rho 3 mRNA is exclusive toganglion cells. Reverse transcriptase PCR (RT-PCR) and in situhybridisation have shown rho transcripts also to be present in other regionsof the brain, specifically those involved in visual signal processing, suchas the superior colliculus and visual cortex.This entry represents Rho 2 subunits.
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptorsprovides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. GABAA receptors can be characterised by their sensitivitytowards a selective antagonist, bicuculline. A GABA receptor has been identified that is insensitive to bicuculline and classical GABAA modulators but has an enhanced affinity for GABA. This receptor, unlike most GABAA receptors, is composed principally of rho subunits and was initially termed 'GABAC' in recognition of its altered pharmacology []. Despite these differences, rho subunits are generally considered to be part of the GABAAfamily of receptor proteins due to similarities in sequence and topology.Whilst early studies supported the view that rho subunits assembled to forma homopentamer, it has been shown that a mutant rho 1 protein is able tocoassemble with GABAA gamma 2 subunits as well as the glycine receptor alphasubunit. Rho subunit mRNA occurs prominently in both human and ratretina [], each subunit showing a characteristic pattern of spatial expression. In rat retina, rho 1 mRNA has been detected only in bipolarcells, whereas rho 2 transcripts have been detected in both bipolar andganglion cells. In retinal tissues, expression of rho 3 mRNA is exclusive toganglion cells. Reverse transcriptase PCR (RT-PCR) and in situhybridisation have shown rho transcripts also to be present in other regionsof the brain, specifically those involved in visual signal processing, suchas the superior colliculus and visual cortex.This entry represents the GABAA Rho subunits.
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. GABAA receptors can be characterised by their sensitivitytowards a selective antagonist, bicuculline. A GABA receptor has been identified that is insensitive to bicuculline and classical GABAA modulators but has an enhanced affinity for GABA. This receptor, unlike most GABAA receptors, is composed principally of rho subunits and was initially termed 'GABAC' in recognition of its altered pharmacology []. Despite these differences, rho subunitsare generally considered to be part of the GABAAfamily of receptor proteins due to similarities in sequence and topology.Whilst early studies supported the view that rho subunits assembled to forma homopentamer, it has been shown that a mutant rho 1 protein is able tocoassemble with GABAA gamma 2 subunits as well as the glycine receptor alphasubunit. Rho subunit mRNA occurs prominently in both human and ratretina [], each subunit showing a characteristic pattern of spatial expression. In rat retina, rho 1 mRNA has been detected only in bipolarcells, whereas rho 2 transcripts have been detected in both bipolar andganglion cells. In retinal tissues, expression of rho 3 mRNA is exclusive toganglion cells. Reverse transcriptase PCR (RT-PCR) and in situhybridisation have shown rho transcripts also to be present in other regionsof the brain, specifically those involved in visual signal processing, suchas the superior colliculus and visual cortex.This entry represents Rho 1 subunits.
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups []. The term clan can be used 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 rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [, , , , ]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice []. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [].The rhodopsin-like GPCRs (GPCRA) 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 [, , ].Endothelins are able to activate a number of signal transduction processes including phospholipase A2, phospholipase C and phospholipase D, as well as cytosolic protein kinase activation. The play an important role in the regulation of the cardiovascular system [, , ]and are the most potent vasoconstrictors identified, stimulating cardiac contraction, regulating the release of vasoactive substances, and stimulating mitogenesis in blood vessels [, ]. As a result, endothelins are implicated in a number of vascular diseases, including the heart, general circulation and brain [, , ]. Endothelins stimulate the contraction in almost all other smooth muscles (e.g., uterus, bronchus, vas deferens, stomach) and stimulate secretion in several tissues e.g., kidney, liver and adrenals [, , ]. Endothelins have also been implicated in a variety of pathophysiological conditions associated with stress including hypertension, myocardial infarction, subarachnoid haemorrhage and renal failure [].Two endothelin receptor subtypes have been isolated and identified, endothelin A receptor(ETA) and endothelin B receptor (ETB) [, , , ], and are members of the seven transmembrane rhodopsin-like G-protein coupled receptor family (GPCRA) which stimulate multiple effectors via several types of G protein []. ETA and ETB receptors are both widely distributed, ETA receptors are mainly located on vascular smooth muscle cells, whereas ETB receptors are present on endothelial cells lining the vessel wall. Endothelin receptors have also been found in the brain, e.g. cerebral cortex, cerebellum and glial cells [, ]. ETA receptors are considered to be the primary vasoconstrictor and growth-promoting receptor, and the binding of endothelin to ETA increases vasoconstriction (contraction of the blood vessel walls) and the retention of sodium, leading to increased blood pressure []. Endothelin B receptor on the other hand not only inhibits cell growth and vasoconstriction in the vascular system but also functions as a "clearance receptor". This receptor-mediated clearance mechanism is particularly important in the lung, which clears about 80% of circulating endothelin-1 [, ].Both receptors are localised to non-vascular structures such as epithelial cells as well as occurring in the central nervous system (CNS) on glial cells and neurones, where they are thought to mediate neurotransmission and vascular functions [].This entry represents the endothelin A receptor.
The IA3 polypeptide of Saccharomyces cerevisiae (also known as Pai3) is an 8kDa inhibitor of the vacuolar aspartic proteinase (proteinase A or saccharopepsin, MEROPS peptidase family A1). It belongs to MEROPS inhibitor family I34, clan JA. No other aspartic proteinase has been found to be inhibited by IA3, and at least 15 aspartic proteinases related to YprA cleave IA3 as a substrate. Ligand- free IA3 has little intrinsic secondary structure, however, upon contact with proteinase A, residues 2-32 of the inhibitor become ordered and adopt a near perfect α-helical conformation occupying the active site cleft of the enzyme. This potent, specific interaction is directed primarily by hydrophobic interactions made by three key features in the inhibitory sequence [].
This entry represents a sub-group of peptidase C39 homologues in which the proposed protease active site is not conserved. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria []. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions [, ].
This family of bacterial proteins includes DNA processing protein A (DprA) from Streptococcus pneumoniae and Smf, the Bacillus subtilis orthologue. DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation []. In Helicobacter pylori, DprA is required for natural chromosomal and plasmid transformation []. It has now been shown that DprA binds cooperatively to single-stranded DNA (ssDNA) and interacts with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the Escherichia coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier []. DprA has a role not only in ensuring production of transformants via interaction with RecA, it is also involved in competence shut-off via interaction with ComE [].
