This entry represents a family of general phage tail assembly chaperone proteins from double-stranded DNA viruses with no RNA stage, many of which are unclassified.
Members of this family are found in Solanaceae spp. plants, a taxonomic group (family) that includes pepper and tobacco
plant species. Synthesis of these proteins is induced by Tobacco mosaic virus and salicylic acid []; indeed theyare thought to be involved in the development of systemic acquired resistance (SAR) after an initial hypersensitive
response to microbial infection [,
]. SAR is characterised by long-lasting resistance to infection by a wide range ofpathogens, extending to plant tissues distant from the initial infection site [
].
This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved TTC sequence motif.
This is the N-terminal domain found in copper resistance protein ScsS present in Proteus mirabilis. ScsC is a powerful disulfide isomerase that is able to refold and reactivate the scrambled disulfide form of the model substrate RNase A. The protein has a thioredoxin 4 domain but, unlike other characterised proteins in this family, it is trimeric. The N-terminal domain is responsible for trimerization of ScsC which is needed for isomerase activity [
].
This family represents the matrix protein, M2, of Influenza C virus. The M1 protein is the product of a spliced mRNA (see
). Small
quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein.
This is a family of proteins of unknown function predominantly found in Halobacteria. This family includes some members which are thought to be peptidoglycan binding proteins.
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process.
Protein kinases fall into three broad classes, characterised with respect to substrate specificity []:Serine/threonine-protein kinasesTyrosine-protein kinasesDual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins)Protein kinase function is evolutionarily conserved from Escherichia coli to human [
]. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases [].Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups [
]:Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis [
]. RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction []. Cytoplasmic / non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases [
].This group represents a group of known and predicted receptor-type tyrosine-protein kinases, including the EGF and ERB receptors, and the melanoma-inducing oncogene product XmrK.
This family of proteins is functionally uncharacterised. Proteins in this family are typically between 237 and 332 amino acids in length. There are two completely conserved residues (C and R) that may be functionally important.
This family represents the matrix protein, M1, of Influenza C virus. The M1 protein is the product of a spliced mRNA. Small quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein (see ).
This is a family of proteins predominantly found in Halobacteria. They are thought to be GNAT (Gcn5-related N-acetyltransferases) family acetyltransferases.
This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 147 and 190 amino acids in length. There is a single completely conserved residue R that may be functionally important.
TRAF3IP1, also known as MIP-T3, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved [
].
This family includes the Bacillus subtilis YjdJ protein
, which is functionally uncharacterised. This is not a homologue of Escherichia coli YjdJ, which belongs to . The proteins in this family are found in bacteria and they are functionally uncharacterised.
This family contains several proteins of unknown function. Proteins in this family include DciA from Pseudomonas aeruginosa. DciA is a replicative helicase operator essential for bacterial replication initiation [
].
This family consists of several hypothetical bacterial proteins of around 230 residues in length. Members of this family are often referred to as YjaH and are found in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown.
Competence protein ComEA, helix-hairpin-helix domain
Type:
Domain
Description:
Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions [
].The development of genetic competence in Bacillus subtilis is a highly regulated adaptive response to stationary-phase stress. For competence to develop, the transcriptional regulator, ComK, must be activated. ComK is required for the expression of genes encoding proteins that function in DNA uptake. In log-phase cultures, ComK is inactive in a complex with MecA and ClpC. The comS gene is induced in response to high culture cell density and nutritional stress and its product functions to release active ComK from the complex. ComK then stimulates the transcription initiation of its own gene as well as that of the late competence operons [
].This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain.
This is the N-terminal domain of adaptive response protein AidB present in E. coli. AidB is upregulated in response to small doses of DNA-methylating agents initiates a response that mitigates the mutagenic and cytotoxic effects of DNA methylation. Tetramer formation is thought to be carried out by the N-terminal domain [].
AlkB proteins are dioxygenases that repair alkylation damage to DNA and RNA [
]. The Escherichia coli alkB gene product protects against cell killing by S(N)2-alkylating agents through DNA repair by a novel direct reversal DNA repair mechanism: the oxidative demethylation of N1-methyladenine or N3-methylcytosine DNA lesions. This reaction occurs on both single- and double-stranded DNA, and requires AlkB-bound non-heme Fe(2+), O(2) and alpha-ketogluterate to oxidize the offending methyl group. This is followed by the release of succinate, CO(2) and formaldehyde, and the restoration of undamaged A or C in DNA [].Nine mammalian AlkB homologues exist (ALKBH1-8, FTO), but only a subset functions as DNA/RNA repair enzymes [
], and only ALKBH1 is included in this entry. In humans, ALKBH1 (ABH1) is responsible for the conversion of 5-methylcytosine to 5-formylcytosine (f5C) in position 34 in mitochondrial tRNAMet [].
