DltA is part of the operon for incorporation of D-Ala residues into lipoteichoic acids (LTAs), which requires the activity of four gene products (DltA to DltD). DltA is a cytoplasmic D-alanine-D-alanyl carrier protein ligase that catalyses the D-alanylation of the D-alanyl carrier protein DltC (or Dcp); DltB is a transmembrane protein thought to be involved in the efflux of activated D-alanine to the site of acylation; and DltD is thought to be a membrane-associated protein that may have multifunctional activities (hydrolysis of mischarged DltC, facilitation of D-alanine ligation to DltC and D-alanylation of LTAs) [
,
].
This family represents D-alanyl carrier protein ligase DltA and similar proteins, including L-proline--[L-prolyl-carrier protein] ligase.DltA is part of the operon for incorporation of D-Ala residues into lipoteichoic acids (LTAs), which requires the activity of four gene products (DltA to DltD). DltA is a cytoplasmic D-alanine-D-alanyl carrier protein ligase that catalyses the D-alanylation of the D-alanyl carrier protein DltC (or Dcp); DltB is a transmembrane protein thought to be involved in the efflux of activated D-alanine to the site of acylation; and DltD is thought to be a membrane-associated protein that may have multifunctional activities (hydrolysis of mischarged DltC, facilitation of D-alanine ligation to DltC and D-alanylation of LTAs) [
,
].L-proline--[L-prolyl-carrier protein]ligase, also known as L-prolyl-AMP ligase, participates in the biosynthesis of undecylprodigiosin [
] where it catalyses the conversion of L-proline to L-prolyl-AMP and the transfer of the L-prolyl group to acyl carrier protein RedO [].
This is a family of major tegument proteins from Herpesviruses. Herpesvirus tegument proteins counteract the intrinsic anti-viral defenses and support the early steps of infection. BNRF1 is the Epstein-Barr virus (EBV) major tegument protein and plays an important role in viral transport from the endosomes to the nucleus [
]. Furthermore, it supports EBV early infection by interacting with host nuclear protein Daxx and disrupting the formation of the Daxx-ATRX chromatin remodeling complex [].
This R3H domain is found in the Saccharomyces cerevisiae protein SQS1 and in fungal and plant proteins with unknown functions, all of which also contain a G-patch domain. SQS1 may be involved in splicing, since overexpression antagonizes the suppression of splicing defects by spp382 mutants [
].The R3H domain is a conserved sequence motif found in proteins from a diverse range of organisms including eubacteria, green plants, fungi and various groups of metazoans, but not in archaea and Escherichia coli. The domain is named R3H because it contains an invariant arginine and a highly conserved histidine, that are separated by three residues. It also displays a conserved pattern of hydrophobic residues, prolines and glycines. It can be found alone, in association with AAA domain or with various DNA/RNA binding domains like DSRM, KH, G-patch, PHD, DEAD box, or RRM. The functions of these domains indicate that the R3H domain might be involved in polynucleotide-binding, including DNA, RNA and single-stranded DNA [
].The 3D structure of the R3H domain has been solved. The fold presents a small motif, consisting of a three-stranded antiparallel β-sheet, against which two α-helices pack from one side. This fold is related to the structures of the YhhP protein and the C-terminal domain of the translational initiation factor IF3. Three conserved basic residues cluster on the same face of the R3H domain and could play a role in nucleic acid recognition. An extended hydrophobic area at a different site of the molecular surface could act as a protein-binding site [
].
This domain is found in bacteria and eukaryotes. This domain is about 120 amino acids in length. This family is the inner membrane complex of parasitic organisms. This is a cytoskeletal structure associated with the pellicle of these parasites.
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 [
,
].This entry specifically identifies the archaeal version of the large ribosomal complex L7 protein. The family is a narrower version of the
model which also recognises the L30 protein. Multifunctional RNA-binding protein that recognises the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Parvoviruses are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides. Parvoviruses have been described that infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contain two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons [
,
].The Parvovirus coat protein VP1 together with VP2 forms a capsomer. Both of these proteins are formed from the same transcript using alternative translation start codons. As a result, VP1 and VP2 differ only in the N terminus region. VP2 is involved in packaging the viral DNA [
]. The mature viron contains three capsid proteins VP1, VP2, and VP3 and a noncapsid protein NS1. VP3 may arise from a third start codon with a favorable translationinitiation context which is present at position 3067 in the ChPV genome and which has been described in the goose and Muscovy duck parvoviruses [
].Parvovirus coat proteins have a β-barrel fold [
].
