In Escherichia coli the TonB protein interacts with outer membrane receptor proteins that carry out high-affinity binding and energy-dependent uptake of specific substrates into the periplasmic space [
]. These substrates are either poorly permeable through the porin channels or are encountered at very low concentrations. In the absence of TonB, these receptors bind their substrates but do not carry out active transport. TonB-dependent regulatory systems consist of six components: a specialised outer membrane-localized TonB-dependent receptor (TonB-dependent transducer) that interacts with its energizing TonB-ExbBD protein complex, a cytoplasmic membrane-localized anti-sigma factor and an extracytoplasmic function (ECF)-subfamily sigma factor [
]. The TonB complex senses signals from outside the bacterial cell and transmits them via two membranes into the cytoplasm, leading to transcriptional activation of target genes. The proteins that are currently known or presumed to interact with TonB include BtuB [], CirA, FatA, FcuT, FecA [], FhuA [], FhuE, FepA [], FptA, HemR, IrgA, IutA, PfeA, PupA and Tbp1. The TonB protein also interacts with some colicins. Most of these proteins contain a short conserved region at their N terminus [].This entry represents the plug domain, which has been shown to be an independently folding subunit of the TonB-dependent receptors [
]. It acts as the channel gate, blocking the pore until the channel is bound by a ligand. At this point it undergoes conformational changes and opens the channel.
Teneurins are a family of phylogenetically conserved transmembrane glycoproteins expressed during pattern formation and morphogenesis [
]. Originally discovered as ten-m and ten-a in Drosophila melanogaster, the teneurin family is conserved from Caenorhabditis elegans (ten-1) to vertebrates, in which four paralogs exist (teneurin-1 to -4 or odz-1 to -4). Their distinct domain architecture is highly conserved between invertebrate and vertebrate teneurins, particularly in the extracellular part. The intracellular domains of Ten-a, Ten-m/Odz and C. elegans Ten-1 are significantly different, both in size and structure, from the comparable domains of vertebrate teneurins, but the extracellular domains of all of these proteins are remarkably similar.The large C-terminal extracellular domain consists of eight EGF-like repeats (see
), a region of conserved cysteines and unique YD-repeats. The N-terminal intracellular domain of vertebrate teneurins contains two EF-hand-like calcium-binding motifs and two polyproline regions involved in protein-protein interactions, followed by a single-span transmembrane domain. The intracellular domain is linked to the cytoskeleton through its interaction with the adaptor protein CAP/ponsin and can be cleaved near (or possibly in) the transmembrane domain and transported to the nucleus [
,
], giving teneurins the potential to act as transcription factors ,
]. There is considerable divergence between intracellular domains of invertebrate and vertebrate teneurins as well as between different invertebrate proteins [,
,
,
,
].This domain is found in the intracellular N-terminal region of the Teneurin family.
This entry includes the C2HC RNF-type zinc finger.Ubiquitination is a post-translational modification that mediates the covalent attachment of ubiquitin (Ub), a small, highly conserved, cytoplasmic protein of 76 amino acid residues, to target proteins. This conjugation is catalyzed by the sequential action of three enzymes: Ub-activating (E1) enzyme, Ub-conjugating (E2) enzyme and Ub ligase (E3). A large number of RING finger (RNF) proteins are present in eukaryotic cells and the majority of them are believed to act as E3 ubiquitin ligases. The closely related proteins RNF125/TRAC-1, RNF114 (also known as Zpf313), RNF138 (or NARF) and RNF166 contain, apart from the RING domain, a C2HC (Cys2-His-Cys)- and two C2H2 (Cys2-His2)-type zinc fingers, as well as an ubiquitin interacting motif (UIM) [
,
,
,
].Some proteins known to contain a C2HC RNF-type zinc finger are listed below:
Mammalian RNF125/T-cell RING protein in activation 1 (TRAC-1)/, a positive regulator of T-cell activation. It negatively regulates RIG-1 mediated antiviral activity via conjugating ubiquitin chains to RIG-1 and MDA5, leading to their degradation by the proteasome.Vertebrate RNF114, acts as negative regulator of NF-kappaB-dependent transcription. It interacts with A20 in T cells and modulates A20 ubiquitylation.Vertebrate RNF138, likely involved in regulating homologous recombination repair pathway.Vertebrate RNF166, potentiates the RNA virus-induced production of IFN-beta via enhancing the ubiquitination of TRAF3 and TRAF6.
Co-chaperones are helper interacting proteins that modulate the chaperone cycle, being involved in substrate specificity and stimulation of chaperone activity of HSP90/70 and include other heat shock proteins, TPR containing proteins, cyclophilins and others. The TPR containing proteins possess an N-terminal TPR domain, which are more closely related to each other than to TPR domains from other proteins with different functionality [
,
], which is involved in HSP90/70 direct interaction. The first N-terminal residues prior to the TRP domain and the C-terminal domain are involved and important for domain interplay and stabilisation of its interactions []. The Hsp90 chaperone machinery in eukaryotes comprises a number of distinct accessory factors, among them TTC4 from human and its homologues Cns1 from yeast and Dpit47 from Drosophila, structurally and functionally conserved from yeast to human. Cns1 is one of the few essential co-chaperones in yeast, important for maintaining translation elongation, specifically chaperoning the elongation factor eEF2. Cns1 interacts with Hgh1 and forms a quaternary complex together with eEF2 and Hsp90 mediating the proper folding and solubility of eEF2. Recently, the C-terminal structure has been solved and is called the "wheel"domain according to its 2D projection. It shows an overall fold consisting of a twisted five-stranded beta sheet surrounded by several alpha helices [
].This entry represents the wheel domain found at the C terminus of yeast Cns1, human TTC4 and Drosophila Dpit47 proteins.
Crossover junction endodeoxyribonuclease RuvC, magnesium-binding site
Type:
Binding_site
Description:
The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination [
]. RuvC protein () cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures
in vivo[
]. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer α-β sandwich containing a 5-stranded β-sheet sandwiched between 5 α-helices [
].This signature pattern covers a region located in the C-terminal part of RuvC that contains two aspartate residues implicated in the binding of a magnesium ion required for function.
This superfamily represents the C-terminal domain of the eukaryotic translation initiation factor (eIF-2B) and are found in initiation factor 2B alpha, beta and delta subunits from eukaryotes; related proteins from archaebacteria and IF-2 from prokaryotes in addition to a subfamily of proteins in eukaryotes, archaea, or eubacteria.Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. The eukaryotic translation initiation factor EIF-2B is a complex made up of five different subunits, alpha, beta, gamma, delta and epsilon, and catalyses the exchange of EIF-2-bound GDP for GTP. This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes; related proteins from archaebacteria and IF-2 from prokaryotes and also contains a subfamily of proteins in eukaryotes, archaeae (e.g. Pyrococcus furiosus), or eubacteria such as Bacillus subtilis and Thermotoga maritima. Many of these proteins were initially annotated as putative translation initiation factors despite the fact that there is no evidence for the requirement of an IF2 recycling factor in prokaryotic translation initiation. Recently, one of these proteins from B. subtilis has been functionally characterised as a 5-methylthioribose-1-phosphate isomerase (MTNA) [
]. This enzyme participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthioribulose-1-phosphate []. The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species.
Secretion of virulence factors in Gram-negative bacteria involves
transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in
animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia.
The type III secretion system is of great interest as it is used to
transport virulence factors from the pathogen directly into the host cell [
] and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis []. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part ofthe flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.One of the outer membrane protein subunit families, termed "O"here for
nomenclature purposes, aids in the structural assembly of the invasion complex [
]. It is essential for the secretion of the Sip toxins in Salmonella and Shigella (SspaO gene). Members of this family also include YscQ protein (Yersinia), and the plant enteropathogen gene Y4YK
(Rhizobium). The flagellar protein FliN also shares partial similarity, probably due to evolution of the type III secretion system from the
flagellar biosynthetic pathway.
The Orange domain is a motif of ~35 amino acids present in eukaryotic
DNA-binding transcription repressors, which regulate cell differentiation,embryonic patterning and other biological processes in both vertebrates and
invertebrates. The Orange domain is located just C-terminal to a basichelix-loop-helix (bHLH) domain in the bHLH-Orange (bHLH-O) proteins. This
family of bHLH repressors is related to the Drosophila hairy andEnhancer-of-split proteins, wherein the Orange domain was first described and
also named helix III/IV region [,
]. The transcription of many vertebrate bHLH-O genes is regulated by the Notch signaling pathway, which controls fate decisions and other developmental processes. Orange domain proteins function as transcription repressors involved in the regulation of differentiation, anteroposterior segmentation and sex determination in flies [].Four subfamilies of bHLH-Orange proteins have been identified, i.e. hairy,
Enhancer of split, Hey (also named HRT or Hesr) and Stra13 (also named SHARP,DEC, CLAST or BHLHB2) [
,
]. All these Orange domain proteins have the bHLH domain and except for the Stra13 subfamily, the othersubfamily members have a conserved tetrapeptide motif in the C-terminal
extremity. The C-terminal motif of the hairy and Enhancer of split proteins isWRPW and this binds the transcriptional corepressor groucho/TLE. For the Hey
subfamily members the C-terminal motif is YXXW. The Orange domain may conferspecificity of function to different family members and/or it may be involved
in dimerization [,
].
In Escherichia coli the TonB protein interacts with outer membrane receptor proteins that carry out high-affinity binding and energy-dependent uptake of specific substrates into the periplasmic space [
]. These substrates are either poorly permeable through the porin channels or are encountered at very low concentrations. In the absence of TonB, these receptors bind their substrates but do not carry out active transport. TonB-dependent regulatory systems consist of six components: a specialised outer membrane-localized TonB-dependent receptor (TonB-dependent transducer) that interacts with its energizing TonB-ExbBD protein complex, a cytoplasmic membrane-localized anti-sigma factor and an extracytoplasmic function (ECF)-subfamily sigma factor []. The TonB complex senses signals from outside the bacterial cell and transmits them via two membranes into the cytoplasm, leading to transcriptional activation of target genes. The proteins that are currently known or presumed to interact with TonB include BtuB [], CirA, FatA, FcuT, FecA [], FhuA [], FhuE, FepA [], FptA, HemR, IrgA, IutA, PfeA, PupA and Tbp1. The TonB protein also interacts with some colicins. Most of these proteins contain a short conserved region at their N terminus [].This entry represents the plug domain superfamily, which has been shown to be an independently folding subunit of the TonB-dependent receptors [
]. It acts as the channel gate, blocking the pore until the channel is bound by a ligand. At this point it undergoes conformational changes and opens the channel.
This entry represents a domain superfamily found in Bacteriophage T4, Gp12. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.This region is occasionally found in conjunction with
. Most of the proteins appear to be phage tail proteins; however some appear to be involved in other processes. For instance the RhiB protein (
) from Rhizobium leguminosarum may be involved in plant-microbe interactions [
]. A related protein, microcystin related protein (MrpB, ) is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (
) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop [
] and three β-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the collar and may bind SO
4. The long unconserved region maybe due to domain swapping in and out of a loop or due to rapid evolution.
The egg peptide speract receptor is a transmembrane glycoprotein of about
500 amino acids []. Topologically, it comprises a large extracellulardomain of about 450 residues, followed by a transmembrane domain and a
short cytoplasmic region of about 12 amino acids. The extracellulardomain contains 4 repeats of a well-conserved region, which spans 115
amino acids and contains 6 conserved cysteines. A similar domain is alsofound towards the C terminus of macrophage scavenger receptor type I [
],a membrane glycoprotein implicated in the pathologic deposition of
cholesterol in arterial walls during artherogenesis, and in the CD5glycoprotein, which acts as a receptor in regulating T-cell proliferation.