Glucose-6-phosphate dehydrogenase assembly protein OpcA
Type:
Family
Description:
OpcA protein may play a role in the functional assembly of glucose-6-phosphate dehydrogenase [
]. The opcA gene is found immediately downstream of zwf, the glucose-6-phosphate dehydrogenase (G6PDH) gene, in a number of species, including Mycobacterium tuberculosis, Streptomyces coelicolor, Nostoc punctiforme (strain ATCC 29133/PCC 73102), and Synechococcus sp. (strain PCC 7942). In the latter, disruption of opcA was shown to block assembly of G6PDH into active oligomeric forms.
The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [
]. CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).The defense reaction is divided into three stages. In the adaptation stage, the invader DNA is cleaved, and a piece of it is selected to be integrated as a new spacer into the CRISPR locus, where it is stored as an identity tag for future attacks by this invader. During the second stage (the expression stage), the CRISPR RNA (pre-crRNA) is transcribed and subsequently processed into the mature crRNAs. In the third stage (the interference stage), Cas proteins, together with crRNAs, identify and degrade the invader [
,
,
].The CRISPR-Cas systems have been sorted into three major classes. In CRISPR-Cas types I and III, the mature crRNA is generally generated by a member of the Cas6 protein family. Whereas in system III the Cas6 protein acts alone, in some class I systems it is part of a complex of Cas proteins known as Cascade (CRISPR-associated complex for antiviral defense). The Cas6 protein is an endoribonuclease necessary for crRNA production whereas the additional Cas proteins that form the Cascade complex are needed for crRNA stability [
]. This entry represents a family of DevR (Cas7)-type Cas proteins that includes DevR from Myxococcus xanthus. DevR is a key regulator of development. DevR mutants are incapable of fruiting body development [
]. The expression of DevR appears to be regulated through a number of means, including both location and autorepression.
There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively [
].The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a β-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered.
This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes
affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high levelof UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for
the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand.
During DNA replication, lesion bypass is an important cellular response to unrepaired damage in the genome. In the yeast
Saccharomyces cerevisiae (Baker's yeast), Rad6 and Rad18 are required for both the error-free and error-prone lesion bypass mechanisms. The Rad18 gene encodes a RING-finger protein with single-stranded DNA binding activity that interacts with theubiquitin-conjugating enzyme Rad6. This entry represents the Rad8 from fungi.
All proteins in this family for which functions are known bind single-stranded DNA and are involved in the the pairing of homologous DNA. RecT from Escherichia coli is a homotetramer which binds to single-stranded DNA and promotes the renaturation of complementary single-stranded DNA, and also plays a role in recombination. It is able to promote the annealing of complementary single
DNA strands and can catalyze the formation of joint molecules [].
P2 (30.2kDa) is the major outer-coat protein of the marine lipid-containing bacteriophage PM2. Each sub-unit of P2 is composed of two beta barrel jelly rolls, disposed normal to the surface of the capsid, which lend pseudo-6-fold symmetry to the molecules, facilitating their close packing within the capsid. There is a Ca2+ ion located between the two beta barrels of P2 that helps PM2 molecular organizations stabilization. This entry represents the N-terminal jelly roll domain of P2 [
].
This is a family of unknown function found in chordata. Family members contain a transmembrane region in the C-terminal and have been shown to be localized to the Golgi apparatus [
].
Malonyl CoA-acyl carrier protein transacylases transfer the malonyl moiety from coenzyme A to acyl-carrier protein. These include proteins involved in fatty acid biosynthesis (FabD), antibiotic biosynthesis (PksC) and the McdH subunit of malonate decarboxylase [
,
,
].