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 [
,
].The L21 superfamily contains proteins from a number of eukaryotic and archaebacterial organisms which include mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.
This entry represents highly hydrophobic proteins that are commonly preceded by a structured RNA element called the yybP-ykoY leader or SraF, which may serve as a riboswitch. From the larger group of TerC homologues (
), this entry contains protein YjbE from Bacillus subtilis. A transport function is proposed.
This family contains proteins that have a signal transduction response regulator receiver domain at the N terminus and a OmpR/PhoB-type DNA-binding domain at the C terminus. Homologues are predominantly from bacteria, but also eukaryotes and archaea. Members of the family are frequently part of a two-component regulatory system, including:
Transcriptional regulatory protein WalR, a member of the two-component regulatory system with WalK involved in the regulation of the ftsAZ operon and others [
]
Heme response regulator HssR, a member of the two-component regulatory system with HssS involved in intracellular heme homeostasis and tempering of staphylococcal virulence.Response regulator protein GraR, a member of the two-component regulatory system with GraS involved in resistance against cationic antimicrobial peptides [
]
Response regulator MprA, a member of the two-component regulatory system with MprB which contributes to maintaining a persistent infection in the host [
]
Response regulator ArlR, a member of the two-component regulatory system with ArlS involved in the regulation of adhesion, autolysis, multidrug resistance and virulence [
]
Response regulator SaeR, a member of the two-component regulatory system with SaeS involved in the regulation of staphylococcal virulence factors [
]
SV2 proteins are abundant synaptic vesicle proteins expressed in two major (SV2A and SV2B) and one minor isoform (SV2C) that resemble transporter proteins. SV2B knockout mice are phenotypically normal while SV2A- and SV2A/SV2B
double knockout mice exhibit severe seizures and die postnatally. Without SV2 proteins, presynaptic Ca2+accumulation during consecutive action potentials causes abnormal increases in neurotransmitter release that destabilise synaptic circuits and induce epilepsy [
].
This entry describes a very small (as short as 33 amino acids) protein of unknown function, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase [
]. It begins with an aromatic motif MWYFXW and appears to contain a membrane-spanning helix. This protein appears to be restricted to the Proteobacteria and exist in a single copy only. We suggest it may be a membrane subunit of the terminal oxidase. The family is named after the Escherichia coli member YbgT (). This model excludes the apparently related protein YccB (
).
Interferon alpha-inducible protein IFI6/IFI27-like
Type:
Family
Description:
This entry represents interferon alpha-inducible proteins IFI6 (also known as IFI-6-16) and IFI27-like (also known as ISG12) which play a role in the apoptotic process and also have pro-apoptotic activity [
,
]. ISG12a is a mitochondrial protein that contributes to IFN-induced apoptosis through perturbation of normal mitochondrial function [].
This entry represents bacteriophage lambda, GpU, a minor tail protein. GpU plays an essential role in tail assembly by capping the rapidly polymerizing tail once it has reached its requisite length and serving as the interaction surface for the completion protein [
]. GpU forms a hexameric ring within the tail structure since it spontaneously forms such rings in the presence of Mg2+ that match the size of the hexameric rings of gpV that comprise the bulk of the tail tube. However, prior to tail assembly, gpU remains monomeric []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homologue of bacterial L16. L16 and L10e exhibit structural differences at the N terminus [
,
,
,
,
,
,
,
].This entry represents a structural domain superfamily with an alpha/β-hammerhead fold, where the β-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16.
The olfactory receptors of terrestrial animals exist in an aqueous environment, yet detect odorants that are primarily hydrophobic. The aqueous solubility of hydrophobic odorants is thought to be greatly enhanced via odorant binding proteins which exist in the extracellular fluid surrounding the odorant receptors [
]. This family is composed of pheromone binding proteins (PBP) and general-odorant binding proteins (GOBP). GOBPs and PBPs form a subgroup of the insect odorant binding proteins (OBPs). PBPs are male-specific and associate with pheromone-sensitive neurons [].
YabA is involved in initiation control of chromosome replication [
]. It interacts with both DnaA and DnaN, acting as a bridge between these two proteins [].
YjbH is a family of Gram-negative β-barrel outer-membrane lipoproteins that act as putative porins. YbjH is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjH and F are predicted to be β-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production [
].
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 S11 [
] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. S14 is the eukaryotic homologue of S11; they constitute the uS11 family that includes bacterial, archaeal and eukaryotic proteins [].