The T1/Leu-1/CD5 glycoprotein is expressed at the surface membrane of all
mature T cells. It has been implicated both in the proliferative response of activated T cells and in T-cell helper function [
]. Thecomplete amino-acid sequence of the T1 precursor has been deduced from cDNA
clones. The protein contains a classical signal peptide; a 347-residue extracellular segment; a transmembrane region; and a 93-residue intra-
cellular segment []. The extracellular region contains several cysteineresidues and comprises 2 speract receptor domains separated by a proline/
threonine-rich region []. CD5 has been shown to function as a receptor,delivering co-stimulatory signals to T-cells, interacting specifically with
the cell-surface protein CD72 (Lyb-2 in mice) exclusive to B-cells [].
It is thought that NAPs act as histone chaperones, shuttling both core and linker histones from their site of synthesis in the cytoplasm to the nucleus. The proteins may be involved in regulating gene expression and therefore cellular differentiation [
,
].The centrosomal protein c-Nap1, also known as Cep250, has been implicated in the cell-cycle-regulated cohesion of microtubule-organizing centres. This 281kDa protein consists mainly of domains predicted to form coiled coil structures. The C-terminal region defines a novel histone-binding domain that is responsible for targeting CNAP1, and possibly condensin, to mitotic chromosomes [
]. During interphase, C-Nap1 localizes to the proximal ends of both parental centrioles, but it dissociates from these structures at the onset of mitosis. Re-association with centrioles then occurs in late telophase or at the very beginning of G1 phase, when daughter cells are still connected by post-mitotic bridges. Electron microscopic studies performed on isolated centrosomes suggest that a proteinaceous linker connects parental centrioles and C-Nap1 may be part of a linker structure that assures the cohesion of duplicated centrosomes during interphase, but that is dismantled upon centrosome separation at the onset of mitosis []. The structure of NAP-1 has a long α-helix, responsible for homodimerization via a previously uncharacterized antiparallel non-coiled-coil, and an alpha/beta domain composed of four-stranded antiparallel β-sheet, implicated in protein-protein interaction [
].
The function to find (FIIND) domain was initially discovered in two proteins, NLRP1 (aka NALP1, CARD7, NAC, DEFCAP) and CARD8 (aka TUCAN, Cardinal) [
]. NLRP1 is a member of the Nod-like receptor (NLR) protein superfamily and is involved in apoptosis and inflammation. To date, it is the only NLR protein known to have a FIIND domain. The FIIND domain is also present in the CARD8 protein where, like in NLRP1, it is followed by a C-terminal CARD domain. Both proteins are described to form an "inflammasome", a macro-molecular complex able to process caspase 1 and activate pro-IL1beta [
]. The FIIND domain is present in only a very small subset of the kingdom of life, comprising primates, rodents (mouse, rat), carnivores (dog) and a few more, such as horse. Publications describing the newly discovered NLRP1 protein failed to identify it as a separate domain; for example, it was taken as part of the adjacent leucine rich repeat domain (LRR) []. Upon discovery of CARD8 it was noted that the N-terminal region shared significant sequence identity with an undescribed region in NLRP1 []. Before getting its final name, FIIND [], this domain was termed NALP1-associated domain (NAD) []. This is a peptidase domain of the ZU5 superfamily that is predicted to be involved in autoproteolytic cleavage [].
This entry is represented by a domain found in Bacteriophage T4, Gp12. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.This region is occasionally found in conjunction with
. Most of the proteins appear to be phage tail proteins; however some appear to be involved in other processes. For instance the RhiB protein (
) from Rhizobium leguminosarum may be involved in plant-microbe interactions [
]. A related protein, microcystin related protein (MrpB, ) is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (
) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop [
] and three β-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the collar and may bind SO
4. The long unconserved region maybe due to domain swapping in and out of a loop or due to rapid evolution.
Tissue inhibitors of metalloproteinases (TIMPs, [
,
,
,
,
]) and their target matrix metalloproteinases (MMPs, MEROPS peptidase family M10A) are important in connective tissue re-modelling in diseases of the cardiovascular system and in the physiological degradation of connective tissue, as well as in pathological states such as tumour invasion and arthritis. TIMPs belong to MEROPS proteinase inhibitor family I35, clan IT.TIMPs complex with extracellular matrix metalloproteinases (such as collagenases) and irreversibly inactivate them. Members of this family are common in extracellular regions of vertebrate species [
]. TIMPs are proteins of about 200 amino acid residues, 12 of which are cysteines involved in disulphide bonds [].The basic structure of such a type of inhibitor is shown in the following schematic representation:
+-----------------------------+ +--------------+
| | | |CxCxCxxxxxxxxxxxxxxxxxCxxxxxxxxxCxxxxxxxCxCxCxCxCxxxxxCxxCxxx
| | | | | | | || +-----------------|-----------------+ +-+ +-----+
+---------------------+'C': conserved cysteine involved in a disulphide bond.
The crystal structure of the human proMMP-2/TIMP-2 complex reveals an interaction between the hemopexin domain of proMMP-2 and the C-terminal domain of TIMP-2, leaving the catalytic site of MMP-2 and the inhibitory site of TIMP-2 distant and spatially isolated. The interfacial contact of these two proteins is characterised by two distinct binding regions composed of alternating hydrophobic and hydrophilic interactions. This unique structure provides information for how specificity for non-inhibitory MMP/TIMP complex formation is achieved [].
The adaptor proteins AP-1 and GGA (Golgi-localized, gamma ear-containing, ADP-
ribosylation factor (ARF)-binding proteins) regulate membrane traffic betweenthe trans-Golgi network (TGN) and endosome/lysosomes through ARF-regulated
membrane association, recognition of sorting signals, and recruitment ofclathrin and accessory proteins. The gamma-adaptin ear (GAE) domain is a C-
terminal appendage or ear of about 120 residues, which is found in gamma-adaptins, the heavy subunits of the AP-1 complex, and in GGAs. The GAE domain,
which is found in associated with other domains such as VHS,coiled-coils and GAT, is involved in the recruitment of accessory proteins,
such as gamma-synergin, Rababptin-5, Eps15 and cyclin G-associated kinase,which modulate the functions of GAE domain containing proteins in the membrane
trafficking events [,
,
,
].The resolution of the 3D-structure of the human gamma-adaptin GAE domain shows that it forms an immunoglobulin-like β-sandwich fold composed of eight
β-strands with two short α-helices. The topology ofthe entire GAE domain is similar to those of the N-terminal subdomains in the
alpha- and beta-adaptin ear domains of the AP-2 complex. However, the GAEdomain has very low sequence identity and homology to the N-terminal
immunoglobulin-like subdomains of the alpha and beta ear domains. The bindingsite for the accessory proteins has been located to a shallow hydrophobic
trough surrounded by charged (mainly basic) residues [,
].This entry represents the entire GAE domain.
The ATP-dependent DNA helicase RecQ (
) is involved in genome maintenance [
]. All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novosynthesis DNA, such as the replication fork, and protein levels peak during S-phase.
A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise
at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that isnecessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)-DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus
contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and theRecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand
synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response.
This superfamily represents a structural domain found in the nitrogen regulatory protein PII, in ATP phosphribosyltransferases (C-terminal domain), in the divalent ion tolerance protein CutA1, and in some bacterial hypothetical proteins. This domain consists of a ferredoxin-like alpha/beta sandwich, which forms trimeric structures with orthogonally packed β-sheets around a three-fold axis. PII is a tetrameric protein encoded by glnB that functions as a component of the adenylation cascade involved in the regulation of GS activity [
]. PII helps regulate the level of glutamine synthetase in response to nitrogen source availability. In nitrogen-limiting conditions, PII is uridylylated to form PII-UMP, which allows the deadenylation of glutamine synthetase, thus activating the enzyme. Conversely, in nitrogen excess, PI-UMP is deuridylated to PII, promoting the adenylation and deactivation of glutamine synthetase [].ATP phosphoribosyltransferase is the first enzyme of the histidine pathway. It is allosterically regulated, controlling the flow of intermediates through the pathway. The C-terminal domain is the regulatory region of the protein, which binds the allosteric inhibitor histidine [
].CutA1 functions in divalent ion tolerance in bacteria, plants and animals [
,
]. Divalent metal ions play key roles in all living organisms, serving as cofactors for many proteins involved in a variety of electron-transfer activities. In Escherichia coli it is thought to be involved in copper ion tolerance, excessive copper ions being toxic [].
The type IV secretion systems (T4SSs) are ancestrally related to bacterial conjugation machines and are able to translocate proteins and/or protein-DNA complexes to the extracellular milieu or the host interior, in many cases contributing to the ability of the bacterial pathogen to colonize the host and evade its immune system [
]. In the pathogenic plant pathogen Agrobacterium tumefaciens T4SS allows the bacterium to transfer a segment of its tumor inducing (Ti-) plasmid DNA into plant cells causing crown gall tumor disease. Proteins in the virB and virD operons catalyze processing of the T-DNA and its transfer to plants. The VirB proteins assemble a secretion apparatus spanning both bacterial membranes to allow transfer of DNA and protein substrates into plant cells. VirB7 and VirB8, along with VirB6, VirB9 and VirB10, are the core components of the Agrobacterium DNA translocation apparatus. Structural studies with the Escherichia coli plasmid pKM101 VirB homologues showed that three proteins, TraN (VirB7 homologue), TraO (VirB9) and TraF (VirB10), form a hetero-tetradecameric structure with 14-fold symmetry forming an outer membrane channel through which the substrates pass. VirB7 stabilizes VirB9 and in its absence bacteria do not accumulate VirB9 preventing assembly of the secretion machine []. Members of the VirB7 family are typically 45-65 residues long, becoming 15-20 residues shorter after removal of the N-terminal signal sequence and covalent attachment to lipid molecules [].
The entry includes the peptidase M14-like domain of cytosolic carboxypeptidase 1 (CCP1; MEROPS identifier M14.028), also known as Nna-1 (Nervous system Nuclear protein induced by Axotomy) or ATP/GTP binding protein (AGTPBP-1), and ATP/GTP-binding protein-like 1 (also known as CCP4) [
,
,
]. The peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CCP1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. CCP1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain []. It has been suggested that this N-terminal domain might act as a folding domain.CCP1 is widely expressed in the developing and adult nervous systems, including cerebellar Purkinje and granule neurons, miral cells of the olfactory bulb and retinal photoreceptors. CCP1 is also induced in axotomized motor neurons [
]. Mutations in CCP1 cause Purkinje cell degeneration (pcd) []. The CCP1 CP domain is required to prevent the retinal photoreceptor loss and cerebellar ataxia phenotypes of pcd mice, and a functional zinc-binding domain is needed for CCP1 to support neuron survival in these mice.