Peptidase A31, hydrogenase expression/formation protein
Type:
Family
Description:
This family of peptidases consists of hydrogenase expression/formation proteins, such as HoxM from Alcaligenes eutrophus and HybD from E. coli. They belong to the MEROPS peptidase family A31.Nickel/iron hydrogenases are synthesized as two subunits, with the larger subunit containing the metallo centre. Once nickel has bound, the large subunit is activated by processing at a conserved site near the C terminus [
]. The HycI endopeptidase releases a 32-residue peptide by cleavage of an Arg+Met bond []. A 15-residue peptide is released from hydrogenase 2 by cleavage of a His+Met bond by the HybD endopeptidase [
].The tertiary structure of HybD has been solved, and shows a twisted beta sheet with three alpha helices on one side and four on the other [
]. The molecule binds a single cadmium ion, which led to the peptidase being incorrectly identified as a metallopeptidase. It is possible that the metal binding site interacts with the nickel in the hydrogenase substrate []. The fold is similar to that of members of family A25, and both families A25 and A31 are included in the same clan, AE.
This entry represents a membrane protein, GltS, which is a glutamate carrier of an Na+-dependent, binding protein-independent, and glutamate-specific transport system [
,
].
Cytochrome B pre-mRNA-processing protein 2 (Cbp2) is required for splicing of the group I intron bI5 of the COB pre-mRNA [
,
]. It can also stimulate the splicing of the omega intron of the precursor of large ribosomal RNA [].
This entry represents a domain found in lipopolysaccharide assembly protein A (LapA). LabA and LapB function together in the assembly of lipopolysaccharide (LPS) [
]. This domain is also found in some uncharacterised proteins, such as Rv3760 from Mycobacterium tuberculosis.
Uncharacterised protein family UPF0288, methanogenesis
Type:
Family
Description:
Members of this protein family are only found in archaeal methanogens. The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis.
This entry represents a family of proteins including Hemolysin coregulated protein, Hcp (also known as TssD).Type VI secretion systems (T6SSs) are multiprotein complexes requiring numerous core proteins (Tss proteins) that function as a toxin delivery systems. The core Tss proteins include cytoplasmic, transmembrane, and outer membrane components. The toxin delivery apparatus includes a needle or tube structure which functions as a puncturing device. This is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. The inner tube is formed of Hcp (TssD), assembled as stacked hexamers [
]. Hcp proteins have also been reported to function as chaperones, by binding to and stabilizing effectors [].
Uncharacterised conserved protein UCP005648, calcium-binding
Type:
Family
Description:
The structure of the Methanobacterium thermoautotrophicum protein encoded by MTH1880 demonstrates the typical alpha + beta fold found in many proteins with different functions [
]. The molecular surface of the protein reveals a small, highly acidic pocket. MTH1880 protein contains a novel motif for calcium-specific binding, but does not show a calcium-induced conformational change typical of calcium sensor proteins. It may function as a calcium buffering protein [].
This is a family of unknown function found in archaebacterial proteins. The family has been solved via structural
genomics techniques and comprises of segregated helical and anti-parallel beta sheet regions. It is a putative metal-binding protein.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [
].
Non-structural protein NSP3A domain-like superfamily
Type:
Homologous_superfamily
Description:
The multi-domain non-structural protein NSP3 is the largest protein encoded by the coronavirus (CoV) genome, with an average molecular mass of about 200 kD. While some of the domains differ between CoV genera, eight domains of NSP3 exist in all known CoVs: the ubiquitin-like domain 1 (Ubl1), the Glu-rich acidic domain (also called "hypervariable region"), a macrodomain (also named "X domain"), the ubiquitin-like domain 2 (Ubl2), the papain-like protease 2 (PL2pro), the NSP3 ectodomain (3Ecto, also called "zinc-finger domain"), as well as the domains Y1 and CoV-Y of unknown functions. There are also two transmembrane regions, TM1 and TM2, which exist in all CoVs [
].The ubiquitin-like domain 1 (Ubl1) and the Glu-rich acidic region are located at the N-terminal of NSP3. These two regions together are also named "NSP3A". In addition to the four β-strands and two α-helices that are common to ubiquitin-like folds, the globular domain of NSP3A contains two short helices [
]. NSP3A is well conserved within different SARS-CoV sequences but exhibits low sequence identity (less than 35%) to other CoV NSP3 proteins []. It is an essential component of the replication/transcription complex and is involved in multiple biological processes, such as proteolysis and RNA processing [].This entry represents NSP3A that has been shown to bind ssRNA. The overall structure of the SARS-CoV Ubl1 domain is similar to human ubiquitin (Ub) and that of each of the two ubiquitin-like domains of human or mouse interferon-stimulated gene 15 (hISG15 or mISG15). It is also similar to the Ras-interacting domain (RID) of RalGDS [
,
].