Mycoplasma genitalium has the smallest known genome of any free-living organism. Its complete genome sequence has been determined by whole genome random sequencing and assembly. Only 470 putative coding regions were identified, including genes for DNA replication, transcription and translation, DNA repair, cellular transport and energy metabolism. One family of hypothetical proteins, which includes products of the
MG067/MG068/MG395 genes, has been shown to have homologues of similarlyunknown function in Mycoplasma pneumoniae.
Members of this protein family have a Sec-independent twin-arginine tranlocation (TAT) signal sequence, which enables tranfer of proteins folded around prosthetic groups to cross the plasma membrane. These proteins have four copies of a repeat of about 23 amino acids that resembles the β-helix repeat. β-helix refers to a structural motif in which successive beta strands wind around to stack parallel in a right-handed helix, as in AlgG and related enzymes of carbohydrate metabolism. The twin-arginine motif suggests that members of this protein family bind some unknown cofactor.
Proteins in this entry include MmcB (
) from Caulobacter crescentus. MmcB is required specifically for MMC-induced mutagenesis. Based on the structural analysis of a close homologue, MmcB is predicted to be an endonuclease [
].
This entry represents GPALPP motifs-containing protein 1 from humans (GPAM1) and similar proteins found in eukaryotes. The function of GPAM1 is not clear. It has been shown to be overexpressed in follicular lymphoma (FL), a frequent type of Mature B-cell non-Hodgkin lymphoma [
].
Fat storage-inducing transmembrane protein family (FIT/FITM, also known as Acyl-coenzyme A diphosphatase
) plays an important role in lipid droplet accumulation. They are endoplasmic reticulum (ER) resident membrane proteins that induce lipid droplet accumulation in cell culture and when expressed in mouse liver [
]; they hydrolyses fatty acyl-CoA to yield acyl-4'-phosphopantetheine and adenosine 3',5'-bisphosphate, with preference of unsaturated long-chain acyl-CoA substrates in the ER []. The ability to store fat in the form of cytoplasmic triglyceride droplets is conserved from yeast to humans, important for maintaining ER structure and for lipid droplets (LDs) biogenesis, which are lipid storage organelles involved in maintaining lipid and energy homeostasis [,
]. The FIT family of proteins are not involved in triglyceride biosynthesis [].In mammals there are two FIT proteins, FIT1, which is muscle specific and FIT2, which is expressed in most other tissues [
,
]. Yeast has two FIT2 orthologues, called Scs3p and Yft2p but no FITM1. FIT1 and FIT2 proteins are six-transmembrane-domain containing proteins with both the N and C termini residing in the cytosol. FIT2 is the more ancient conserved homologue of the FIT family; this family of proteins do not share sequence similarity to known proteins or domains.
This entry represents a group of proteins from enterobacteria, including Cell division protein DrpB from Escherichia coli. DrpB is a non-essential division protein that localizes to the septal ring in low ionic strength medium [
].
Bacterial microcompartments (BMCs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. They are found across bacteria where they play functionally diverse roles including CO(2) fixation and the catabolism of a range of organic compounds. They function as organelles by sequestering particular metabolic processes within the cell. A shell or capsid, which is composed of a few thousand protein subunits, surrounds a series of sequentially acting enzymes and controls the diffusion of substrates and products (including toxic or volatile intermediates) into and out of the lumen. Although functionally distinct BMCs vary in their encapsulated enzymes, all are defined by homologous shell proteins. The shells of BMCs are made primarily of a family of proteins whose structural core is the BMC domain, and variations upon this core provide functional diversity [
,
,
]. This entry represents Carboxysome shell protein CcmK and similar proteins from cyanobacteria. CcmK is one of the shell proteins of the carboxysome, a polyhedral BMC where RuBisCO (ribulose bisphosphate carboxylase) is sequestered for primary carbon production. It assembles into hexamers which make sheets that form the facets of the polyhedral carboxysome [
,
]. The formation of hexamers might play a role in environmental adaptability [].
This entry identifies proteins that are decribed as citrate utilization protein B, restricted to the proteobacteria. CitB [
] has been identified in Salmonella and Escherichia coli as the signal transduction component of a two-component system for citrate in which CitA acts as a citrate transporter.This domain is also a C-terminal domain in the Rhodobacter capsulatus (Rhodopseudomonas capsulata) CobZ gene, which in most other species exists as the separate CitB gene adjacent to CobZ. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene [
]) and is complemented by the characterised precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, haem and Fe-S cluster cofactors and is believed to require dioxygen as a substrate.
Members of this family are widely (though sparsely) distributed bacterial proteins, about 230 residues in length and in fungal proteins, which are around 400 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown.