DNA replication in eukaryotes results from a highly coordinated interaction between proteins, often as part of protein complexes, and the DNA template. One of the key early steps leading to DNA replication is formation of the pre-replication complex, or pre-RC. The pre-RC is formed by the sequential binding of the origin recognition complex (ORC), Cdc6 and Cdt1 proteins, and the MCM complex. Activation of the pre-RC into the initiation complex (IC) is achieved via the action of S-phase kinases, eventually leading to the loading of the replication machinery.Recently, a novel replication complex, GINS (for Go, Ichi, Nii, and San; five, one, two, and three in Japanese), has been identified [, ]. The precise function of GINS is not known. However, genetic and two-hybrid interactions indicate that it mediates the loading of the enzymatic replication machinery at a step after the action of the S-phase kinases []. Furthermore, GINS may be a part of the replication machinery itself, since it is found associated with replicating DNA [, ]. Electron microscopy of GINS shows that it forms a ring-like structure [], reminiscent of the structure of PCNA [], the DNA polymerase delta replication clamp. This observation, coupled with the observed interactions for GINS, indicates that the complex may represent the replication clamp for DNA polymerase epsilon [].The GINS complex is essential for initiation of DNA replication in Xenopus egg extracts []. This 100kDa stable complex includes Sld5, Psf1, Psf2, and Psf3. Homologues of these components are found also in other eukaryotes []. The archaeal GINS complex contains two subunits (SSO0772/gins23 and SO1049/gins15 in Sulfolobus) that are poorly conserved homologues of the eukaryotic GINS subunits []. Only Gins23 is included in this entry.The eukaryotic GINS subunits are homologous. The four subunits of the complex consist of two domains each, termed the α-helical (A) and β-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3 [].
Haemagglutinin (HA) is one of two main surface fusion glycoproteins embedded in the envelope of influenza viruses, the other being neuraminidase (NA). There are sixteen known HA subtypes (H1-H16) and nine NA subtypes (N1-N9), which together are used to classify influenza viruses (e.g. H5N1). The antigenic variations in HA and NA enable the virus to evade host antibodies made to previous influenza strains, accounting for recurrent influenza epidemics []. The HA glycoprotein is present in the viral membrane as a single polypeptide (HA0), which must be cleaved by the host's trypsin-like proteases to produce two peptides (HA1 and HA2) in order for the virus to be infectious. Once HA0 is cleaved, the newly exposed N-terminal of the HA2 peptide then acts to fuse the viral envelope to the cellular membrane of the host cell, which allows the viral negative-stranded RNA to infect the host cell. The type of host protease can influence the infectivity and pathogenicity of the virus.The haemagglutinin glycoprotein is a trimer containing three structurally distinct regions: a globular head consisting of anti-parallel β-sheets that form a β-sandwich with a jelly-roll fold (contains the receptor binding site and the HA1/HA2 cleavage site); a triple-stranded, coiled-coil, α-helical stalk; and a globular foot composed of anti-parallel β-sheets [, ]. Each monomer consists of an intact HA0 polypeptide with the HA1 and HA2 regions linked by disulphide bonds. The N terminus of HA1 provides the central strand in the 5-stranded globular foot, while the rest of the HA1 chain makes its way to the 8-stranded globular head. HA2 provides two alpha helices, which form part of the triple-stranded coiled-coil that stabilises the trimer, its C terminus providing the remaining strands of the 5-stranded globular foot.This entry represents haemagglutinin from influenza virus A. The influenza A HAs can be divided into group 1 encompassing H1, H2, H5, H6, H8, H9, H11, H12, H13, H16, H17, and H18, and group 2 including H3, H4, H7, H10, H14, and H15 subtypes []. This entry also includes HA from Bat-derived influenza-like viruses H17N10 () [].
Quinolinate synthetase catalyses the second step of the de novobiosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid []. This synthesis requires two enzymes, an FAD-containing "B protein"and an "A protein". B protein converts L-aspartate to iminoaspartate. The A protein, NadA, converts iminoaspartate to quinolate. NadA harbours a [4Fe-4S]cluster []. The structure of NadA is composed of three similar domains related by pseudo threefold symmetry. Each domain has three layers (alpha/beta/alpha) with parallel beta sheet.
Peroxisomal acyl-CoA oxidases (ACO) catalyze the first set in the peroxisomal fatty acid beta-oxidation, the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. In a second oxidative half-reaction, the reduced FAD is reoxidized by molecular oxygen. ACO is generally a homodimer. There are several subtypes of AXO's, based on substrate specificity. Palmitoyl-CoA oxidase (ACOX1) acts on straight-chain fatty acids and prostanoids [, ]; whereas, the closely related Trihydroxycoprostanoly-CoA oxidase (ACOX2) has the greatest activity for 2-methyl branched side chains of bile precursors []. Pristanoyl-CoA oxidase (ACOX3), acts on 2-methyl branched fatty acids [, ].
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups []. The term clan can be used 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 rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [, , , , ]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice []. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [].The rhodopsin-like GPCRs (GPCRA) 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 [, , ].Cholecystokinins (CCKs) and gastrins are naturally-occurring peptides that share a common C-terminal sequence, GWMDF; full biological activity resides in this region. In the periphery, the principal physiological actions of CCK include gall bladder contraction, pancreatic enzyme secretion and regulation of secretion/absorption in the gastrointestinal tract. In the CNS, CCK induces analgesia, satiety and a decrease in exploratory behaviour. In mesolimbic andmesocortical neurons, CCK coexists with dopamine. It is found throughout the digestive tract, with high concentrations in the duodenum and jejunum. It is also found in peripheral nerves to other smooth muscles and to secretory glands, and is one of the most abundant peptides in the brain. The highest levels of the CCKA receptor are found in peripheral tissues, notably the pancreas, stomach, intestine and gall bladder. It has only a limited distribution in the brain. The receptor has been implicated in the pathogenesis of schizophrenia, Parkinson's disease, drug addiction and feeding disorders.
Membrane-spanning four-domains subfamily A (MS4A) includes B-cell-specific antigen CD20 (MS4A1), high affinity immunoglobulin epsilon receptor beta chain (MS4A2), hematopoietic-cell-specific protein HTm4 (MS4A3), and related proteins. These proteins share a similar structure with four transmembrane domains and have amino acid identities of 25-40% []. They are predominantly expressed in hematopoietic cells, but some can be found in other tissues including testis and brain [, ].MS4A1 (B-lymphocyte antigen CD20) [], MS4A2 (high affinity IgE receptor subunit beta) [, ], and MS4A4B []have been shown to have an important role in immunity.Several variants within the MS4A gene cluster have been implicated in Alzheimer's disease [].