Cystatins (also known as cysteine proteinase inhibitors) are structurally conserved, low molecular weight endogenous cysteine protease inhibitors found in most body compartments and fluids. They play an intra and/or extra-cellular role to inhibit cysteine enzymes (i.e cathepsins), crucial to maintain the protease-inhibitor balance, thus regulating damaging proteolytic activities [
]. It is thought that cystatins may influence the intra- and extracellular catabolism of proteins and peptides, regulate proteolytic processing of prohormones and proenzymes, protect against penetration of normal tissues by malignant cells or microorganisms and modulate local inflammatory processes such as rheumatoid arthritis and purulent bronchiectasis [].Cystatins have been categorised into three classes. Stefins (type I) are unglycosylated proteins of about 100 amino acids lacking disulphide bridges. Type II cystatins are about 120 amino acids and have two intra-chain disulphide bonds. Most of them are found both in tissues and body fluids including saliva. Kininogens (type III) are single chain glycoproteins containing three cystatin-like domains [
].Cystatin 9 (CST9) is a small ~18kDa human protein member of the type 2 cystatin superfamily [
]. It may play a role in hematopoietic differentiation or inflammation. It may be targeted through the Golgi via the secretory pathway []. It has been shown to have immunomodulatory and antibacterial effects against Francisella tularensis infection of the lung [].This entry represents cystatin 9 and cystatin 9-like proteins.
Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell
exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia.The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell
[] and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis []. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.One of the outer membrane protein subunit families, termed "K"here for nomenclature purposes, aids in the structural assembly of the invasion
complex []. It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.
This entry represents the TetR-like C-terminal domain found in HTH-type transcriptional repressor KstR2 as well as fatty acid metabolism regulator proteins. In Mycobacterium smegmatis, KstR2 is involved in cholesterol catabolism [
], while YsiA in Bacillus subtilis is involved in fatty acid degradation [].TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity [
]. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response []. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis []. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain [].
The ATP-dependent DNA helicase RecQ (
) is involved in genome maintenance [
]. All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novosynthesis DNA, such as the replication fork, and protein levels peak during S-phase.
A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise
at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that isnecessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)-DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus
contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and theRecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand
synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response.
Rod, the Rough deal protein (also known as Kinetochore-associated protein 1) displays a dynamic intracellular staining pattern, localising first to kinetochores in pro-metaphase, but moving to kinetochore microtubules at metaphase. Early in anaphase the protein is once again restricted to the kinetochores, where it persists until the end of telophase. This behaviour is in all respects similar to that described for ZW10 [
], and indeed the two proteins function together, localisation of each depending upon the other []. These two proteins are found at the kinetochore in complex with a third, Zwilch, in both flies and humans. The C- terminus is the most conserved part of the protein. During pro-metaphase, the ZW10-Rod complex, dynein/dynactin, and Mad2 all accumulate on unattached kinetochores; microtubule capture leads to Mad2 depletion as it is carried off by dynein/dynactin; ZW10-Rod complex accumulation continues, replenishing kinetochore dynein. The continuing recruitment of the ZW10-Rod complex during metaphase may serve to maintain adequate dynein/dynactin complex on kinetochores for assisting chromatid movement during anaphase[]. The ZW10-Rod complex acts as a bridge whose association with Zwint-1 links Mad1 and Mad2, components that are directly responsible for generating the diffusible 'wait anaphase' signal, to a structural, inner kinetochore complex containing Mis12 and KNL-1AF15q14, the last of which has been proved to be essential for kinetochore assembly in Caenorhabditis elegans. Removal of ZW10 or Rod inactivates the mitotic checkpoint [].
XIAP, also called baculoviral IAP repeat-containing protein 4 (BIRC4), is a potent suppressor of apoptosis that directly inhibits specific members of the caspase family of cysteine proteases, including caspase-3, -7, and -9 [
,
]. It promotes proteasomal degradation of caspase-3 and enhances its anti-apoptotic effect in Fas-induced cell death []. The ubiquitin-protein ligase (E3) activity of XIAP also exhibits in the ubiquitination of second mitochondria-derived activator of caspases (Smac) []. The mitochondrial proteins, Smac/DIABLO and Omi/HtrA2, can inhibit the antiapoptotic activity of XIAP []. XIAP has also been implicated in several intracellular signaling cascades involved in the cellular response to stress, such as the c-Jun N-terminal kinase (JNK) pathway, the nuclear factor-kappaB (NF-kappaB) pathway, and the transforming growth factor-beta (TGF-beta) pathway [,
,
]. Moreover, XIAP can regulate copper homeostasis through interacting with MURR1 []. BIRC8, also called inhibitor of apoptosis-like protein 2 (IAP-like protein 2 or ILP-2), or testis-specific inhibitor of apoptosis, is a tissue-specific homologue of E3 ubiquitin-protein ligase XIAP. It has been implicated in the control of apoptosis in the testis by direct inhibition of caspase 9 [
]. Both XIAP and BIRC8 contain three N-terminal baculoviral IAP repeat (BIR) domains, a ubiquitin-association (UBA) domain and a RING domain at the carboxyl terminus.This entry represents the UBA domain found in XIAP and BIRC8.
This entry represents a group of transmembrane proteins, including myelin protein P0, myelin protein zero-like protein 1/2/3, sodium channel subunit beta-2 and v-set and immunoglobulin domain-containing protein 1.
The saposin B-type domain is a ~80 amino acid domain present in saposins and
related proteins that interact with lipids. The domain is named after thesmall lysosomal proteins, saposins, which serve as sphingolipid hydrolase
activator proteins in vertebrates. The mammalian saposins are synthesized as asingle precursor molecule (prosaposin) which contains two saposin A-type
domains in the extremities that are removed in the activation reaction, and four saposin B-type domains yielding the active saposins A,B, C and D after proteolytic cleavage. Saposin-like proteins (SAPLIPs) can
have different functions, such as enzymatic activities, as cofactors ofenzymes involved in lipid metabolism, as components of lung surfactant
reducing the surface tension, as part of a complex involved in stageregulation of Dictyostelium, as antimicrobial effector molecules, or as a
stimulator of dendritic outgrowth [,
,
,
].The 3D structures of different SAPLIPs have been resolved, and show that the
saposin B-type domain is formed by a four/five helical bundle. The saposin B-type domain is characterised by six conservedcysteine residues involved in three disulfide bridges: one between helices 2
and 3, one between the first and the last helix and one from the N-terminalpart of the first helix to the C terminus. In plant aspartic proteinases the
two subdomains that are connected by the disulfide bridges occur in inversedorder, these are called "swaposin"domains [
,
,
]. In these phytepsin proteinsthe two half saposin B-type domains occur in combination with the aspartyl
protease signature [,
].
A number of proteins, some of which are known to be receptors for growth factors, have been found to contain a cysteine-rich domain of about 110 to 160 amino acids in their N-terminal part, that can be subdivided into four (or in some cases, three) modules of about 40 residues containing 6 conserved cysteines. Some of the proteins containing this domain are listed below [
,
,
]:Tumor Necrosis Factor type I and type II receptors (TNFR). Both receptors bind TNF-alpha and TNF-beta, but are only similar in the cysteine-rich region. TNFR contains four cysteine-rich domain modules (CRDs), termed CRD1 through CRD4. CRD2 and CRD3 are known as TNF-binding domains [
].Shope fibroma virus soluble TNF receptor (protein T2)Lymphotoxin alpha/beta receptorLow-affinity nerve growth factor receptor (LA-NGFR) (p75)CD40 (Bp50), the receptor for the CD40L (or TRAP) cytokineCD27, the receptor for the CD27L cytokineCD30, the receptor for the CD30L cytokineT-cell protein 4-1BB, the receptor for the 4-1BBL putative cytokine FAS antigen (or APO-1), the receptor for FASL, a protein involved in apoptosis (programmed cell death)T-cell antigen OX40, the receptor for the OX40L cytokineWsl-1, a receptor (for a yet undefined ligand) that mediates apoptosisVaccinia virus protein A53 (SalF19R)It has been shown [
] that the six cysteines all involved in intrachaindisulphide bonds. A schematic representation of the structure of the 40 residue
module of these receptors is shown below:+-------------+ +--------------+
| | | |xCxxxxxxxxxxxxxCxCxxCxxxxxxxxxCxxxxCxx
| |+------------+
'C': conserved cysteine involved in a disulphide bond.
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4.
Methylation at CpG dinucleotide, the most common DNA modification in
eukaryotes, has been correlated with gene silencing associated with variousphenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [
,
].The MBD folds into an alpha/beta sandwich structure comprising a layer of
twisted beta sheet, backed by another layer formed by the alpha1 helix and ahairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [
].
The natural resistance-associated macrophage protein (NRAMP) family consists of animal NRAMP1, NRAMP2, yeast proteins Smf1 and Smf2 and bacterial homologues [
,
,
,
,
,
,
]. The NRAMP family includes functional related proteins defined by a conserved hydrophobic core of ten transmembrane domains. These membrane proteins are divalent cation transporters which have a high degree of sequence conservation, particularly, the residues contributing to ion interaction are strongly conserved (DPNG and MPH motifs) [,
].NRAMP1 is an integral membrane protein expressed exclusively in cells of the immune system and is recruited to the membrane of a phagosome upon phagocytosis, where it plays an essential role in host defense against pathogens. Mutations in NRAMP1 may genetically predispose an individual to susceptibility to diseases including leprosy and tuberculosis [
]. NRAMP2 (DMT1) is a multiple divalent cation transporter broadly expressed in the duodenum, kidney, brain, testis and placenta. It transports Fe2+, Mn2+ and Cd+2, whereas Zn2+ is a poor substrate. Ca+2 and Mg+2 are not transported, which is important because their high concentrations in duodenum, where NRAMP2 is expressed at high levels, would interfere with the absorption of Fe2+ []. It is the major transferrin-independent iron uptake system in mammals ,
].NRAMP related members of this family have substrate specificity for Mn2+ and/or Mg2+, such as the yeast proteins Smf1 and Smf2 [
] and a group of bacterial transporters (NrmT, for Nramp-related magnesium transporter) [].
The major intrinsic protein (MIP) family is large and diverse, possessing over 100 members that form transmembrane channels. These channel proteins function in water, small carbohydrate (e.g., glycerol), urea, NH3, CO2 and possibly ion transport, by an energy independent mechanism. They are found ubiquitously in bacteria, archaea and eukaryotes.The MIP family contains two major groups of channels: aquaporins and glycerol facilitators. The known aquaporins cluster loosely together as do the known glycerol facilitators. MIP family proteins are believed to form aqueous pores that selectively allow passive transport of their solute(s) across the membrane with minimal apparent recognition. Aquaporins selectively transport water (but not glycerol) while glycerol facilitators selectively transport glycerol but not water. Some aquaporins can transport NH3 and CO2. Glycerol facilitators function as solute nonspecific channels, and may transport glycerol, dihydroxyacetone, propanediol, urea and other small neutral molecules in physiologically important processes. Some members of the family, including the yeast FPS protein and tobacco NtTIPA may transport both water and small solutes. The structures of various members of the MIP family have been determined by means of X-ray diffraction [
,
,
], revealing the fold to comprise a right-handed bundle of 6 transmembrane (TM) α-helices [,
,
]. Similarities in the N-and C-terminal halves of the molecule suggest that the proteins may have arisen through tandem, intragenic duplication of an ancestral protein that contained 3 TM domains []. This superfamily represents the aquaporin-like structural domain.
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger domain is found in Mcm10 proteins and DnaG-type primases [
].
Transcription regulator HTH, AsnC-type, conserved site
Type:
Conserved_site
Description:
The many bacterial transcription regulation proteins which bind DNA through a
'helix-turn-helix' motif can be classified into subfamilies on the basis ofsequence similarities. One such family is the AsnC/Lrp subfamily [
]. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria andarchaea, as an important regulatory system of the amino acid metabolism and related processes [
]. Members of the Lrp family are small DNA-binding proteins with molecular masses of around
15kDa. Target promoters often contain anumber of binding sites that typically lack obvious inverted repeat elements, and to which binding isusually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure
has been solved. In the crystal structure LrpA forms an octamer consistingof four dimers. The structure revealed that the N-terminal part of the protein consists of a
helix-turn-helix (HTH) domain, a fold generally involved in DNA binding.The C terminus of Lrp-like proteins has a β-fold, where the two α-helices are located at one side of the four-stranded antiparallel β-sheet.