Members of this family are widely (though sparsely) distributed bacterial proteins, about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown.
This entry represents transcription attenuation protein MtrB. MtrB is required for transcription attenuation control in the Trp operon. This trans-acting factor seems to recognise a 10 bases nucleotide sequence in the Trp leader transcript causing transcription termination. It binds the leader RNA only in presence of L-tryptophan [
].
This entry includes synaptonemal complex protein 2 (SYCP2) and synaptonemal complex protein 2-like (SYCP2L).SYCP2 is one of the major components of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase [
].SYCP2L has partial sequence homology to a SYCP2 and is the major component of nucleolar cortical skeleton in Xenopus oocytes [
]. In humans, SYCP2L promotes primordial oocytes survival, thus being associated with age at natural menopause (ANM) [].
Regulated endocrine-specific protein 18 (RESP18) is a major glucocorticoid-responsive protein that is mainly distributed in the peripheral endocrine and neuroendocrine tissues [
]. The protein shares sequence homology with the luminal region of IA-2, a dense core vesicle (DCV) transmembrane protein involved in insulin secretion [].The function of RESP18 is unknown, but it may may play an important regulatory role in corticotrophs and peptidergic neurons [
].
Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA [
].
Nitrogen fixation is catalysed by the nitrogenase complex and can be inhibited by carbon monoxide. The CowN protein protects against this inhibition, allowing nitrogen fixation-dependent growth to occur in the presence of carbon monoxide [
]. The mechanism by which CowN confers this protection is not known.
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 [
,
].Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA [
]. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.
The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [
], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.The core structure of S18 is composed of three helices arranged in a close or partly open bundle fold with right-handed twist going up-and down.
This family is found in bacteria and viruses, and is approximately 160 amino acids in length. Some annotation suggests that it may be a tail fibre protein. There are two completely conserved residues (K and W) in these proteins that may be functionally important.
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 L14 is one of the proteins from the large ribosomal subunit.
In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.
This entry represents a conserved hypothetical protein about 240 residues in length found so far in Proteobacteria including Shewanella oneidensis and Ralstonia solanacearum, usually as part of a paralogous family. The function is unknown.
This entry represents the probable protein kinase UbiB (also known as as AarF), which is required for ubiquinone biosynthesis [
,
,
]. It may function in regulating Q8 biosynthesis via its putative kinase activity [].
This entry contains proteins of unknown function, which include HutD from Pseudomonas fluorescens and Ves from Escherichia coli K12.HutD from P. fluorescens is a component of the histidine uptake and utilisation operon. HutD is operonic with the well characterised repressor protein HutC. Genetic analysis using transcriptional fusions (lacZ) and deletion mutants shows that hutD is necessary to maintain fitness in environments replete with histidine. HutD probably sets an upper bound on the level of hut operon transcription [
]. The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of HutD from Pseudomonas aeruginosa show that urocanate (the first breakdown product of histidine) docks with the active site of HutD.
Proteins of the Ves family have no known function. Ves is induced by various environmental stresses, including low temperature, osmotic shock and oxygen. Expression is induced more than 10 fold by reducing temperature from 37 to 25 degrees Celsius [
].
This entry represents an uncharacterised protein family that occurs only among the roughly 8 percent of prokaryotic species that carry homologues of the integral membrane protein exosortase (see
), a proposed protein-sorting system transpeptidase.
This protein family contains proteins with a median length of about 175, including a strongly conserved N-terminal region of about 55 amino acids, a conserved extreme C-terminal region of about 15 amino acids, and highly variable sequence in between the two.
This family represents the plant homologues of C. elegans uncoordinated protein 93 (also called putative potassium channel regulatory protein unc-93), including UNC93-like protein 3 from Arabidopsis thaliana. It maintains K+ homeostasis through abscisic acid (ABA) signalling pathway, which positively regulates abiotic stress tolerance and plant growth [
].
MauL is one of the products from the methylamine utilization gene cluster in Methylobacterium extorquens AM1 [
]. Mutants generated by insertions in mauL were not able to grow on methylamine or any other primary amine as carbon sources. MauL belongs to the blue or type I copper protein family, which are involved in electron transfer reactions, with the Cu centre transitioning between the oxidized Cu(II) form and the reduced Cu(I) form [].
Ribosomal protein L13 is one of the proteins from the large ribosomal subunit [
]. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.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 [
,
].The structure of the L13 domain is composed of three layers (alpha/beta/alpha) with parallel β-sheet of four strands.