G protein pathway suppressor 2 is involved in G protein-mitogen-activated protein kinase (MAPK) signaling cascades. When overexpressed in mammalian cells, this protein could potently suppress a RAS- and MAPK-mediated signal and interfere with JNK activity, suggesting that the function of this protein may be signal repression [
]. This protein is a component of the N-CoR-HDAC3 [] and alsothe SMRT corepressor complexes [
].
This family consists of outer dense fibre protein 2 and related proteins.
Outer dense fibre protein 2 (Odf2), also known as cenexin, seems to be a major component of sperm tail outer dense fibres (ODFs). ODFs are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail and may help to maintain the passive elastic structures and elastic recoil of the sperm tail. Odf2 may have a modulating influence on sperm motility. It functions as a general scaffold protein that is specifically localized at the distal/subdistal appendages of mother centrioles [,
].
Kinase associated protein B (KapB) is one of the major histidine kinases that provide phosphate input in the phosphorelay to produce SpoOA approximately P, the key transcription factor controlling the initiation of sporulation in Bacillus subtilis [
]. It forms an anti-parallel beta sheet with an extending alpha helical region.
Activating transcription factor 7-interacting protein
Type:
Family
Description:
Activating transcription factor 7-interacting protein (MCAF) family consists of MCAF1 and MCAF2 [
]. MCAF1 (also known as MBD1-containing chromatin-associated factor 1) is a recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation. It can both act as an activator or a repressor depending on the context [
,
]. MCAF2 might be involved in the transcription modulation during gonad development [
].
The function of mitochondrial ribosomal small-subunit protein MRP51 is not entirely clear, but deletion of the MRP51 gene completely blocks mitochondrial gene expression [
].
This entry represents the MmpL family of membrane transport proteins, which may be involved in lipid transport [
]. Mycobacterium tuberculosis MMPL10 is required for the biosynthesis of polyacyltrehalose (PAT) and the transport of diacyltrehalose (DAT) and possibly PAT to the cell surface [], while MMPL4 is a part of an export system required for biosynthesis and secretion of siderophores [].
Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation [
].Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Protein-export membrane protein SecD/SecF-like, archaeal-type
Type:
Family
Description:
Characterised members of the RND superfamily all probably catalyze substrate efflux via an H antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families; one of them is the SecDF protein-secretion accessory protein (SecDF) family, which is found in Gram-negative and Gram-positive bacteria, as well as archaea [
].This entry consists of uncharacterised putative transporters of the SecDF family, mainly from archaea.
The arginine exporter protein ArgO is involved in the export of arginine and is important to control the intracellular level of arginine and the correct balance between arginine and lysine [
].
Uncharacterised conserved protein UCP019240, SpoVT/AbrB-related
Type:
Family
Description:
This entry represents a small family of archaeal proteins, including SpoVT-AbrB domain-containing protein from Pyrococcus horikoshii (PHS018,
), which consists of six-stranded Greek-key barrel fold and two α-helices, with a very similar overall appearance to the double-psi and swapped-hairpin β-barrel [
]. Members of this group are predicted regulators of stationary/sporulation gene expression with an SpoVT/AbrB like domain.
Uncharacterised protein family UPF0285, methanogenesis
Type:
Family
Description:
This group represents uncharacterised conserved proteins. They share distant sequence similarity with members of
. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
This entry represents TraI, which is a component of the relaxosome complex. In the process of conjugative plasmid transfer the relaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein [
,
]. TraI contains four domains: a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [
,
]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [
,
].Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.This entry represents 50S ribosomal protein L31 from the type A subfamily.
This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA-binding regions have been identified in Bluetongue virus 17 (
) at residues 2-11, 153-166 and 274-286 [
]. NS2 multimers also possess nucleotidyl phosphatase activity []. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs [].
This family, which includes Haemophilus influenzae protein HI_1624, is functionally uncharacterised. Some family members were previously annotated as prokaryotic transmembrane nickel uptake transporters, NikM. This has been shown to be incorrect, as the proteins matched do not exhibit transmembrane properties, nor do they contain conserved residues associated with NikM proteins [
].
Biofilm-dependent modulation protein Bdm, putative
Type:
Family
Description:
This entry represents a group of tightly conserved proteins from Enterobacteriaceae which are annotated as being biofilm-dependent modulation protein homologues. This entry includes Bdm, whose expression is reduced in biofilms and is repressed by a high salt concentration [
].