LrpA forms a homodimer mainly through interactions between the β-strands of this C-terminaldomain, and an octamer through further interactions between the second α-helix and fourth β-strand
of the motif. Hence, the C-terminal domain of Lrp-like proteins appears tobe involved in ligand-response and activation [
].This entry represents a conserved site that spans the complete helix-turn-helix motif and extends one residue downstream and one upstream of the HTH extremities.
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This group represents a predicted uncharacterised protein with a topoisomerase zinc finger domain.
This entry includes the bacterial nitrogenase iron protein NifH [
], chloroplast encoded chlL (or frxC) [], and archaeal Ni-sirohydrochlorin a,c-diamide reductive cyclase complex component CfbC [].Nitrogenase (
) is responsible for biological nitrogen fixation. Nitrogenase is an oligomeric complex which consists of two components: component 1 which contains the active site for the reduction of nitrogen to ammonia and component 2 (also called the iron protein) [
,
]. Component 2 is a homodimer of a protein (gene nifH) which binds a single 4Fe-4S iron sulfur cluster. In the nitrogen fixation process NifH is first reduced by a protein such as ferredoxin; the reduced protein then transfers electrons to component 1 with the concomitant consumption of ATP [].There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) and in the central section there are two conserved cysteines which have been shown, in NifH, to be the ligands of the 4Fe-4S cluster.Protochlorophyllide reductase is involved in light-independent chlorophyll biosynthesis. The light-independent reaction uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This enzyme complex is composed of three subunits: ChlL, ChlN and ChlB. ChlL (also known as frxC) is present as a homodimer, and binds one 4Fe-4S cluster per dimer. Theconserved domains, including the ATP-binding motif and the Fe-S binding motif found in the three subunits, are similar to those in nitrogenases [
].
The transcription factor NF-kB (Nuclear Factor-kappaB) was first identified as a DNA-binding protein specific for the 10-base pair kB site in the immunoglobulin k light-chain enhancer of B lymphocytes [
], but has subsequently been found in many different cell types. NF-kB represents a group of structurally related proteins that share a 300 amino acid `Rel homology domain' (RHD) []: members include p50 (NF-kB1), p52 (NF-kB2), p65 (RelA), c-Rel, v-Rrel, RelB, and the Drosophila proteins Dorsal and Dif. These proteins exist as homo- and heterodimers that bind to kB sites in the enhancer regions of several target genes, most of which are involved in cellular defence mechanisms and differentiation.The RHD, which is located N-terminally, is responsible for protein
dimerisation, DNA binding and nuclear localisation. The more variableC-terminal transactivation domain is found in RelA, RelB and c-Rel, but not in p50 or p52. Nevertheless, p50 and p52 play critical roles in modulating
the specificity of NF-kB function. DNA binding requires the entire RHD, by contrast with other eukaryotic and prokaryotic transcription factors, where muchsmaller DNA-binding domains confer full specificity and binding
affinity for the target []. The structure of the transcription factor NF-kB p50 homodimer bound to a palindromic kB site shows the RHD to fold into 2 distinct subdomains, similar to the β-sandwich structure of the immunoglobulins [].NF-kB is expressed in the cytoplasm of virtually all cell types, where its activity is controlled by a family of regulatory proteins, called inhibitors of NF-kB (IkB) [
,
].
This family consists of several insect specific haemolymph juvenile hormone binding proteins (JHBP). Juvenile hormone (JH) has a profound effect on insects. It regulates embryogenesis, maintains the status quo of larva development and stimulates reproductive maturation in the adult forms. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph [
]. The crystal structure of the JHBP from Galleria mellonella (Wax moth) shows an unusual fold consisting of a long α-helix wrapped in a much curved antiparallel β-sheet, the so-called TULIP domain []. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulphide bond linking the long helix and the β-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance [,
].Proteins in this entry includes protein Daywake (dyw) and Takeout (to) from fruit flies [
]. Dyw functions in neurons as a day-specific anti-siesta gene, with little effect on sleep levels during the nighttime or in the absence of light []. Protein Takeout is implicated in circadian control of feeding behaviour [,
] and affects male courtship behaviour [].
NF-kappaB is a pleiotropic transcription factor present in almost all cell types. It is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappaB is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RelA/p65, RelB, NFKB1/p50, c-Rel and NFKB2/p52 [
]. Each individual NF-kappaB subunit, and perhaps each dimer, carries out unique functions in regulating transcription. Dimer-specific functions can be conferred by selective protein-protein interactions with other transcription factors, coregulatory proteins, and chromatin proteins [].NF-kB1 and NF-kB2 are synthesised as large precursors, called p105 and p100, which undergo processing to generate the NF-kB subunits p50 and p52, respectively [
]. The processing of p105 and p100 is mediated by the ubiquitin/proteasome pathway, and involves selective degradation of their C-terminal regions containing ankyrin repeats []. Unlike RelA, RelB and c-Rel, p50 and p52 do not contain transactivation domains in their C-termini. Nevertheless, they play critical roles in modulating the specificity of NF-kB function [].This entry represents the N-terminal sub-domain of the Rel homology domain (RHD) of NF-kappaB subunit precursor p100, which can be processed to produce a 52kDa protein (p52). p52 can form homodimers. It can also form heterodimers with different NF-kappaB family members, such as RelB, p65 and c-Rel [
,
]. p100 inhibits c-Rel and reduces the expression of IL-23 in dendritic cells [].
Bacterial type IV pili are surface filaments critical for diverse biological processes including surface and host cell adhesion, colonisation, biofilm formation, twitching motility, DNA uptake during natural transformation and virulence [
,
]. The proteins necessary to form the type IV pili inner-membrane complex, are included in the pilMNOPQ operon which encodes the cytoplasmic actin-like protein PilM, PilN, PilO, the periplasmic lipoprotein PilP and the outer-membrane secretin PilQ. The inner-membrane PilM/N/O/P complex is required for the optimal function of the outer-membrane secretin PilQ. This cluster is highly conserved across the type IV pilus-producing bacterial species, and all of these proteins have been shown to be essential for twitching motility [,
].The type IV pilus inner membrane component PilM is required for competency and pilus biogenesis [
,
]. PilM associates with PilNO heterodimers by binding the conserved cytoplasmic N terminus of PilN. Binding to PilN induce conformational changes that allow PilM to bind its own N-terminal and form dimers. It also binds ATP, which facilitates PilN interaction [
,
]. This protein is required for the assembly of the type IV fimbria in P. aeruginosa and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.This entry also includes Competence protein A from Haemophilus influenzae in which this cluster is annotated as comA/B/C/D/E.
TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response
[,
,
]. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair [
]. It also regulates CHD3 nucleosome remodelling during the DNA double-strand break (DSB) response []. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response []. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription []. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase []. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization []. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity [,
].This entry represents the RING-HC finger found in TIF1-beta.
This domain can be found in human SRP9 protein and its homologues, such as the Srp21 protein from budding yeasts [
]. These proteins are part of the signal recognition particle (SRP) [].The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [
,
]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome. In eukaryotes this retards its elongation until SRP docks the ribosome-polypeptide complex to the RER membrane via the SR receptor []. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [].
This entry represents proteins contain an SRP9 domain, such as human signal recognition particle 9kDa protein (SRP9), a component of the signal recognition particle (SRP) [
] and its homologues, such as the Srp21 protein from budding yeasts [].The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [
,
]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome. In eukaryotes this retards its elongation until SRP docks the ribosome-polypeptide complex to the RER membrane via the SR receptor []. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [].
Paxillin is a cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion) [
,
]. Extensive tyrosine phosphorylation occurs during integrin-mediated cell adhesion, embryonic development, fibroblast transformation and following stimulation of cells by mitogens that operate through the 7TM family of G-protein-coupled receptors []. Paxillin binds in vitro to the focal adhesion protein vinculin, as well as to the SH3 domain of c-Src, and, when tyrosine phosphorylated, to the SH2 domain of v-Crk []. An N-terminal region has been identified that supports the binding of both vinculin and the focal adhesion tyrosine kinase, pp125Fak [
].Paxillin is a 68kDa protein containing multiple domains, including four tandem C-terminal LIM domains (each of which binds 2 zinc ions); an N-terminal proline-rich domain, which contains a consensus SH3 binding site; and three potential Crk-SH2 binding sites [
]. The predicted structure of paxillin suggests that it is a unique cytoskeletal protein capable of interaction with a variety of intracellular signalling and structural molecules important in growth control and the regulation of cytoskeletal organisation [,
].This entry represents the second Lim domain of Paxillin, which function as an adaptor or scaffold to support the assembly of multimeric protein. This domain shows two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms [
,
].
The crystal structures of four growth factors; nerve growth factor, transforming growth factor-beta, platelet-derived growth factor, and human chorionic gonadotropin from four separate superfamilies revealed that these proteins are structurally related and share a common overall topology [
]. These proteins show very little sequence homology, but they all have an unusual arrangement of six cysteines linked to form a "cystine-knot"conformation. The active forms of these proteins are dimers, either homo- or heterodimers [
]. Because of their shape, there appears to be an intrinsic requirement for the cystine-knot growth factors to form dimers. This extra level of organisation increases the variety of structures built around this simple structural motif [].Glycoprotein hormones [
,
] (or gonadotropins) are a family of proteins which include the mammalian hormones follitropin (FSH), lutropin (LSH), thyrotropin (TSH) and chorionic gonadotropin (CG), as well as at least two forms of fish gonadotropins. All these hormones consist of two glycosylated chains (alpha and beta). In mammalian gonadotropins, the alpha chain is identical in the four types of hormones but the beta chains, while homologous, are different.The beta chains are proteins of about 100 to 140 amino acid residues which contain the cysteine-knot domain [
], as shown in the following schematic representation.+----------------------+
| +------------|-----------------------------+| +-|------------|--------+ |
| | | | | |xxxCxxxxxxxCxCxxCxCxxxxxxxCxxxxxxxxCxxxxxxxCxCxCxxCxxxxxCxxxxxxxxxxx
| | | | | || | | | +--+
+-|------------------------+ |+--------------------------+
'C': conserved cysteine involved in a disulphide bond.
Herpesvirus major capsid protein, upper domain superfamily
Type:
Homologous_superfamily
Description:
The Herpesvirus major capsid protein (MCP) is the principal protein of the icosahedral capsid, forming the main component of the hexavalent and probably the pentavalent capsomeres. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces [
]. The MCP can be considered as having three domains: floor, middle and upper. The floor domains form a thin largely continuous layer, or shell, and are the only parts that interact directly to form intercapsomeric connections. They also interact with the internal scaffolding protein during capsid assembly []. The remainder of the protein extends radially outward from the capsid producing the hexamer and pentamer capsomere structures. The middle domains are involved in binding to the triplexes that lie between and link adjacent capsomeres []. The upper domains form the tops of the hexamer and pentamer towers and are the binding sites for the small capsid protein VP26 in the hexons and for tegument proteins in the pentons.The upper domain of MCP forms a pyramid structure composed predominantly of loops and α-helices [
]. This domain appears to form a compact, stable structure and may act as a rigid core around which the more flexible middle and floor domains are able to undertake the conformational changes required for capsid assembly.