Proteins in this entry are encoded by a gene that is found in flagellar operons of Bacillus-related organisms. The function is unknown. A tentative assignment as a regulator has been made in some sources.
This entry includes inactive rhomboid proteins (iRhom1/2), which are catalytically inactive rhomboid protease homologues that play crucial roles within the secretory pathway, including protein degradation, trafficking regulation, and inflammatory signaling [
]. These are metazoan specific pseudoproteases which regulate ADAM17 protease, a sheddase of the epidermal growth factor (EGF) receptor ligands and TNF, acting as trafficking factors that escort ADAM17 from the ER to the later secretory pathway. They are required for the cleavage and release of a variety of membrane-associated proteins []. iRhoms share a common structure comprising 7-helix transmembrane-spanning domains (TMDs) which is a conserved rhomboid fold, an extended N-terminal cytosolic domain and a luminal loop [,
].These proteins have been linked to the development and progression of several autoimmune diseases including rheumatoid arthritis, lupus nephritis, as well as hemophilic arthropathy [
] and also in neurological disorders such as Alzheimer's and Parkinson's diseases, inflammation, cancer and skin diseases [].
This HMM represents a protein family largely restricted to the Actinobacteria (high-GC Gram-positives), although it is also found in the Chloroflexi. Distant similarity to the phosphatidylinositol 3- and 4-kinase is suggested by the matching of some members to .
This entry represents the L12 protein of the large (50S) subunit of the archaeal ribosome. Archaeal L12 is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12 is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative [
].
The PEP-CTERM/exosortase system has been previously identified through in silico analysis [
]. This entry describes a PEP-CTERM-like variant C-terminal protein sorting signal, as found at the C terminus of twenty otherwise unrelated proteins in Verrucomicrobiae bacterium DG1235. The variant motif, VPDSG, seems an intermediate between the VPEP motif () of typical exosortase systems and the classical LPXTG of sortase in Gram-positive bacteria [
].
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.
This family consists of several NOA36 proteins (also known as zinc finger protein 330) which contain 29 highly conserved cysteine residues. In mitosis it associates with centromeres and concentrates at the midbody in cytokinesis [
].
This entry consists of several fungal-specific membrane proteins, including Sur7 and Rim9. Sur7 carries four transmembrane domains and is a long-lived component of eisosomes, which are large immobile cell cortex structures associated with endocytosis [
]. It is involved in sporulation [].This entry also includes PalI which is part of a pH signal transduction cascade. Based on the similarity of PalI to the yeast Rim9 meiotic signal transduction component it has been suggested that PalI might be a membrane sensor for ambient pH [
].
Bacillus subtilis strain 168 produces the lantibiotic sublancin 168, a broad spectrum bacteriocin. SunI has been identified as the sublancin immunity protein. It belongs to a novel class of bacteriocin antagonists with a particular topology consisting of one N-terminal transmembrane domain and the bulk of the protein facing the cytoplasm [
].
This is a family of exported virulence proteins from largely Acinetobacteria and a few Fimicutes, Gram-positive bacteria. It is exported in conjunction with EspA as an interacting pair [
,
,
].
The proteins in this entry are functionally uncharacterised. However, they show protein sequence similarity with Sjoegren syndrome/scleroderma autoantigen 1 protein (
).
Coiled-coil domain-containing protein 91 (also known as GGA-binding partner or accessory protein p56) colocalizes and interacts with GGA proteins, which are adaptors involved in clathrin-mediated transport between the trans-Golgi network and endosomal system [
]. p56 cooperates with the GGAs and clathrin in the sorting of cathepsin D to lysosomes [].
PAP-1 (for Pim-1-associated protein) is thought to be a target for Pim-1 kinase [
]. It has been implicated as the defective gene in RP9, one type of autosomal dominant retinitis pigmentosa []. PAP-1 has a role in pre-mRNA splicing and this activity is dependent on its phosphorylation state []. PAP-1 interacts with Prp3p; both were found to be components of the U4/U6.U5-tri-snRNP complex, one form of the spliceosome [].
CrgA is a transmembrane (TM) protein, first described in Streptomyces as being required for sporulation through the coordination of several aspects of reproductive growth. In Mycobacterium tuberculosis, CrgA is a central component of the divisome, and consists of 93 residues with two predicted TM helices (TM1: residues 29-51 and TM2: residues 66-88). CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and also stabilizes the divisome. Reduced production of CrgA results in elongated cells and reduced growth rate, and loss of CrgA impairs peptidoglycan synthesis. CrgA has homologs in other actinomycetes [
].