Membrane-bound lytic murein transglycosylase A is a murein-degrading enzyme. It may play a role in recycling of muropeptides during cell elongation and/or cell division [, ].
UVSSA is part of a UV-induced ubiquitinated protein complex involved in transcription-coupled nucleotide excision repair (TC-NER) in response to UV damage. It stabilise the TC-NER master organizing protein ERCC6 (also known as CSB) by delivering the deubiquitinating enzyme USP7 to TC-NER complexes [].
The tubulin heterodimer consists of one alpha- and one beta-tubulin polypeptide. In humans, five tubulin-specific chaperones termed TBCA/B/C/D/E are essential for bring the alpha- and beta-tubulin subunits together into a tightly associated heterodimer. Following the generation of quasi-native beta- and alpha-tubulin polypeptides (via multiple rounds of ATP-dependent interaction with the cytosolic chaperonin), TBCA and TBCB bind to and stabilise newly synthesised beta- and alpha-tubulin, respectively. The exchange of beta-tubulin between TBCA and TBCD, and of alpha-tubulin between TBCB and TBCE, resulting in the formation of TBCD/beta and TBCE/alpha. These two complexes then interact with each other and form a supercomplex (TBCE/alpha/TBCD/beta). Interaction of the supercomplex with TBCC causes the disassembly of the supercomplex and the release of E-site GDP-bound alpha/beta tubulin heterodimer, which becomes polymerization competent following spontaneous exchange with GTP [].This entry represents tubulin binding cofactor A (TBCA) from animal, plants and fungi. Human TBCA functions as a molecular chaperone for beta-tubulin []. Budding yeast TBCA, also known as Rbl2, may bind transiently to free beta-tubulin, which then passes into an aggregated form that is not toxic []. The sequence identity of Rbl2 and human TBCA is only 32%, they appear to be structurally distinct and may interact with beta-tubulin by different mechanisms [].
Lipoate-protein ligase A catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes [, ]. It is also ableto catalyze very poorly the transfer of lipoyl and octanoyl moiety from their acyl carrier protein [].
This entry represents 1,2-phenylacetyl-CoA epoxidase, subunit A (also known as PaaA). E. coli PaaA and PaaC are components of 1,2-phenylacetyl-CoA epoxidase multicomponent enzyme system which catalyses the reduction of phenylacetyl-CoA (PA-CoA) to form 1,2-epoxyphenylacetyl-CoA. PaaA is the catalytic subunit involved in the incorporation of one atom of molecular oxygen into phenylacetyl-CoA [, ].
Lipopolysaccharide (LPS) in the outer leaflet of the outer membrane (OM) constitutes the major amphiphilic component of the envelope of most Gram-negative bacteria. This entry represents lipopolysaccharide assembly protein A (LapA) from Gammaproteobacteria. LabA and another heat shock protein, LapB, function together in the assembly of lipopolysaccharide (LPS) [].
Alternative ribosome-rescue factor A (arfA) rescues ribosomes stalled at the 3' end of non-stop mRNAs [, ]. It binds the 30S subunit, contacting 16S rRNA with the N terminus near the decoding centre and its C terminus in the mRNA entry channel; contacts change in the presence of release factor 2 (RF2, also named PrfB) [, , , , ].
An operon encoding 4 proteins required for bacterial cellulose biosynthesis(bcs) in Acetobacter xylinus (Gluconacetobacter xylinus) has been isolated via genetic complementationwith strains lacking cellulose synthase activity []. Nucleotide sequence analysis showed the cellulose synthase operon to consist of 4 genes, designated bcsA, bcsB, bcsC and bcsD, all of which are required for maximal bacterial cellulose synthesis in A. xylinum.The calculated molecular mass of the protein encoded by bcsA is 84.4kDa []. Sequence analysis suggests that the gene product is an integral membrane protein with several transmembrane (TM) domains []. It is postulated that the protein is anchored in the membrane at the N-terminal end by a single hydrophobic helix. Two potential N-glycosylation sites are predicted from sequence analysis, consistent with earlier observations that BcsA is a glycoprotein. The function of BcsA is unknown. The sequence shares a high degree of similarity with Escherichia coli YhjO.Cellulose synthase catalyzes the beta-1,4 polymerisation of glucose residues in the formation of cellulose. In bacteria, the substrate is UDP-glucose. The synthase consists of two subunits (or domains in the frequent cases where it is encoded as a single polypeptide), the catalytic domain modelled here and the regulatory domain (). The regulatory domain binds the allosteric activator cyclic di-GMP [, ]. The protein is membrane-associated and probably assembles into multimers such that the individual cellulose strands can self-assemble into multi-strand fibrils.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ].Ribosome-binding factor A [](gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (; topoisomerases II, IV and VI) break double-strand DNA [].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [].Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically [].
Whereas bacterial and archaeal RNasesH2 are active as single polypeptides, the Saccharomyces cerevisiae (Baker's yeast) homologue, Rnh2Ap, when expressed in Escherichia coli, fails to produce an active RNase H2. For RNase H2 activity three proteins are required [Rnh2Ap (Rnh201p), Ydr279p (Rnh202p) and Ylr154p (Rnh203p)]. Deletion of any one of the proteins or mutations in the catalytic site in Rnh2A leads to loss of RNase H2 activity []. RNase H2 is an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. This entry represents the catalytic chain of RNase H2, which is found as a single polypeptide in prokaryotes and is part of a three protein complex in eukaryotes. In Saccharomyces cerevisiae (Baker's yeast) it is represented by .
Escherichia coli, Haemophilus spp and Campylobacter spp. all produce a toxin that is seen to cause distension in certain cell lines [, ], which eventually disintegrate and die. This novel toxin, termed cytolethal distending toxin (cdt), has three subunits: A, B and C. Their sizes are approx. 27.7, 29.5 and 19.9kDa respectively [], and they appear to be entirely novel []. Further research on the complete toxin has revealed that it blocks the cellcycle at stage G2, through inactivation of the cyclin-dependent kinase Cdk1, and without induction of DNA breaks. This leads to multipolar abortive mitosis and micronucleation, associated with centrosomal amplification [].The roles of each subunit are unclear, but it is believed that they haveseparate roles in pathogenicity.This entry represents the A subunit.