Paxillin is a cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion) [
,
]. Extensive tyrosine phosphorylation occurs during integrin-mediated cell adhesion, embryonic development, fibroblast transformation and following stimulation of cells by mitogens that operate through the 7TM family of G-protein-coupled receptors [
]. Paxillin binds in vitro to the focal adhesion protein vinculin, as well as to the SH3 domain of c-Src, and, when tyrosine phosphorylated, to the SH2 domain of v-Crk []. An N-terminal region has been identified that supports the binding of both vinculin and the focal adhesion tyrosine kinase, pp125Fak [].Paxillin is a 68kDa protein containing multiple domains, including four tandem C-terminal LIM domains (each of which binds 2 zinc ions); an N-terminal proline-rich domain, which contains a consensus SH3 binding site; and three potential Crk-SH2 binding sites [
]. The predicted structure of paxillin suggests that it is a unique cytoskeletal protein capable of interaction with a variety of intracellular signalling and structural molecules important in growth control and the regulation of cytoskeletal organisation [,
].This entry represents the C-terminal fourth Lim domain of Paxillin, which function as an adaptor or scaffold to support the assembly of multimeric protein. This domain shows two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms [
,
].
This entry include nebulin and nebulin-related-anchoring protein (N-RAP). Nebulin is a giant filamentous protein (600-900 kD) that plays a role in numerous cellular processes including regulation of muscle contraction, Z-disc formation, and myofibril organization and assembly in skeletal muscle. It contains an N-terminal LIM domain, many nebulin repeats/super repeats, and a C-terminal SH3 domain. The N terminus of nebulin is located near the pointed end of the thin filament and contains a binding site for the actin filament capping protein tropomodulin (Tmod). The super repeat region of nebulin has been shown to interact with kelch-like family member 40 (KLHL40). The C terminus of nebulin is located within the highly specialized boundary of the sarcomere (Z-disc), and plays an important role in myofibril assembly, mechanosensing, signaling, force generation and transmission, and sarcolemmal resilience. The SH3 domain of nebulin interacts with multiple proteins, such as alpha-actinin, XIRP2 and titin []. Mutations in nebulin can cause nemaline myopathy, characterised by muscle weakness which can be severe and can lead to neonatal lethality []. Nebulin-related-anchoring protein (N-RAP) is a muscle-specific protein that may serve as a scaffold for premyofibril assembly [
,
]. N-RAP contains a N-terminal LIM domain (LIM), the C-terminal actin-binding nebulin super repeats and the nebulin-related simple repeats (IB) in between the two []. The N-terminal IB region is essential for alpha-actinin organisation, while the N-RAP super repeats are essential for sarcomeric actin organisation [].
The crystal structures of four growth factors; nerve growth factor, transforming growth factor-beta, platelet-derived growth factor, and human chorionic gonadotropin from four separate superfamilies revealed that these proteins are structurally related and share a common overall topology [
]. These proteins show very little sequence homology, but they all have an unusual arrangement of six cysteines linked to form a "cystine-knot"conformation. The active forms of these proteins are dimers, either homo- or heterodimers [
]. Because of their shape, there appears to be an intrinsic requirement for the cystine-knot growth factors to form dimers. This extra level of organisation increases the variety of structures built around this simple structural motif [].Glycoprotein hormones [
,
] (or gonadotropins) are a family of proteins which include the mammalian hormones follitropin (FSH), lutropin (LSH), thyrotropin (TSH) and chorionic gonadotropin (CG), as well as at least two forms of fish gonadotropins. All these hormones consist of two glycosylated chains (alpha and beta). In mammalian gonadotropins, the alpha chain is identical in the four types of hormones but the beta chains, while homologous, are different.The beta chains are proteins of about 100 to 140 amino acid residues which contain the cysteine-knot domain [
], as shown in the following schematic representation.+----------------------+
| +------------|-----------------------------+| +-|------------|--------+ |
| | | | | |xxxCxxxxxxxCxCxxCxCxxxxxxxCxxxxxxxxCxxxxxxxCxCxCxxCxxxxxCxxxxxxxxxxx
| | | | | || | | | +--+
+-|------------------------+ |+--------------------------+
'C': conserved cysteine involved in a disulphide bond.
Wnt-1 (previously known as int-1) [
] is a proto-oncogene induced by theintegration of the mouse mammary tumor virus. It is thought to play a role in
intercellular communication and seems to be a signalling molecule important inthe development of the central nervous system (CNS). The sequence of wnt-1 is
highly conserved in mammals, fish, and amphibians.Wnt-1 is a member of a large family of related proteins [
,
] that are allthought to be developmental regulators. These proteins are known as wnt-2
(also known as irp), wnt-3 up to wnt-15. At least four members of this familyare present in Drosophila; one of them, wingless (wg), is implicated in
segmentation polarity.All these proteins share the following features characteristics of secretory
proteins: a signal peptide, several potential N-glycosylation sites and 22conserved cysteines that are probably involved in disulfide bonds. The Wnt
proteins seem to adhere to the plasma membrane of the secreting cells and aretherefore likely to signal over only few cell diameters.Signal transduction by the Wnt family of ligands is mediated by the binding to
the extracellular domain fz of Frizzled receptors. It can lead to either theactivation of dishvelled proteins, inhibition of GSK-3 kinase, nuclear
accumulation of beta-catenin and activation of Wnt target genes or be coupledto the inositol signaling pathway and PKC activation, depending on the type of
Frizzled receptor [,
].This entry represents a conserved region including three cysteines.
This group represents alpha-1B-glycoproteins and several leukocyte immunoglobulin-like receptors. There are five domains in human alpha 1B-glycoprotein. Mongoose antihemorrhagic factor (AHF1) is a protein, which is homologous to human alpha 1BG, and a supergene family of immunoglobulins [
]. Alpha-1B-glycoproteins have been found associated with a number of diseases. They have been detected in the urine of children with steroid-resistant minimal change nephrotic syndrome (SRINS) [
]. It is also found associated with bladder cancer, having been detected in all tumor-bearing patient samples but not samples obtained from non-tumor-bearing individuals []. When the 1694 bp was cloned from human liver Marathon cDNA, which is the alpha-1B glycoprotein precursor gene, it was found that it may be a novel member of immunoglobulin superfamily and could be involved in cell recognition and the regulation of cell behavior [].Polymorphism of Alpha-1-B-glycoprotein (A1BG) has been found in the plasma of several human populations of the Indian subcontinent [
]. Human leukocyte antigen-G (HLA-G) is a non-classical HLA class-I molecule that is expressed by placental trophoblast cells. HLA-G probably stimulates leukocyte immunoglobulin-like receptor B1 (LILRB1) receptors on decidual leukocytes. In this way, a foetus may affect the local maternal immune response [
]. Human killer immunoglobulin-like receptor (KIR) genes are important for restraining natural killer cytotoxicity toward cells with autologous HLA, while targeting cells lacking or expressing low levels of self-HLA molecules [].LILRB1 is expressed by most leukocytes and LILRB2 is expressed primarily by monocytes, macrophages and dendritic cells [
].
The apical membrane of many tight epithelia contains sodium channels that
are primarily characterised by their high affinity to the diuretic blockeramiloride [
,
,
,
]. These channels mediate the first step of active sodiumreabsorption essential for the maintenance of body salt and water
homeostasis []. In vertebrates, the channelscontrol reabsorption of
sodium in kidney, colon, lung and sweat glands; they also play a role intaste perception.
Members of the epithelial Na
+channel (ENaC) family fall into four
subfamilies, termed alpha, beta, gamma and delta []. The proteins exhibitthe same apparent topology, each with two transmembrane (TM) spanning
segments, separated by a large extracellular loop. In most ENaC proteinsstudied to date, the extracellular domains are highly conserved and contain
numerous cysteine residues, with flanking C-terminal amphipathic TM regions,postulated to contribute to the formation of the hydrophilic pores of the
oligomeric channel protein complexes. It is thought that the well-conservedextracellular domains serve as receptors to control the activities of the
channels.Vertebrate ENaC proteins are similar to degenerins of Caenorhabditis elegans
[]: deg-1, del-1, mec-4, mec-10 and unc-8. These proteins can be mutated to cause neuronal degradation, and are also thought to form sodium channels.Structurally, the proteins that belong to this family consist of about 510
to 920 amino acid residues. They are made of an intracellular N terminusregion followed by a transmembrane domain, a large extracellular loop, a
second transmembrane segment and a C-terminal intracellular tail [].
CAS, serine rich four helix bundle domain superfamily
Type:
Homologous_superfamily
Description:
This superfamily represents a serine rich protein that is found in the docking protein p130(cas) (Crk-associated substrate). The protein folds into a four helix bundle which is associated with protein-protein interactions [
].
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [
,
,
]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [
,
]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome.EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, facilitates the movement of peptidyl-tRNA from the A to the P site, being critical for the structural transition to take place [
].Included in this entry is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins that is homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA [
,
,
,
,
,
,
,
,
].
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH [
].TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [
,
].The TFIIB zinc finger adopts a zinc ribbon fold characterised by two β-hairpins forming two structurally similar zinc-binding sub-sites [
]. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I [].
Tumour necrosis factor family protein, CD30 ligand type
Type:
Family
Description:
Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [
,
,
]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [,
]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide [].There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The following cytokines can be grouped into a family on the basis of sequence, functional, and structural similarities [
,
,
]: Tumor Necrosis Factor (TNF) (also known as cachectin or TNF-alpha) [
,
] is a cytokine which has a wide variety of functions. It can cause cytolysis of certain tumor cell lines; it is involved in the induction of cachexia; it is a potent pyrogen, causing fever by direct action or by stimulation of interleukin-1 secretion; finally, it can stimulate cell proliferation and induce cell differentiation under certain conditions.Lymphotoxin-alpha (LT-alpha) and lymphotoxin-beta (LT-beta), two related cytokines produced by lymphocytes and which are cytotoxic for a wide range of tumor cells in vitro and in vivo [
]. T cell antigen gp39 (CD40L), a cytokine which seems to be important in B-cell development and activation.CD27L, a cytokine which plays a role in T-cell activation. It induces the proliferation of costimulated T cells and enhances the generation of cytolytic T cells. CD30L, a cytokine which induces proliferation of T cells.FASL, a cytokine involved in cell death [
].4-1BBL, a inducible T cell surface molecule that contributes to T-cell stimulation.OX40L, a cytokine that co-stimulates T cell proliferation and cytokine production [
].TNF-related apoptosis inducing ligand (TRAIL), a cytokine that induces apoptosis [
].TNF-alpha is synthesised as a type II membrane protein which then undergoes post-translational cleavage liberating the extracellular domain. CD27L, CD30L, CD40L, FASL, LT-beta, 4-1BBL and TRAIL also appear to be type II membrane proteins. LT-alpha is a secreted protein. All these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. The PROSITE pattern for this family is located in a β-strand in the central section of the protein which is conserved across all members.This group represents a tumour necrosis factor family protein, CD30 ligand type, also known as Tumor necrosis factor ligand superfamily member 8. It is a cytokine that binds to TNFRSF8/CD30, inducing proliferation of T-cell [
].
Phosphatidylinositol-glycan-specific phospholipase D is an extracellular
amphiphilic glycoprotein [,
]. It hydrolyses theinositol phosphate linkage in proteins anchored by phosphatidylinositol glycans,
releasing these proteins from the membrane.The enzyme catalyses the reaction: glycoprotein
phosphatidylinositol + H2O = phosphatidate + glycoprotein inositol
This family of proteins is functionally uncharacterised. These proteins are related to Escherichia coli YsaB (
). This family of proteins is found in bacteria. Proteins in this family are lipoproteins and they are approximately 100 amino acids in length.