The Drosophila protein Futsch has homology to MAP1B and controls synaptic growth at the Drosophila neuromuscular junction through the regulation of the synaptic microtubule cytoskeleton. Futsch protein colocalises with microtubules and identifies cytoskeletal loops that traverse the lateral margin of select synaptic boutons. Futsch mutations disrupt synaptic microtubule organisation, reduce bouton number, and increase bouton size. These deficits can be partially rescued by neuronal overexpression of a Futsch MAP1B homology domain [
]. The translation of Futsch is repressed by fragile X messenger ribonucleoprotein 1 (FMR1/FMRP), an RNA binding protein that acts as a negative translational regulator []. The N- and C-terminal domains of Futsch are homologous to the vertebrate MAP1B microtubule-associated protein. The central domain of Futsch is highly repetitive [
]. This entry represents the Futsch repeats.
Sak3 (also known as ORF35) from Lactococcus phage p2 is a novel single-strand annealing protein that stimulates homologous recombination [
]. Mutations in Sak3 can reduce sensitivity to the antiviral abortive infection mechanism AbiK [].
This domain covers the NSP16 region of the coronavirus polyprotein. It was originally named NSP13 and later changed to NSP16 to distinguish it from the helicase region [
]. NSP16 is a 7-methylguanine-triphosphate-adenosine (m7GpppA)-specific, SAM-dependent 2'-O-MTase that has selective RNA binding properties and is a cap-0 binding protein. It contains a highly conserved catalytic tetrad (K-D-K-E) that is a hallmark of RNA 2'O-MTases [,
,
]. NSP16 plays a key role in viral replication as it is involved in immune response evasion through the 2'-O-methylation of coronavirus RNA, which is essential for preventing recognition by the host. It mimics the human protein CMTr1 and, unlike CMTr1, it requires NSP10 as a binding partner to activate its enzymatic activity []. Structural analysis in NSP16 from SARS-CoV-2 identified a cryptic pocket (also present in other coronavirus such as SARS-CoV-1 and MERS) not present in human CMTr1, and the fact that NSP16 is one of the most conserved proteins of SARS-CoV-2 and related viruses, make it an interesting target for developing new antiviral treatment for COVID-19 and other diseases caused by coronaviruses [].
The unique coronavirus (CoV) transcription/replication machinery comprised of multiple virus-encoded non structural proteins (NSP) plays a vital role during initial and intermediate phases of the viral life cycle. This entry represents NSP14, encoded as part of polyprotein pp1ab and excised by NSP5. Its N-terminal exoribonuclease (ExoN) domain plays a proofreading role for prevention of lethal mutagenesis, and the C-terminal domain functions as an S-adenosyl methionine (SAM)-dependent (guanine-N7) methyl transferase (N7-MTase) for mRNA capping [,
,
,
,
,
]. NSP14 forms the nsp14-nsp10 complex involved in RNA viral proofreading [,
].
This entry includes non-structural protein 14 (NSP14) from gammacoronavirus.Nonstructural protein 14 (NSP14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain [
,
,
]. ExoN is important for proofreading and therefore, the prevention of lethal mutations []. The association of NSP14 with NSP10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The NSP10/NSP14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. NSP14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or NSP14 has been found to interfere with protein translation of cellular mRNAs [,
]. NSP14 inhibits host translation, an activity that is enhanced when NSP14 forms the complex with NSP10. This abolishes the type I interferon (IFN-I)-dependent induction of interferon-stimulated genes (ISGs), and therefore, is one of the SARS-CoV-2 mechanisms to impair host innate immune responses [].
This entry includes non-structural protein 14 (NSP14) from deltacoronavirus.
Nonstructural protein 14 (NSP14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain [,
,
]. ExoN is important for proofreading and therefore, the prevention of lethal mutations []. The association of NSP14 with NSP10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The NSP10/NSP14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. NSP14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or NSP14 has been found to interfere with protein translation of cellular mRNAs [,
]. NSP14 inhibits host translation, an activity that is enhanced when NSP14 forms the complex with NSP10. This abolishes the type I interferon (IFN-I)-dependent induction of interferon-stimulated genes (ISGs), and therefore, is one of the SARS-CoV-2 mechanisms to impair host innate immune responses [].