A large group of bacterial exotoxins are referred to as "A/B toxins", essentially because they are formed from two subunits []. The "A"subunitpossesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B"subunit [].Bordetella pertussis is the causative agent of whooping cough, and is a Gram-negative aerobic coccus. Its major virulence factor is the pertussis toxin, an A/B exotoxin that mediates both colonisation and toxaemic stagesof the the disease [, ]. Recombinant, inactive forms of the 5 subunits that make up the toxin have proven to be good vaccines.The S1 ("A") subunit of pertussis toxin causes the characteristic sound of the "whoop"in whooping cough. It achieves this through ADP-ribosylation of host Gi alpha-units, an adenylate cyclase inhibitor [, ]. Uninhibited, this enzyme produces elevated levels of cAMP, leading to increased cell exudate and inflammation in the lungs [].The crystal structure of pertussis toxin has been determined to 2.9A resolution []. The catalytic A-subunit (S1) shares structural similarity with other ADP-ribosylating bacterial toxins, although differences in the C-terminal portion explain its unique activation mechanism. Despite itsheterogeneous subunit composition, the structure of the cell-bindingB-oligomer (S2, S3, two copies of S4, and S5) resembles the symmetricalB-pentamers of the cholera and shiga toxin families, but it interactsdifferently with the A-subunit and there is virtually no sequence similarity between B-subunits of the different toxins.
Most bacteria use an enzyme belonging to the phospholipase D family as cardiolipin synthase. In contrast, eukaryotes and most actinobacteria use a cardiolipin synthase of the CDP-alcohol phosphatidyltransferase family [].This entry represents the ClsA sub-subfamily of cardiolipin synthases that belong to the phospholipase D family. These proteins catalyse the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (diphosphatidylglycerol) and glycerol []. Bacillus subtilis has three genes (clsA, ywjE and ywiE) for CL synthase; the main role in CL synthesis being played by clsA [].
Members of this family include FapA (flagellar assembly protein A), , found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction [].
A novel genetic system characterised by six major proteins, included a ParB homologue and a ThiF homologue, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Coenzyme A disulphide reductase () has been characterised in Staphylococcus aureus, Pyrococcus horikoshii, and Borrelia burgdorferi (Lyme disease spirochete), and inferred in several other species on the basis of high levels of CoA and an absence of glutathione as a protective thiol. Coenzyme A disulphide reductase specifically catalyses the NAD(P)H-dependent reduction of coenzyme A disulphide using FAD and NAD(P)H [, , ]. In some species the enzymes show a distinct preference for NADH or NADPH, while others can use either substrate equally well. The reduction of disulphides occurs by a thiol-disulphide exchange reaction, but involves only a single catalytic cysteine residue that forms a stable mixed disulphide with CoA during catalysis. This enzyme contains 2 FAD binding domains and a single NAD(P)H binding domain [].This entryrepresents a distinct subgroup of coenzyme A disulphide reductases, so far found only in Staphylococcus species. These enzymes are specific for NADPH [].
The crystallins are water-soluble structural proteins that occur in high concentration in the cytoplasm of eye lens fibre cells. Four major groups of crystallin have been distinguished on the basis of size, charge and immunological properties: alpha-, beta- and gamma-crystallins occur in all vertebrate classes (though gamma-crystallins are low or absent in avian lenses); and delta-crystallin is found exclusively in reptiles and birds [, ].Alpha-crystallin occurs as large aggregates, comprising two types of related subunits or chains (A and B) that are highly similar to the small (15-30kDa) heat shock proteins (HSPs), particularly in their C-terminal halves. The relationship between these families is one of classic gene duplication and divergence, from the small HSP family, allowing adaptation to novel functions. Divergence probably occurred prior to evolution of the eye lens, alpha-crystallin being found in small amounts in tissues outside the lens [].Alpha-crystallin has chaperone-like properties including the ability to prevent the precipitation of denatured proteins and to increase cellular tolerance to stress []. It has been suggested that these functions are important for the maintenance of lens transparency and the prevention of cataracts. This is supported by the observation that alpha-crystallin mutations show an association with cataract formation.This group represents the A subunit (or chain) of alpha-crystallin.
The E. coli interleukin [IL]receptor mimic protein A (IrmA), is a small (13kDa) Uropathogenic E. coli (UPEC) protein that was originally identified in a large reverse genetic screen as a broadly protective vaccine antigen. It has a fibronectin III (FNIII)-like fold that forms a domain-swapped dimer with structural mimicry to the binding domain of the IL-2 receptor (IL-2R), the IL-4 receptor (IL-4R) and, to a lesser extent, the IL-10 receptor (IL-10R). IrmA binds to all three cytokines, with the greatest affinity observed for IL-4. It is suggested that IrmA may contribute to manipulation of the innate immune response during UPEC infection [].
Rfa3 (also known as RPA14) is a component of the replication protein A (RPA) complex, which binds to and removes secondary structure from ssDNA. The RPA complex is involved in DNA replication, repair, and recombination [].
Rfa1 (also known as RPA70) is a component of the replication protein A (RPA) complex, which binds to and removes secondary structure from ssDNA. The RPA complex is involved in DNA replication, repair, and recombination [].
Rfa2 (also known as RPA32) is a component of the replication protein A (RPA) complex, which binds to and removes secondary structure from ssDNA. The RPA complex is involved in DNA replication, repair, and recombination [].
This entry represents a domain found in lipopolysaccharide assembly protein A (LapA). LabA and LapB function together in the assembly of lipopolysaccharide (LPS) []. This domain is also found in some uncharacterised proteins, such as Rv3760 from Mycobacterium tuberculosis.
Heme A synthase catalyzes the oxidation of the C8 methyl side group on heme O porphyrin ring into a formyl group [].This entry represents the type 2 subfamily, found in some bacteria and eukaryota.
Rab proteins constitute a family of small GTPases that serve a regulatory role in vesicular membrane traffic [, ]; C-terminal geranylgeranylation is crucial for their membrane association and function. This post-translational modification is catalysed by Rab geranylgeranyl transferase (Rab-GGTase), a multi-subunit enzyme that contains a catalytic heterodimer and an accessory component, termed Rab escort protein (REP)-1 [, ]. REP-1 presents newly-synthesised Rab proteins to the catalytic component, and forms a stable complex with the prenylated proteins following the transfer reaction.cDNA cloning of component A of rat Rab geranylgeranyl transferase (REP) confirms its resemblance to Rab3A guanine nucleotide dissociation inhibitor (GDI) and its identity with the human choroideremia gene product []. A genetic defect in REP underlies human choroideremia. Choroideraemia (or tapetochoroidal dystrophy) is a common form of X-linked blindness characterised by progressive dystrophy of the choroid, retinal pigment epithelium and retina [, , ].