This entry represents a domain of unknown function predominantly found in uncharacterised proteins from Pandoravirus. Some members of this entry are thought to be F-box domain-containing proteins. The conserved F-box domain, present in numerous proteins, is involved in protein-protein interaction.
This domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [
,
]. Proteins containing this domain include NIN-like proteins (NLPs) and RWP-RK domain proteins (RKDs). RWP-RK domain may serve in dimerisation and DNA binding [].
Several proteins in this superfamily are annotated as being putative molybdopterin-guanine dinucleotide biosynthesis proteins, but this has not been confirmed. Members of this superfamily also include proteins containing the N-terminal domain of the bacteria NE0471 protein. The function of these proteins is not known.
This protein family includes Mab-21 and Mab-21-like proteins and similar animal proteins. In Caenorhabditis elegans these proteins are required for several aspects of embryonic development [
,
]. This entry also includes inositol 1,4,5-triphosphate receptor-interacting proteins, which are predicted to contain a partial Mab-21 domain [].
This entry represents an uncharacterised alpha/beta domain fused to E1 proteins. This protein is usually present in gene neighbourhoods with genes encoding a JAB protein and a predicted metal-binding protein. In related E1 proteins, the E1-N domain is replaced by an E2/UBC superfamily domain [
].
It has been shown that several proteins share two sequence motifs [
]. Two of these proteins, vertebrate and plant inositol monophosphatase (), and vertebrate inositol polyphosphate 1-phosphatase (
), are enzymes of the inositol phosphate second messenger signalling pathway, and share similar enzyme activity. Both enzymes exhibit an absolute requirement for metal ions (Mg2 is preferred), and their amino acid sequences contain a number of conserved motifs, which are also shared by several other proteins related to MPTASE (including products of fungal QaX and qutG, bacterial suhB and cysQ, and yeast hal2) [
]. The function of the other proteins is not yet clear, but it is suggested that they may act by enhancing the synthesis or degradation of phosphorylated messenger molecules []. Structural analysis of these proteins has revealed a common core of 155 residues, which includes residues essential for metal binding and catalysis. An interesting property of the enzymes of this family is their sensitivity to Li+. The targets and mechanism of action of Li+ are unknown, but overactive inositol phosphate signalling may account for symptoms of manic depression [].An interesting property of the enzymes of this family is their sensitivity
to Li+ at levels achieved in patients undergoing therapy for manicdepression. The targets and mechanism of action of Li+ are unknown, but
overactive inositol phosphate signalling may account for symptoms of thedisease [
,
]. It has been proposed that these Li+-sensitive proteins could represent targets for Li+ in manic depressive disease [,
,
].
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The TTF zinc finger domain is found in transposases and transcription
factors. It is present in eukaryotic proteins but has not been identified in any from fungi and nematodes.
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as
, which are involved in cell growth regulation.
Peptidase S26A, signal peptidase I, conserved site
Type:
Conserved_site
Description:
Signal peptidases (SPases) [
] (also known as leader peptidases) remove the signal peptides from secretory proteins. In prokaryotes three types of SPases are known: type I (gene lepB) which is responsible for the processing of the majority of exported pre-proteins; type II (gene lsp) which only processlipoproteins, and a third type involved in the processing of pili subunits.
SPase I (EC 3.4.21.89) is an integral membrane protein that is anchored in the cytoplasmic membrane by one (in Bacillus subtilis) or two (in Escherichia coli) N-terminal transmembrane domains with the main part of the protein protuding in the periplasmic space. Two residues have been shown [
,
] to be essential for the catalytic activity of SPase I: a serine and an lysine.SPase I is evolutionary related to the yeast mitochondrial inner membrane
protease subunit 1 and 2 (genes IMP1 and IMP2) which catalyse the removal ofsignal peptides required for the targeting of proteins from the mitochondrial
matrix, across the inner membrane, into the inter-membrane space [].In eukaryotes the removal of signal peptides is effected by an oligomeric
enzymatic complex composed of at least five subunits: the signal peptidasecomplex (SPC). The SPC is located in the endoplasmic reticulum membrane. Two
components of mammalian SPC, the 18 Kd (SPC18) and the 21 Kd (SPC21) subunitsas well as the yeast SEC11 subunit have been shown [
] to share regions ofsequence similarity with prokaryotic SPases I and yeast IMP1/IMP2.
This entry represents a conserved region of unknown biological significance which is located in the C-terminal section of S26 peptidases (SPase I and IMP1/2).
Peptidase S26A, signal peptidase I, serine active site
Type:
Active_site
Description:
Signal peptidases (SPases) [
] (also known as leader peptidases) remove the signal peptides from secretory proteins. In prokaryotes three types of SPases are known: type I (gene lepB) which is responsible for the processing of the majority of exported pre-proteins; type II (gene lsp) which only processlipoproteins, and a third type involved in the processing of pili subunits.
SPase I (EC 3.4.21.89) is an integral membrane protein that is anchored in the cytoplasmic membrane by one (in Bacillus subtilis) or two (in Escherichia coli) N-terminal transmembrane domains with the main part of the protein protuding in the periplasmic space. Two residues have been shown [
,
] to be essential for the catalytic activity of SPase I: a serine and an lysine.SPase I is evolutionary related to the yeast mitochondrial inner membrane
protease subunit 1 and 2 (genes IMP1 and IMP2) which catalyse the removal ofsignal peptides required for the targeting of proteins from the mitochondrial
matrix, across the inner membrane, into the inter-membrane space [].In eukaryotes the removal of signal peptides is effected by an oligomeric
enzymatic complex composed of at least five subunits: the signal peptidasecomplex (SPC). The SPC is located in the endoplasmic reticulum membrane. Two
components of mammalian SPC, the 18 Kd (SPC18) and the 21 Kd (SPC21) subunitsas well as the yeast SEC11 subunit have been shown [
] to share regions ofsequence similarity with prokaryotic SPases I and yeast IMP1/IMP2.
This entry represents the putative active site serine located in S26 peptidases (SPase I and IMP1/2).
The cold-shock domain (CSD) is an ancient β-barrel fold of about 70 aminoacids that binds single-stranded nucleic acids (both RNA and DNA). CSD-
containing proteins have been found in all three domains of life and functionin a variety of processes that are related, for the most part, to post-
translational gene regulation. CSDs were first found in bacterial cold-shockproteins (CSPs). CSPs are small, abundant proteins that are essentially
composed of one CSD. Some members of this family are strongly induced aftercold shock and are involved in adaptation to low temperatures, while others
function during normal growth conditions. Bacterial CSPs bind to single-stranded nucleic acids and function as RNA chaperones, rescuing RNAs trapped
in unproductive folding states. This general molecular function enables CSPsto participate in the regulation of practically any step of gene expression
involving RNA, including transcription, translation, and RNA turnover. Sincetheir discovery in bacterial CSPs, CSDs have been found in many other
bacterial and eukaryotic proteins. In multicellular organisms, CSDs areusually embedded in larger proteins [
,
,
,
,
].The CSD adopts a five-stranded antiparallel β-barrel structure, which is
similar to the oligonucleotide/oligosaccharide fold (OB-fold). Many CSDs contain the motifs [YF]-G-F-I and [VF]-[VF]-H, which
are known as the ribonucleoprotein (RNP)-1 and RNP-2 motifs and include mostof the residues involved in the interaction with nucleic acids. RNP-1 and
RNP-2 are located in strands beta2 and beta3, respectively [,
,
,
].This conserved region is located at the N-terminal. The beginning of this region is highly similar to the RNP-1 RNA-binding motif [
].
The YjgF/YER057c/UK114 family (also known as the Rid family) of proteins is conserved in all domains of life [
]. A phylogenetic analysis applied by Lambrecht et al.has divided the Rid family into a widely distributed archetypal RidA (YjgF) subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other [
]. Although the family members share high levels of protein sequence and structure similarity, their functions vary widely across different species []. Structurally, these proteins are homotrimers with clefts between the monomeric subunits that are proposed to have some functional relevance [
,
,
].This family includes: YjgF (also known as RidA or 2-iminobutanoate/2-iminopropanoate deaminase), which displays enamine/imine deaminase activity and can accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA) [
,
]
the yeast growth inhibitor YER057c (protein HMF1) that appears to play a role in the regulation of metabolic pathways and cell differentiation [
]
the mammalian 14.5kDa translational inhibitor protein UK114, also known as L-PSP (liver perchloric acid-soluble protein), with endoribonucleolytic activity that directly affects mRNA translation and can induce disaggregation of the reticulocyte polysomes into 80 S ribosomes [
]
RutC from E. coli, which is essential for growth on uracil as sole nitrogen source and is thought to reduce aminoacrylate peracid to aminoacrylate [
] YabJ from B. subtilis, which is required for adenine-mediated repression of purine biosynthetic genes [
]
The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation [
,
,
]. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. This domain is also found in the Saccharomyces cerevisiae SNF12 protein, the eukaryotic initiation factor 2 (eIF2) []and the Arabidopsis thaliana At1g31760 protein [].MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription [
]. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded β-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 α-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain.The SWIB and MDM2 domains are homologous and share a common fold.
In eukaryotes, glutathione S-transferases (GSTs) participate in the detoxification of reactive electrophilic compounds by catalysing their
conjugation to glutathione. The GST domain is also found in S-crystallins from squid, and proteins with no known GST activity, such as eukaryotic elongation factors 1-gamma and the HSP26 family of stress-related proteins, which include auxin-regulated proteins in plants and stringent starvation proteins in Escherichia coli. The major lens polypeptide of Cephalopoda is also a GST [,
,
,
].Bacterial GSTs of known function often have a specific, growth-supporting role in biodegradative metabolism: epoxide ring opening and tetrachlorohydroquinone reductive dehalogenation are two examples of the reactions catalysed by these bacterial GSTs. Some regulatory proteins, like the stringent starvation proteins, also belong to the GST family [
,
]. GST seems to be absent from Archaea in which gamma-glutamylcysteine substitute to glutathione as major thiol.Soluble GSTs activate glutathione (GSH) to GS-. In many GSTs, this is accomplished by a Tyr at H-bonding distance from the sulphur of GSH. These enzymes catalyse nucleophilic attack by reduced glutathione (GSH) on nonpolar compounds that contain an electrophilic carbon, nitrogen, or sulphur atom [
].Glutathione S-transferases form homodimers, but in eukaryotes can also form heterodimers of the A1 and A2 or YC1 and YC2 subunits. The homodimeric enzymes display a conserved structural fold, with each monomer composed of two distinct domains [
]. The N-terminal domain forms a thioredoxin-like fold that binds the glutathione moiety, while the C-terminal domain contains several hydrophobic α-helices that specifically bind hydrophobic substrates.This entry represents the N-terminal domain of GST.