This entry includes non-structural protein 14 (Nsp14) from alphacoronavirus.Nonstructural protein 14 (NSP14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain [
,
,
]. ExoN is important for proofreading and therefore, the prevention of lethal mutations []. The association of NSP14 with NSP10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The NSP10/NSP14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. NSP14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or NSP14 has been found to interfere with protein translation of cellular mRNAs [,
]. NSP14 inhibits host translation, an activity that is enhanced when NSP14 forms the complex with NSP10. This abolishes the type I interferon (IFN-I)-dependent induction of interferon-stimulated genes (ISGs), and therefore, is one of the SARS-CoV-2 mechanisms to impair host innate immune responses [
].
This entry includes non-structural protein 14 (NSP14) from betacoronavirus. There are not yet publicly available structures of SARS-CoV-2 NSP14, but computed homology model based on the structure of SARS-CoV-1 NSP14 (
), revealed that they share ~95% sequence identity. Superposition of the methyltransferase catalytic centers of SARS-CoV-1 and SARS-CoV-2 NSP14 showed 100% conservation of active site residues, including both the cap binding residues and the S-adenosylmethionine (SAM) binding residues. The active site of the exoribonuclease proofreading domain of NSP14 contains a DEDDH motif, which is identical to the corresponding motif found in SARS-CoV-1 NSP14 [
]. Nonstructural protein 14 (NSP14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain [
,
,
]. ExoN is important for proofreading and therefore, the prevention of lethal mutations []. The association of NSP14 with NSP10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The NSP10/NSP14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. NSP14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or NSP14 has been found to interfere with protein translation of cellular mRNAs [,
]. NSP14 inhibits host translation, an activity that is enhanced when NSP14 forms the complex with NSP10. This abolishes the type I interferon (IFN-I)-dependent induction of interferon-stimulated genes (ISGs), and therefore, is one of the SARS-CoV-2 mechanisms to impair host innate immune responses [].
Diphthine--ammonia ligase/Uncharacterised protein MJ0570
Type:
Family
Description:
This entry includes diphthine--ammonia ligases from eukaryotes and the uncharacterised protein MJ0570 from archaea. Diphthine--ammonia ligases are amidases that catalyse the last step of diphthamide biosynthesis using ammonium and ATP [
,
].
Gas vesicles provide cells with buoyancy, enabling them to remain at the water surface. These organelles are generally synthesized by halophilic archaea and cyanobacteria, as well as some other prokaryotes. A cluster of 12-14 gvp genes (gvpMLKJIHGFEDACNO) is responsible for gas vesicle synthesis in Halobacterium sp. [
]. GvpF and GvpL are essential for gas vesicle formation and display sequence similarity to one another, both containing predicted coiled-coil domains that are often involved in self-oligomerisation; and are structural components of the vesicle [].
This family includes the neuron-enriched endosomal proteins NSG1 (NEEP21), NSG2 (P19) and NSG3 (calcyon, Caly). They interact with distinct elements of the endosomal and synaptic scaffolding machinery [
]. NSG1 and NSG2 may not be resident endosomal proteins, and are also known as neuronal vesicle trafficking-associated proteins 1 and 2 respectively []. NSG1/NEEP21 plays a role in the trafficking of multiple receptors, including the cell adhesion molecule L1/NgCAM, the neurotransmitter receptor GluA2, and beta-APP []. The role of NSG2 is not known.It was originally thought that the Neuron-specific vesicular protein calcyon (previously known as D1 dopamine receptor-interacting, calcyon), interacted directly with the D1 dopamine receptor (DRD1) to modulate neocortical and hippocampal neuronal excitability as well as cAMP-dependent signalling [
]. However, this work was retracted, as it was shown that a direct interaction with the dopamine D1 receptor had been misinterpreted []. However, it has been shown that calcyon induces D1DR to stimulate intracellular Ca2+ release, and this suggests a possible functional interaction between calcyon and D1DR, despite there being, as yet, no direct interaction between them. A recent study suggested that calcyon-containing vesicles might transport D1DR by associating calcyon with D1DR through their assembly to clathrin []. However, as a single transmembrane protein, it is currently not clear how calcyon can regulate the internalization of D1DR from the plasma membrane to endocytic vesicles.Calcyon is a brain-specific protein, mainly localized in the intracellular endosomal vesicles of dendritic spines in dopamine expressing pyramidal cells in the prefrontal cortex and hippocampus and dorsal striatum region [
]. Neuron-specific vesicular protein calcyon has implicated in clathrin-mediated endocytosis. It is exclusively expressed in neurons, and localized in moving vesicles and it thought to play a role in brain plasticity []. Defective calcyon proteins have been implicated in both attention-deficit/hyperactivity disorder (ADHD) [,
] and schizophrenia [].