Fasciclin-like arabinogalactan proteins (FLAs) proteins from Arabidopsis, a subclass of arabinogalactan proteins (AGPs), can be classified in four groups (A-D) based on pair-wise sequence similarity, domain structure, and phylogenetic analysis []. Group A FLAs are characterised by a single fasciclin domain that is flanked by AGP regions and a C-terminal GPI-anchor signal; group B contain two fasciclin domains flanking an AGP region and lack a C-terminal GPI anchor signal sequence; group C have a variable domain structure with one or two fasciclin domains, one or two AGP regions, and a C-terminal GPI anchor signal; FLAs 4 and 19 to 21 formed group D as they have low similarity to each other or to any of the other FLAs [].This family represents Group A Fasciclin-like arabinogalactan proteins (FLAs) from plants, which includes FLAs 6, 7, 9,11,12 and 13 from Arabidopsis []. They are probably cell surface adhesion proteins.
The regulator of ribonuclease activity A (RraA) family includes a number of closely related sequences from bacteria and plants. The Escherichia coli member has been characterised, and its crystal structure determined []. It acts as a regulator of the endonuclease RNase E [](see ) by binding to it and inhibiting RNA processing [].
This entry represents LmtA from Leptospira. It methylates a phosphate on the Kdo2 sugar of lipid A. Members of this family belong to the broader family of phospholipid methyltransferase , which includes a characterised yeast enzyme that acts on a range of unsaturated phospholipids [].
This entry represents a domain found predominantly at the N terminus of various prokaryotic alpha-glucosyltransferases. According to whether the domain exists as a whole molecule or as a half molecule determines the number of sugar residues that the molecule transfers. Two-domain proteins are processive in that they transfer more than one sugar residue, processively; single domain proteins transfer just one sugar moiety [, ].
This enzyme catalyzes the synthesis of GMP from XMP in the reaction ATP + xanthosine 5'-phosphate + L-glutamine +H(2)O = AMP + diphosphate + GMP + L-glutamate.The enzyme is a heterodimer composed of a glutamine amidotransferase subunit (A) and a GMP-binding subunit and contains 1 glutamine amidotransferase type-1 domain.
Phospholipase A and acyltransferase 4 (PLAAT4, also known as RARRES3, TIG3 , RIG1) exhibits both phospholipase A1/2 and acyltransferase activities [, , , ]. It has been identified as a tumour suppressor [, ]and is a regulator of keratinocyte proliferation and terminal differentiation [, ].
This entry describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product [].
This entry represents the stage IV sporulation protein A (), an ATPase that has a role at an early stage in the morphogenesis of the spore coat and is required for proper coat localisation to the forespore [, , ]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the subset of endospore-forming species. This protein contains an ATPase domain at the N-terminal, a structural middle domain and a C-terminal domain that is key for targeting SpoIVA to the outer forespore membrane [].
This entry includes the A chain of coagulation factor XIII (FXIIIa; ). FXIII is a heterotetramer consisting of two A and two B chains. FXIII is activated by thrombin, and activated FXIII (FXIIIa) covalently cross-links the fibrin chains, making an insoluble clot. Activation of FXIII involves thrombin-induced cleavage of the peptide bond between Arg37 and Gly38 of the A subunit, resulting in the release of an N-terminal activation peptide. In a second step, calcium induces dissociation of the A-subunit dimer from the B subunit. Activated FXIIIa catalyzes the introduction of gamma-glutamyl-epsilon-lysine peptide bonds between fibrin gamma- and alpha-chains. The B subunit serve a carrier function for the A subunit in plasma []. Interestingly, FXIIIa is also present in the cytoplasm of platelets, monocytes, monocyte-derived macrophages, dendritic cells, chondrocytes, osteoblasts, and osteocytes. It may be invovled in wound healing process and maintaining pregnancy [].
Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS moleculesare variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A []. The polysaccharide component consists of a variable repeat-structure polysaccharideknown as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS []. The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids []. These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units.The bacterial lipid A biosynthesis protein, or lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase , transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA during lipopolysaccharide core biosynthesis [].
This entry represents subunit A, one of the three subunits of the anaerobic sulphite reductase of Salmonella, and close homologues from various Clostridium species, where the three-gene neighbourhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substrates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulphite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulphide gas from sulphite.
This entry represents lactate utilization protein A, which is involved in L-lactate degradation and allows cells to grow with lactate as the sole carbon source.
Members of this family closely resemble quinoproteins and quinohemoproteins such as PQQ-dependent methanol, glucose, and shikimate dehydrogenases, but restricted to species of Acidobacteria unable to synthesize PQQ. Seven members occur in Candidatus Solibacter usitatus Ellin6076, eleven in Acidobacteriaceae bacterium KBS 96, etc. Members have N-terminal signal sequences. They lack the pair of adjacent Cys residues, involved in electron transfer, typical for family , and they lack CxxCH motifs for cytochrome c-like heme-binding. What cofactor these paralogous families of enzymes might use is unclear.
This family of proteins is regulated by the ferric uptake regulator protein Fur []. This family does not regulate the lutABC operon encoding iron sulfur-containing enzymes necessary for growth on lactate [].
This entry represents glyoxysomal malate synthases and one of two bacterial forms, designated malate synthase A.Malate synthase and isocitrate lyase are the two characteristic enzymes of the glyoxylate cycle. The glyoxylate cycle allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle []. Isocitrate lyase, first catalyzes the aldol cleavage of isocitrate to succinate (an intermediate of the tricarboxylic acid cycle) and glyoxylate. Then malate synthase catalyzes the condensation of acetyl CoA with glyoxylate to yield malate (another intermediate of the tricarboxylic acid cycle) [].
This entry represents Spo11, a meiotic recombination protein found in eukaryotes, and subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, , , ]. These two types of proteins share structural homology.DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination [].
Coenzyme A (CoA) transferases belong to an evolutionary conserved [, ]family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. They have been identified in many prokaryotes and in mammalian tissues. The bacterial enzymes are heterodimers of two subunits (A and B) of about 25 Kd each while eukaryotic SCOT consists of a single chain which is colinear with the two bacterial subunits. This signature corresponds to a region in the N terminus of the B subunit which contains a glutamate that is involved in the catalytic mechanism.
Coenzyme A (CoA) transferases belong to an evolutionary conserved [, ]family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. They have been identified in many prokaryotes and in mammalian tissues. The bacterial enzymes are heterodimer of two subunits (A and B) of about 25 Kd each while eukaryotic SCOT consist of a single chain which is colinear with the two bacterial subunits. This entry corresponds to a region in the N-terminal of the A subunit that may be implicated in the binding of CoA to the enzyme.
The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB []. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs [].
This family consists of several bacterial Na+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na+-translocating NADH: ubiquinone oxidoreductase (Na+-NQR) generates an electrochemical Na+potential driven by aerobic respiration [].