The major intrinsic protein (MIP) family is large and diverse, possessing over 100 members that form transmembrane channels. These channel proteins function in water, small carbohydrate (e.g., glycerol), urea, NH3, CO2 and possibly ion transport, by an energy independent mechanism. They are found ubiquitously in bacteria, archaea and eukaryotes.The MIP family contains two major groups of channels: aquaporins and glycerol facilitators. The known aquaporins cluster loosely together as do the known glycerol facilitators. MIP family proteins are believed to form aqueous pores that selectively allow passive transport of their solute(s) across the membrane with minimal apparent recognition. Aquaporins selectively transport water (but not glycerol) while glycerol facilitators selectively transport glycerol but not water. Some aquaporins can transport NH3 and CO2. Glycerol facilitators function as solute nonspecific channels, and may transport glycerol, dihydroxyacetone, propanediol, urea and other small neutral molecules in physiologically important processes. Some members of the family, including the yeast FPS protein and tobacco NtTIPA may transport both water and small solutes. The structures of various members of the MIP family have been determined by means of X-ray diffraction [
,
,
], revealing the fold to comprise a right-handed bundle of 6 transmembrane (TM) α-helices [,
,
]. Similarities in the N-and C-terminal halves of the molecule suggest that the proteins may have arisen through tandem, intragenic duplication of an ancestral protein that contained 3 TM domains []. This entry represents a conserved region which is located in the cytoplasmic loop between the second and third transmembrane regions of MIP family members.
Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions [
,
]; they fall into several subgroups according to the nature of their iron-sulphur cluster(s). One group,originally found in chloroplast membranes, has been termed 'chloroplast-type' or 'plant-type', and includes ferredoxins
from plants, algae, archaea, rhodobacter and a toluene degrading pseudomonas. Here, the active centre is a2Fe-2S cluster, where the irons are tetrahedrally coordinated by both inorganic sulphurs and sulphurs provided by 4
conserved Cys residues []. In chloroplasts, 2Fe-2S ferredoxins function as electron carriers in thephotosynthetic electron transport chain and as electron donors to various cellular proteins. In
hydroxylating bacterial dioxygenase systems, they serve as intermediate electron-transfer carriers betweenreductase flavoproteins and oxygenase [
].Several oxidoreductases contain redox domains similar to 2Fe-2S ferredoxins, including ferredoxin/ferredoxin
reductase components of several bacterial aromatic di- and monooxygenases, phenol hydroxylase, methane monooxygenase, vanillate demethylase oxidoreductase, phthalate dioxygenase reductase, bacterial fumarate
reductase iron-sulphur protein, eukaryotic succinate dehydrogenase and xanthine dehydrogenase. 3D structures are known for a number of 2Fe-2S ferredoxins [
] and for the ferredoxin reductase/ferredoxin fusion protein phthalate dioxygenase reductase [
]. The fold belongs to the alpha + beta class, with 3 helices and 4 strands forming a barrel-like structure, and an extruded loop containing 3 of the 4 cysteinyl residues of the
iron-sulphur cluster.In the 2Fe-2S ferredoxins, four cysteine residues bind the iron-sulphur cluster. Three of these cysteines are clustered together in the same region of the protein. This sequence cover the three cysteine residues involved in iron-sulphur binding.
Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour [
]. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry contains several methyl-accepting chemotaxis proteins, as well as related prokaryotic signalling receptors. All these proteins are composed of the same structural domains as found in classical MCPs.
This entry represents a domain found in prokaryotic members of the GtrA family, which are predicted to be integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides. GtrA is involved in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation. Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane [
]. Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyses the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b) []. This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and Listeria monocytogenes strains. Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose [].This domain usually covers most of the length of these sequences.This domain is also found at the C terminus of the glycosyltransferase 2 (GH2) family member Dolichol-phosphate mannosyltransferase from Pyrococcus furiosus (DPMS) and similar prokaryotic proteins. This protein transfers mannose from GDP-mannose to dolichol monophosphate to form dolichol phosphate mannose (Dol-P-Man) which is the mannosyl donor in pathways leading to N-glycosylation, glycosyl phosphatidylinositol membrane anchoring, and O-mannosylation of proteins. This entry represents the transmembrane (TM) domain that shows four TM helices (TMHs) arranged as two TMH dimers [
].
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [
,
,
,
,
]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [
]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a set of zinc fingers found in bacteriophage transcriptional activators and some bacterial proteins [
]. These zinc fingers all contain the consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].
Iron is essential for growth in both bacteria and mammals. Controlling the
amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein
molecules can accomplish this. Such iron-protein complexes include haem in blood, lactoferrin in tears/saliva, and transferrin in blood plasma. Some
bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores (enterobactins) to
scavenge iron from iron-binding host proteins []. The control of such siderophore gene expression in Escherichia coli is under
the regulation of the negative repressor protein FUR []. When complexed with Fe2+, it down-regulates the transcription not only of the siderophore
genes, but also of the moieties that release Fe2+ ions bound to the hydrox-amate enterobactin proteins in the microbial cytoplasm [
]. An example of the latter is FhuF from the Gram-negative microbes Yersinia pestis,
Salmonella typhi, and E. coli []. In conjunction with the siderophore system, this gene has been demonstrated to be essential for
growth and virulence in pathogenic enterobacteria [].FhuF (Ferric siderophore reductase) is a member of the [2Fe-2S]ferric iron reductase family. However,
in place of the symmetrical tetrahedral arrangement at the ferric ironbinding site, an unusual Cys-Cys C-terminal group distorts the site in this
protein []. This property makes FhuF inherently unstable, and another setof regulatory genes, designated "suf", is thought to maintain its activity
in the cytoplasm. FhuF, involved in the reduction of ferric iron in cytoplasmic ferrioxamine B [], binds both the iron-loaded and the apo forms of ferrichrome [].
In eukaryotes, glutathione S-transferases (GSTs) participate in the detoxification of reactive electrophilic compounds by catalysing their
conjugation to glutathione. The GST domain is also found in S-crystallins from squid, and proteins with no known GST activity, such as eukaryotic elongation factors 1-gamma and the HSP26 family of stress-related proteins, which include auxin-regulated proteins in plants and stringent starvation proteins in Escherichia coli. The major lens polypeptide of Cephalopoda is also a GST [,
,
,
].Bacterial GSTs of known function often have a specific, growth-supporting role in biodegradative metabolism: epoxide ring opening and tetrachlorohydroquinone reductive dehalogenation are two examples of the reactions catalysed by these bacterial GSTs. Some regulatory proteins, like the stringent starvation proteins, also belong to the GST family [
,
]. GST seems to be absent from Archaea in which gamma-glutamylcysteine substitute to glutathione as major thiol.Soluble GSTs activate glutathione (GSH) to GS-. In many GSTs, this is accomplished by a Tyr at H-bonding distance from the sulphur of GSH. These enzymes catalyse nucleophilic attack by reduced glutathione (GSH) on nonpolar compounds that contain an electrophilic carbon, nitrogen, or sulphur atom [
].Glutathione S-transferases form homodimers, but in eukaryotes can also form heterodimers of the A1 and A2 or YC1 and YC2 subunits. The homodimeric enzymes display a conserved structural fold, with each monomer composed of two distinct domains [
]. The N-terminal domain forms a thioredoxin-like fold that binds the glutathione moiety, while the C-terminal domain contains several hydrophobic α-helices that specifically bind hydrophobic substrates.
TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response
[,
,
]. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair [
]. It also regulates CHD3 nucleosome remodelling during the DNA double-strand break (DSB) response []. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response []. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription []. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase []. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization []. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity [,
].This entry represents the B-box-type 2 zinc finger from TIF1-beta, characterised by a CHC3H2 zinc-binding consensus motif.
TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response
[,
,
]. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair [
]. It also regulates CHD3 nucleosome remodelling during the DNA double-strand break (DSB) response []. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response []. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription []. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase []. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization []. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity [,
].This entry represents the B-box-type 1 zinc finger from TIF1-beta, which is characterized by a C6H2 zinc-binding consensus motif.
GPS (for GPCR proteolytic site) motif is found in a number of G-protein-coupled receptors (GPCRs) including CIRLs/latrophilins and in other membrane-associated proteins like the sea urchin receptor for egg jelly protein (REJ) [
].For the CIRL-1, CIRL-2, CIRL-3 and CD-97 proteins, it has been shown that they are each made of two non-covalently bound subunits resulting from the endogenous proteolytic cleavage of a precursor protein. Because the cysteine-rich domain of CIRL-1 and possibly other receptors is involved in the endogenous proteolytic processing of CIRL-1 and possibly other receptors, it has been named GPS for GPCR proteolytic site. As the amino acids surrounding the putative cleavage site are the most conserved residues in the GPS domain, it has been suggested that all proteins containing it may be cleaved at this position [
,
,
].GPS motifs are about 50 residues long and contain either 2 or 4 cysteine residues that are likely to form disulphide bridges. Based on conservation of these cysteines the following pairing can be predicted.+-----------------+
| |+-----------------+---------------+ |
| | | |XXXCXXXXXXXXXXXXXXXXXCXXXXXXXXXXXXXXXCXCXXLTXXXXXXX
^cleavage siteThe GPS motif is an integral part, and the most conserved region, of a much larger (320-residue approximately) domain that has been termed GPCR-Autoproteolysis INducing (GAIN) domain. The GAIN domain represents an autoproteolytic fold whose function is relevant for GPCR signalling and may regulate this process [
,
]. The GPS motif is an essential element for receptor function and needs to be within the context of the GAIN domain to mediate autoproteolysis [].
This entry represents the RNA recognition motif 1 (RRM1) of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing [
]. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm []. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm [,
]. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV) [
]. hnRNP A1 contains two RNA recognition motifs (RRMs) [
,
], followed by a long glycine-rich region at the C terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.
This entry represents the RNA recognition motif 2 (RRM2) of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing [
]. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm []. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm [,
]. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV) [
]. hnRNP A1 contains two RNA recognition motifs (RRMs) [
,
], followed by a long glycine-rich region at the C terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.
Members of this transpeptidase family are, in most cases, designated sortase B, product of the srtB gene. This protein shows only distant similarity to the sortase A family, for which there may be several members in a single bacterial genome. Typical SrtB substrate motifs include NAKTN, NPKSS, etc, and otherwise resemble the LPXTG sorting signals recognised by sortase A proteins. Sortase B sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope [
,
]. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference []. Sortase B cleaves surface protein precursors between threonine and asparagine at a conserved NPQTN motif with subsequent covalent linkage to peptidoglycan []. It is required for anchoring the heme-iron binding surface protein IsdC to the cell wall envelope and the gene encoding Sortase B is located within the isd locus in S. aureus [,
,
] and B. anthracis []. It may also play a role in pathogenesis []. Sortase B contains an N-terminal region that functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring. At the C terminus, it contains the catalytic TLXTC signature sequence, where X is usually a serine []. Genes encoding SrtB and its targets are generally clustered in the same locus.
This superfamily represents the C-terminal region of aspartic peptidases belonging to the MEROPS peptidase family A22 (presenilin family), subfamily A22A, the type example being presenilin 1 from Homo sapiens (Human).Presenilins are polytopic transmembrane (TM) proteins, mutations in which
are associated with the occurrence of early-onset familial Alzheimer'sdisease, a rare form of the disease that results from a single-gene
mutation [,
]. Alzheimer's disease is associated with the formation of extracellular deposits of amyloid, which contain aggregates of the amyloid-beta peptide. The β-peptides are released from the Alzheimer's amyloid precursor protein (APP) by the action of two peptidase activities: "beta-secretase"cleaves at the N terminus of the peptide, and "gamma-secretase"cleaves at the C terminus. The gamma-secretase cleavage occurs in a transmembrane segment of APP. Presenilin, which exists in a complex with nicastrin, APH-1 and PEN-2, has been identified as gamma-secretase from its deficiency [
] and mutation of its active site residues [], but proteolytic activity has only been directly demonstrated on a peptide derived from APP [
].Presenilin-1 is also known to process notch proteins [
] and syndecan-3 [].Presenilin has nine transmembrane regions with the active site aspartic acid residues located on TM6, within a Tyr-Asp motif, and TM7, within a Gly-Xaa-Gly-Asp motif [
]. The protein autoprocesses to form an amino-terminal fragment (TMs 1-6) and a C-terminal fragment (TMs 7-9) []. The tertiary structure of the human gamma-sectretase complex has been solved []. Nicastrin is extracellular, whereas presenilin-1, APH-1 and PEN-2 are all transmembrane proteins. The transmembrane regions of all three proteins form a horseshoe shape.