NS1 is a homodimeric RNA-binding protein found in influenza virus that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA [].
Heme A synthase catalyzes the oxidation of the C8 methyl side group on heme O porphyrin ring into a formyl group [].The type 1 subfamily of this enzyme is found in Gram-positive bacteria. Bacillus subtilis CatA is involved in sporulation [].
This domain is found in Legionella ubiquitin-specific protease A (LupA). LupA removes a ubiquitin modification from LegC3 which inactivates the cognate effector. This domain is typical of eukaryotic ubiquitin proteases involved in deconjugation of ubiquitin or ubiquitin-like proteins from their targets [].
DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (; topoisomerases II, IV and VI) break double-strand DNA [].Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [].This entry represents subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea, but also in a few eukayotes, such as the plant Arabidopsis thaliana []. This enzyme assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein that mediates double-strand DNA breaks during meiotic recombination in eukaryotes []. The core of subunit A is a dimer, with a deep groove in which the DNA molecule is thought to bind, with the monomers separating during DNA transport. Therefore, though related to type IIA topoisomerases, topoisomerase VI may have a distinctive mechanism of action.
The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of α-helices and β-strands []. The vWF domain fold is predicted to be a doubly-wound, open, twisted β-sheet flanked by α-helices []. 3D structures have been determined for the I-domains of integrins alpha-M (CD11b; with bound magnesium) []and alpha-L (CD11a; with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11band CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. Identification and characterisation of the theta subunit was first reportedin 1999 []. Cloning of the full-length cDNA was performed using a humanwhole-brain library, yielding a deduced open reading frame of 627 aminoacids. This polypeptide was found to be most similar to the beta 1 subunitwith regard to sequence identity, and was able to co-assemble with alpha 2,beta 1 and gamma 1 subunits, yielding heteromeric assemblies with a 4-foldincrease in sensitivity towards GABA. Furthermore, theta mRNA was found to have a unique spatial distribution, with significant expression withinmonoaminergic neurons of both human and monkey brain.
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. A cDNA encoding the human GABAA receptor beta 2 subunit has been cloned andsequenced []. Expression of recombinant human GABAA receptors containingdifferent beta subunits (beta 1, beta 2 or beta 3) in both transfectedcells and Xenopus laevis oocytes, has revealed the influence of the beta subunit onthe pharmacology of the receptor. For a number of benzodiazepine bindingsite compounds, a barbiturate, and several neurosteroids, neither theaffinity nor the efficacy of the compounds is influenced by the type ofbeta subunit present in the receptor molecule []. These observationssuggest that the beta subunit does not significantly influence thebenzodiazepine, barbiturate, or steroid site pharmacologies of human GABAAreceptor subtypes [].
This is the first domain in Tp47, an unusual penicillin-binding protein (PBP) from Treponema pallidum. It is mainly composed of β-strands and is sequentially non-contiguous. The first three domains in Tp47 interact with each other through intimate domain-domain interfaces. Domain A contacts domain B through its N-terminal segment. Domain A also interacts tightly with domain C. Tp47 is unusual in that it displays beta-lactamase activity, and thus it does not fit the classical structural and mechanistic paradigms for PBPs. Tp47 appears to represent a new class of PBP [].
The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, butthe majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. ) and Drosophila melanogaster (Fruit fly) Cinnamon () [].This entry represents the MoaA protein (molybdenum cofactor biosynthesis protein A), also known as cyclic pyranopterin monophosphate synthase or GTP 3',8-cyclase. MoaA is a member of the wider S-adenosylmethionine(SAM)-dependent enzyme family which catalyze the formation of protein and/or substrate radicals by reductive cleavage of SAM via a [4Fe-4S]cluster. Monomeric and homodimeric forms of MoaA have been observed in vivo, and it is not clear what the physiologically relevant form of the enzyme is []. The core of each monomer consists of an incomplete TIM barrel, formed by the N-terminal region of the protein, containing a [4Fe-4S]cluster. The C-terminal region of the protein, which also contains a [4Fe-4S]cluster consists of a β-sheet covering the lateral opening of the barrel, an extended loop and three α-helices. The N-terminal [4Fe-4S]cluster is coordinated with 3 cysteines and an exchangeable SAM molecule, while the C-terminal [4Fe-4S], also coordinated with 3 cysteines, is the binding and activation site for GTP [].
This entry represents complement C1q subcomponent subunit A. C1q is a complex of nine proteins, six are disulfide-linked dimers of the A and B chains, and three are disulfide-linked dimers of the C chain []. C1q combines with C1r and C1s to form the first complement in the complement activation cascade, C1. C1qA contains an N-terminal collagen-like domain and a C-terminal C1q domain []. Complexes with C1r and C1s are formed via the collagen-like domain, whereas the C1q-like domain provides the means of interaction with C-reactive protein and IgG []. Deficiency of C1qA is associated with subacute cutaneous lupus erythematosus [].
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Serotonin (5-hydroxytryptamine, 5-HT) is widely distributed in both the central and peripheral nervous system, where it acts as a neurotransmitterand neuromodulator []. It has been implicated in several aspects of brain function, including regulation of affective states, ingestive behavior and addiction. 5-HT can activate a number of different receptor subtypes that produce diverse neuronal responses, principally through activation of G-protein-mediated signalling pathways. Signalling through the 5-HT3 receptor (5-HT3R) differs, since this subtype belongs to the ligand-gated ion channel (LGIC) superfamily, which also includes the inhibitory gamma-aminobutyric acid type A and glycine receptors, and excitatory nicotinic acetylcholine receptors (nAChR) []. 5-HT3 receptor function has been implicated in a variety of neural processes, including pain perception, emesis, anxiety and drug abuse.Like the other members of the LGIC superfamily, the 5HT3R exhibits a high degree of sequence similarity, and therefore putative structural similarity, with nAChRs []. Thus, functional 5HT3Rs comprise a pentamer: the ion channel is formed at the centre of a rosette formed between five homologous subunits. Two classes of 5-HT3R subunit are currently known, termed 5-HT3A and 5-HT3B. Whilst homomeric pentamers of 5-HT3A form functional receptors, heteromeric assemblies display channel conductances, cation permeabilities and current-voltage relationships typical of characterised neuronal 5-HT3 channels [].The proposed topology of 5-HT3R subunits comprises four putative transmembrane (TM) domains (designated M1-4); a large extracellular N-terminal region (~200 amino acids); and a variable cytoplasmic loop between M3 and M4. The M2 domains from each subunit are thought to form the channel pore. The agonist binding site is formed by the N terminus, which, on binding, induces a conformational change in the channel pore, a process often referred to as "gating"[]. Opening of the pore allows cation flux through the neuronal membrane and depolarises the membrane potential. Thus, 5-HT3Rs may be thought of as excitatory receptors [].Cloning of the 5-HT3A subunit from a neuroblastoma expression library wasreported in 1991 []. Whilst recombinant expression of 5-HT3A yieldsfunctional receptors, the channel conductance and permeability to cationsare different from that observed for native receptors []. Alternative exonsplicing gives rise to two isoforms of 5-HT3A, termed 5-HT3AS and 5-HT3ALfor short and long variants, respectively. The 5-HT3RA subunit is widelyexpressed throughout the peripheral and central nervous systems, includingseveral regions of the brain.
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes withinsome classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. The existence of a pi subunit was first reported in 1997, where it wasdetected in a number of human and rat tissues. The subunit shares 30-40%amino acid identity with other members of the GABAA receptor subunit family.The polypeptide is found in several peripheral tissues, including theuterus, where its function appears to be related to tissue contractility: pisubunits can co-assemble with other GABAA receptor subunits to formrecombinant receptors with altered sensitivity to pregnenalone [].
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. Alpha subunitslargely determine benzodiazepine binding properties []. Mutagenesis and agonist/antagonist binding studies have suggested a close functional and structural association of alpha-subunits with the agonist/antagonist binding site, and involvement of N-terminal portions of the extracellular domains of all subunits in the gating of the channel [].
GOLGA3 (Golgin160, Mea2) is a Golgi complex-associated protein that has been implicated in spermatogenesis [, ], as well as in apoptosis [, ], trafficking [], and positioning of the Golgi [].
Cucumoviruses are tripartite RNA plant viruses believed to share a closeevolutionary relationship with Brome mosaic virus (BMV). The cucumoviruses include: Cucumber mosaic virus [], Peanut stunt virus []and Tomato aspermy virus []. The viral coat proteins show a high degree of sequencesimilarity [].The core structure of cucumber mosaic virus (CMV) and chlorotic mottle virus (CCMV), both members of the Bromoviridae family, are highly homologous. In CCMV, the structures of the A, B, and C subunits are nearly identical except in their N termini. In contrast, the structures of two loops in subunit A of CMV differ from those in B and C []. This entry represents the structural domain of subunit A of the cucumber mosaic virus and other cucumovirusus [].
Haemolysins are exotoxins that attack blood cell membranes and cause cell rupture. The mechanism of action is not well defined. Haemolysin A is induced by sodium ribonucleate, and is produced by pathogenic bacterial strains. Haemolysin A from Treponema hyodysenteriae causes swine dysentery []. The homologous protein from Mycobacterium tuberculosis is known as 16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA and exhibits hemolytic activity in vitro. It catalyses the 2'-O-methylation at nucleotides C1409 in 16S rRNA and C1920 in 23S rRNA [, , ].
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. The epsilon subunit was first identified in 1997. Northern blot analysis of several humanbrain tissues showed that epsilon transcripts were relatively enriched inamygdala and thalamus, compared to whole brain, and particularly abundant inthe subthalmic nucleus. Heteromeric recombinant receptors containing theepsilon subunit in place of the more usual gamma subunit were found to be insenstitive to the potentiating effects ofanaesthetic agents [].
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. Delta cDNA was first reported in rat, mouse and humans []. Delta mRNAwas found to be present in regions of the brain that were low in gamma 2, and insensitivity towards "classical"BZs was observed in receptorscontaining the delta subunit. Furthermore, delta subunits are thought to preferentially pair with the alpha 6 polypeptides over other subtypes, and are often found in place of gamma subunits.
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups []. The term clan can be used 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 rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [, , , , ]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice []. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [].GPCR Fungal pheromone mating factor receptors form a distinct family of G-protein-coupled receptors, and are also known as Class D GPCRs.The Fungal pheromone mating factor receptors STE2 and STE3 are integral membrane proteins that may be involved in the response to mating factors on the cell membrane [, , ]. The amino acid sequences of both receptors contain high proportions of hydrophobic residues grouped into 7 domains,in a manner reminiscent of the rhodopsins and other receptors believed tointeract with G-proteins. However, while a similar 3D framework has been proposed to account for this, there is no significant sequence similarity either between STE2 and STE3, or between these and the rhodopsin-type family: the receptors thereofore bear their own unique '7TM' signatures which is why they have been given their own GPCR group: Class D Fungal mating pheromone receptors.The STE3 gene in Saccharomyces cerevisiae is the cell-surface receptor that binds the13-residue lipopeptide a-factor. Several related fungal pheromone receptorsequences are known: these include pheromone B alpha 1 and B alpha 3, andpheromone B beta 1 receptors from Schizophyllum commune; pheromone receptor1 from Ustilago hordei; and pheromone receptors 1 and 2 from Ustilago maydis.Members of the family share about 20% sequence identity.U. maydis, a tetrapolar fungal species, has two genetically unlinkedloci that encode the distinct mating functions of cell fusion (the a locus)and subsequent sexual development and pathogenicity (the b locus) [].The a locus exists in two alleles, the mating type in each of which isdetermined by a set of two genes; one encodes a precursor for a lipopeptidemating factor, while the other specifies the receptor for the pheromonesecreted by cells of opposite mating type []. U. maydis thus employs anovel strategy to determine its mating type by providing the primarydeterminants of cell-cell recognition directly from the mating type locus[]. The bipolar species, U. hordei, contains both a and b loci;physical linkage of these loci in this bipolar fungus accounts for itsdistinct mating system [].This entry represents mating-type a receptors.
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases,which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane []. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [, ].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins [].This entry represents subunit A from the V1 complex of V-ATPases. There are three copies each of subunits A and B (), both of which participate in nucleotide binding. However, only subunit A is catalytic, functioning in ATP hydrolysis to drive the rotation of the D and F subunits of V1, as well as the V0 complex c-ring rotor subunit for proton translocation [, ].
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include:F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane []. They are also found in bacteria [].A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [, ].P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.P-ATPases (also known as E1-E2 ATPases) ([intenz:3.6.3.-]) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.This superfamily represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [, ].