This entry represents the PH domain of Arf-GAP with SH3 domain, ANK repeat and PH domain-containing proteins (ASAPs). ASAPs (ASAP1, ASAP2, and ASAP3) function as Arf-specific GTPase-activating proteins (GAPs), participate in rhodopsin trafficking, are associated with tumour cell metastasis, modulate phagocytosis, promote cell proliferation, facilitate vesicle budding, Golgi exocytosis, and regulate vesicle coat assembly via a Bin/Amphiphysin/Rvs domain [
,
,
]. Each member has a BAR, PH, Arf GAP, Ank repeat and proline rich domains. ASAP1 and ASAP2 also have a SH3 domain at the C terminus []. The ASAP family is named for the first identified member, ASAP1 [].PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner [
]. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity []. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane []. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes [].
This entry represents a chromo (CHRromatin Organization MOdifier) structural domain, which consists of an SH3-like β-barrel capped by a C-terminal helix. Chromo domains are conserved modules of around 60 amino acids that are implicated in the recognition of lysine-methylated histone tails and nucleic acids. Chromo domains were originally identified in Drosophila modifiers of variegation, proteins that alter the structure of chromatin to the condensed morphology of heterochromatin. Domains with a chromo domain structural fold include:Chromo domain, which lacks the first strand of the SH3-like β-barrel.Shadow chromo domain, in which the first strand of the SH3-like β-barrel is altered by insertions.Chromo barrel domain, which is a typical SH3-like β-barrel fold (similar sequence motif to the canonical chromo domain).Histone-like DNA-binding proteins from Archaea [
].Chromo domains can be found in various nuclear proteins, including heterochromatin protein 1 (HP1) (N-terminal chromo domain and C-terminal chromo shadow domain), where the chromo domain recognises histone tails with specifically methylated lysines [
]; polycomb protein Pc, which is essential for maintaining the silencing state of homeotic genes during development (chromo domain important for chromatin targeting) []; histone methyltransferase clr4, which regulates silencing and switching at the mating-type loci and to affect chromatin structure at centromeres []; and the ATP-dependent helicase CHD1, which regulates ATP-dependent nucleosome assembly and mobilisation through conserved double chromo domains and a SWI2/SNF2 helicase/ATPase domain [].Chromo barrel domains are found in various histone acetyltransferases, such as MYST1 from Mus musculus (Mouse) and MOF from Drosophila melanogaster (Fruit fly) [
]. This domain can also be found in the human mortality factor 4-like protein, MRG15.
Serine proteases, trypsin family, serine active site
Type:
Active_site
Description:
The catalytic activity of the serine proteases from the trypsin family is
provided by a charge relay system involving an aspartic acid residue hydrogen-bonded to a histidine, which itself is hydrogen-bonded to a serine. The
sequences in the vicinity of the active site serine and histidine residues arewell conserved in this family of proteases [
]. A partial list of proteasesknown to belong to the trypsin family is shown below.
Acrosin.Blood coagulation factors VII, IX, X, XI and XII, thrombin, plasminogen, and protein C.Cathepsin G.Chymotrypsins.Complement components C1r, C1s, C2, and complement factors B, D and I.Complement-activating component of RA-reactive factor.Cytotoxic cell proteases (granzymes A to H).Duodenase I.Elastases 1, 2, 3A, 3B (protease E), leukocyte (medullasin).Enterokinase (EC 3.4.21.9) (enteropeptidase).Hepatocyte growth factor activator.Hepsin.Glandular (tissue) kallikreins (including EGF-binding protein types A, B, and C, NGF-gamma chain, gamma-renin, prostate specific antigen (PSA) and tonin).Plasma kallikrein.Mast cell proteases (MCP) 1 (chymase) to 8.Myeloblastin (proteinase 3) (Wegener's autoantigen).Plasminogen activators (urokinase-type, and tissue-type).Trypsins I, II, III, and IV.Tryptases.Snake venom proteases such as ancrod, batroxobin, cerastobin, flavoxobin,and protein C activator.Collagenase from common cattle grub and collagenolytic protease from Atlantic sand fiddler crab.Apolipoprotein(a).Blood fluke cercarial protease.Drosophila trypsin like proteases: alpha, easter, snake-locus.Drosophila protease stubble (gene sb).Major mite fecal allergen Der p III.In addition to proteins from eukaryotic species listed above, are a number of bacterial family members, including:
Achromobacter lyticus protease I.Lysobacter alpha-lytic protease.Streptogrisin A and B (Streptomyces proteases A and B).Streptomyces griseus glutamyl endopeptidase II.Streptomyces fradiae proteases 1 and 2.This entry represents the serine active site of serine proteases belonging to peptidase family S1.
Arenaviridae are single stranded RNA viruses. The arenaviridae S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin"structure. The mature glycoproteins that result are G1 and G2 and the N protein [
].Tacaribe virus (TACV) is an arenavirus that is genetically and antigenically
closely related to Junin arenavirus (JUNV), the aetiological agent of Argentinehaemorrhagic fever (AHF). It is well established that TACV protects experimental animals fully against an otherwise lethal challenge with JUNV. It has been established that it is the heterologous glycoprotein that protects against JUNV challenge. A recombinant vaccinia virus that expresses JUNV glycoprotein precursor (VV-GJun) protected seventy-two percent of the animals inoculated with two doses of VV-GJun against the lethal JUNV challenge [
].The GPC complex contains a cleaved stable signal peptide (SSP) in addition to the canonical receptor-binding (G1) and transmembrane fusion (G2) subunits. SSP is essential for intracellular transport of the GPC complex to the cell surface and for its membrane-fusion activity.This superfamily represents the zinc binding domain of GPC, available data is derived from studies on Junin arenavirus (JUNV). The face of the domain that contains the two zinc-binding clusters is well conserved among arenaviruses, and cluster II serves as a binding site for Cys-57 in the SSP. It is believed that the zinc-mediated anchoring of SSP contributes to positioning the ectodomain loop of SSP relative to the G2 ectodomain to modulate membrane fusion [
].
Lysosome-associated membrane glycoprotein, conserved site
Type:
Conserved_site
Description:
Lysosome-associated membrane glycoproteins (lamp) [
] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+
| | | | | | | |xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx
+--------------------------++Hinge++--------------------------++TM++C+In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [
] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region [
]. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. There are two signatures in this entry, one is centred on the first conserved cysteine of the duplicated domains. The second corresponds to a region that includes the extremity of the second domain, the totality of the transmembrane region and the cytoplasmic tail.
P pili tip fibrillum PapE protein, Enterobacteriaceae
Type:
Family
Description:
The Gram-negative pathogen Escherichia coli causes several common bacterial
illnesses in humans, including diarrhoea, neonatal meningitidis and urinary tract infections. Attachment to host tissues is essential for successful invasion, and requires interaction between a bacterial adhesive protein and
its target receptor. This protein is usually supported on a larger structure made up of heteropolymeric fibres [
]. Pyelonephritogenic E. coli specifically invade the uroepithelium by expressing between 100 and 300 pili on their cell surface. Pili are macromolecular structures that allow
binding to a digalactoside receptor in the urinary tract.
P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the
bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope [
]. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane.PapE can vary its structure and antigenic properties according to the
serotype strain of bacteria [], and therefore has the ability to evade host immune responses. A recent study into the assembly of P pili [] showed that both PapA and PapE automatically self-assemble into pilus rods and tip fibrillae, respectively, once released from the PapD chaperone.
Synaptotagmin-like proteins (Slps) contain a N-terminal RabBD (Rab-binding) domain and two C-terminal C2 domains, C2A and C2B [
]. The characteristic feature of the Slp family is the N-terminal domain (referred to as SHD for Slp Homology Domain), which is not found in other C-type tandem C2 proteins []. SHD functions as a specific Rab27A/B-binding domain []. This entry represents the C2B domain. The C2 domain is a Ca
2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking. C2 domains are unique among membrane targeting domains in that they show wide range of lipid selectivity for the major components of cell membranes, including phosphatidylserine and phosphatidylcholine. This C2 domain is about 116 amino-acid residues and is located between the two copies of the C1 domain in Protein Kinase C and the protein kinase catalytic domain [
]. Regions with significant homology [] to the C2-domain have been found in many proteins. The C2 domain is thought to be involved in calcium-dependent phospholipid binding [] and in membrane targetting processes such as subcellular localisation. The 3D structure of the C2 domain of synaptotagmin has been reported
[], the domain forms an eight-stranded β-sandwich constructed around a conserved 4-stranded motif, designated a C2 key []. Calcium binds in a cup-shaped depression formed by the N- and C-terminal loops of the C2-key motif. Structural analyses of several C2 domains have shown them to consist of similar ternary structures in which three Ca2+-binding loops are located at the end of an 8 stranded antiparallel β-sandwich.
Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain
Type:
Domain
Description:
Aconitase (aconitate hydratase;
) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [,
]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is smaller than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) [].Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [,
]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated [
].IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis [
]. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [
,
]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.3-isopropylmalate dehydratase (or isopropylmalate isomerase;
) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family [
]. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S]cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [
,
]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase , converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis [
]. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast [].This entry represents a region containing 3 domains, each with a 3-layer alpha/beta/alpha topology. This region represents the [4Fe-4S] cluster-binding region found at the N-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the C-terminal of bacterial AcnB. This domain is also found in the large subunit of isopropylmalate dehydratase (LeuC).
Aconitase (aconitate hydratase;
) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop [
,
]. Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is smaller than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) [].Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) [,
]. As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated [
].IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis [
]. Although IRP2 is homologous to IRP1, IRP2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes []. In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica [
,
]. In S. enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.3-isopropylmalate dehydratase (or isopropylmalate isomerase;
) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family []. Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S]cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively [
,
]. LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase , converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis [
]. Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus []. It is also found in the higher plant Arabidopsis thaliana, where it is targeted to the chloroplast [].This entry represents a region containing 3 domains, each with a 3-layer alpha/beta/alpha topology. This region represents the [4Fe-4S] cluster-binding region found at the N-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the C-terminal of bacterial AcnB. This domain is also found in the large subunit of isopropylmalate dehydratase (LeuC).
VirB5 proteins are an essential component of most type IV secretion systems. VirB5/TraC is a single domain protein consisting of a three helix bundle and a loose globular appendage [
]. Structural and functional studies indicate that VirB5 proteins participate in protein-protein interactions important for pilus assembly and function.
This domain conceptually resembles
, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure.
This entry represents a group of peptidoglycan biosynthesis proteins including stage V sporulation protein B (SpoVB), sporulation protein YkvU and probable cell division protein YtgP [
]. The integral membrane protein SpoVB has been implicated in the biosynthesis of the peptidoglycan component of the spore cortex in Bacillus subtilis [].
This entry represents the NS7b protein of Rousettus bat coronavirus (CoV) HKU9 and related proteins from betacoronaviruses in the nobecovirus subgenera (D lineage). The NS7b protein of lineage D betacoronavirus is an accessory protein whose function is unknown [
]. It is not related to NS7b proteins from other betacoronavirus lineages.