Coenzyme A (CoA) transferases belong to an evolutionary conserved [, ]family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. They have been identified in many prokaryotes and in mammalian tissues. The bacterial enzymes are heterodimer of two subunits (A and B) of about 25 Kd each while eukaryotic SCOT consist of a single chain which is colinear with the two bacterial subunits.CoA-transferases are found in organisms from all kingdoms of life. They catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids. There are at least three families of CoA-transferases, which differ in sequence and reaction mechanism:Family I consists of CoA-transferases for 3-oxoacids (, ), short-chain fatty acids (, ) and glutaconate (). Most use succinyl-CoA or acetyl-CoA as CoA donors.Family II consists of the homodimeric alpha-subunits of citrate lyase and citramalate lyase (, ). These enzymes catalyse the transfer of acyl carrier protein (ACP) with a covalently bound CoA derivative, but can accept free CoA thioesters as well.Family III consists of formyl-CoA:oxalate CoA-transferase [], succinyl-CoA:(R)-benzylsuccinate CoA-transferase [], (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase [], succinyl-CoA:mesaconate CoA-transferase []and butyrobetainyl-CoA:(R)-carnitine CoA-transferase []. These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate- and stereo-specific manner [].This family consists of 3-oxoacid CoA-transferases and related CoA-transferases from family I.
The tubulin heterodimer consists of one alpha- and one beta-tubulin polypeptide. In humans, five tubulin-specific chaperones termed TBCA/B/C/D/E are essential for bring the alpha- and beta-tubulin subunits together into a tightly associated heterodimer. Following the generation of quasi-native beta- and alpha-tubulin polypeptides (via multiple rounds of ATP-dependent interaction with the cytosolic chaperonin), TBCA and TBCB bind to and stabilise newly synthesised beta- and alpha-tubulin, respectively. The exchange of beta-tubulin between TBCA and TBCD, and of alpha-tubulin between TBCB and TBCE, resulting in the formation of TBCD/beta and TBCE/alpha. These two complexes then interact with each other and form a supercomplex (TBCE/alpha/TBCD/beta). Interaction of the supercomplex with TBCC causes the disassembly of the supercomplex and the release of E-site GDP-bound alpha/beta tubulin heterodimer, which becomes polymerization competent following spontaneous exchange with GTP [].This entry represents tubulin binding cofactor A (TBCA) from animal, plants and fungi. Human TBCA functions as a molecular chaperone for beta-tubulin []. Budding yeast TBCA, also known as Rbl2, may bind transiently to free beta-tubulin, which then passes into an aggregated form that is not toxic []. The sequence identity of Rbl2 and human TBCA is only 32%, they appear to be structurally distinct and may interact with beta-tubulin by different mechanisms []. The structure of TBCA has three helices forming a bundle closed fold with left-handed twist topology going up-and-down.
This group includes nucleic acid independent RNA polymerases, such as polynucleotide adenylyltransferase (), which adds the poly (A) tail to mRNA. This group also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA ().CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)]., one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction [, ]. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase [], Escherichia coli poly(A) polymerase I [, ], human mitochondrial CCAase [, ], and Saccharomyces cerevisiae CCAase (CCA1) [, , ]. CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates [, ]. This family belongs to the Pol beta-like NT superfamily [, ]. Escherichia coli CCAase is related to this group but has not been included in this alignment as this enzyme lacks the N-terminal helix conserved in the remainder of the NT superfamily.In the Pol beta-like NT superfamily [, ], the majority of enzymes have two carboxylates, Dx[D/E], together with a third more distal carboxylate, which coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are fairly well conserved in this family.
Hydroxymethylglutaryl-CoA synthase () catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA [].HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria []. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [, ].This entry represents the sequence surrounding the catalytic cysteine required for nucleophilic attack in the first step of the reaction, the acetylation of the enzyme by acetyl-CoA.
Hydroxymethylglutaryl-CoA synthase () catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA [].HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria []. In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi []. In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes [, ].This entry represents the C-terminal domain of HMG-CoA synthase enzymes from both eukaryotes and prokaryotes.
PB1-F2 is a protein found in almost all known strains of Influenza A virus - a negative sense ssRNA Orthomyxovirus []. It originates from translation of the viral polymerase gene in an alternative reading frame []. PB1-F2 consists of two independent structural domains, two closely neighbouring short helices at the N terminus, and an extended C-terminal helix []. Although the protein has originally been described to induce apoptosis, it has now been shown that PB1-F2 more likely acts as an apoptosis promoter in concert with other apoptosis-inducing agents []. PB1-F2 promotes apoptosis by localising to the mitochondria where it destabilises the membrane. This will cause release of cytochrome C which activates the caspase cascade of apoptosis through the endogenous pathway []. In this way it acts like the Bcl-2 protein family which are physiological apoptotic regulators in cells [].
This domain is found in Propionyl-coenzyme A carboxylase (PCC), present in Roseobacter denitrificans. PCC is a mitochondrial biotin-dependent enzyme that is essential for the catabolism of certain amino acids, cholesterol, and fatty acids with an odd number of carbon atoms. Since this domain mediates biotin carboxylase-carboxyltransferase interactions it is referred to as the BT domain. The BT domain is located between biotin carboxylase and the biotin carboxyl carrier protein domains. The BT domain shares some structural similarity with the pyruvate carboxylase tetramerization domain of pyruvate carboxylase [].
This group of serine peptidases belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). The protein fold of the peptidase domain for members of this family resembles that of D-Ala-D-Ala-carboxypeptidase B, the type example for clan SE.Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endo-peptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S27) of serine protease have been identified, these being grouped into 6 clans (SA, SB, SC, SE, SF and SG) on the basis of structural similarity and other functional evidence. Structures are known for four of the clans (SA, SB, SC and SE): these appear to be totally unrelated, suggesting at least four evolutionary origins of serine peptidases and possibly many more [].Not with standing their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C clans have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (SA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].Bacterial cell walls are complex structures containing amino acids and amino sugars, with alternating chains of N-acetylglucosamine and N-acetyl-muramic acid units linked by short peptides []: the link peptide in Escherichia coli is L-alanyl-D-isoglutamyl-L-meso-diaminopimelyl-D-alanine. The chains are usually cross-linked between the carboxyl of D-alanine and the free amino group of diaminopimelate. During the synthesis of peptidoglycan, the precursor has the described tetramer sequence with an added C-terminal D-alanine [].D-Ala-D-Ala carboxypeptidase A is involved in the metabolism of cell components []; it is synthesised with a leader peptide to target it to the cell membrane []. After cleavage of the leader peptide, the enzyme is retained in the membrane by a C-terminal anchor. There are three families of serine-type D-Ala-D-Ala peptidase, which are also known as low molecular weight penicillin-binding proteins.Family S11 contains only D-Ala-D-Ala peptidases, unlike families S12 and S13, which contain other enzymes, such as class C beta-lactamases and D-amino-peptidases []. Although these enzymes are serine proteases, some members of family S11 are partially inhibited by thiol-blocking agents [].