The imprinted GNAS cluster, located on chromosome 2 in mice and chromosome 20 in humans, contains transcripts that are maternally, paternally, and/or biallelically expressed. Neuroendocrine secretory protein 55 (NESP55) is encoded by an upstream exon of the GNAS1 gene, which is expressed exclusively from the maternal allele [
]. It is a neuroendocrine secretory granule protein originally identified by screening cDNA libraries from bovine chromaffin cells with antibody against secretogranin II []. It belongs to the granin family, whose members are involved in endocrine and neuronal secretory pathways [].NESP55 has been shown to act as biomarkers for endocrine and neuroendocrine tumours and implicated in cell growth [
]. It has been linked to pseudohypoparathyroidism type Ib (PHP-1b), an imprinted human disorder associated with methylation changes at one or several differentially methylated regions at the GNAS locus [].
This entry represents bacterial plasmid segregation protein ParM, also known as StbA [
,
]. ParM is involved in the control of plasmid partition and required for the accurate segregation of the plasmid, which forms filaments to drive partition.
A probable protein export sorting signal, PEP-CTERM, has been described previously [
]. It is predicted to interact with a putative transpeptidase we designate exosortase. This entry describes a variant with conserved motif VPLPA, rather than VPEP. It appears to be the recognition sequences for exosortase D. This variant is found prominently in two members of the Rhodobacterales, namely Jannaschia sp. CCS1 and Roseobacter denitrificans OCh 114 []. One interesting member protein has a full-length duplication and therefore two copies of this putative sorting domain.
Cass2 from Vibrio cholerae is an integron-associated protein that has been shown to bind cationic drug compounds with submicromolar affinity [
]. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species. The structure of Cass2 defines a monomeric β-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators.
The function of PB1A10.08 is not known. In a fission yeast study, it was identified as belonging to a group of late genes that are induced after meiotic divisions and whose expression remains high until the completion of sporulation [
].
PQQ-dependent catabolism-associated beta-propeller protein
Type:
Family
Description:
Members of this protein family contain a variable number of repeats each of the YVTN family β-propeller repeat. Members occur invariably as part of a transport operon that is associated with PQQ-dependent catabolism of alcohols such as phenylethanol.
Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (
) and a von Willebrand factor type A domain (
).
This entry represents a group of proteins from Firmicutes, including ClpXP adapter protein SpxH, also known as YjbH in Bacillus subtilis. This protein is required for efficient degradation of the RNA polymerase-binding transcription factor Spx by the protease ClpXP under non-stress conditions. It is organised into a DsbA-like thioredoxin domain, a linker and a C-terminal domain reminiscent of the winged helix-turn-helix fold [
,
,
].
This entry represents PylB, which is part of a three-gene cassette that directs the biosynthesis of pyrrolysine, the twenty-second amino acid, that is incorporated in some species at a UAG canonical stop codon [
]. PylB possesses signature residues suggesting it to be a radical SAM protein, which mediate radical-catalysed reactions. It catalyses the isomerisation of L-lysine to (2R,3R)-3-methylornithine [,
].
This family consists of several hypothetical proteins from bacteria and from Dictyostelium discoideum (Slime mold). The function of this family is unknown.
Cell division protein ZapD enhances FtsZ-ring assembly. It directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity [
].
The translocon-associated protein (TRAP, also known as the signal sequence receptor) complex is required for the efficient translocation of secretory and membrane proteins in the endoplasmic reticulum, and is also involved in the endoplasmic reticulum stress-mediated unfolded protein response pathway. This entry represents the gamma subunit of the translocon-associated proteins. Trap-gamma (also known as SSR3) appears to be required for vascular network formation in murine placental development [
].
This family is named after the human herpesvirus protein, but has been characterised in cytomegalovirus as UL47. Cytomegalovirus UL47 is a component of the tegument, which is a protein layer surrounding the viral capsid. UL47 co-precipitates with UL48 and UL69 tegument proteins, and the major capsid protein UL86. A UL47-containing complex is thought to be involved in the release of viral DNA from the disassembling virus particle [
].
This entry includes a group of envelope small membrane protein, including GP2b (also known as protein E) from Porcine reproductive and respiratory syndrome virus. It may function as a viroporin in the virion envelope that facilitates uncoating of the virus in order to release the genomic RNA into the cytoplasm for subsequent replication [
].
This family consists of several hypothetical bacterial proteins but contains one sequence Ree1 (
) from Saccharomyces cerevisiae [
]. Members of this family are typically around 200 residues in length. The function of this family is unknown.
The proteins in this entry are also known as secreted effector proteins. Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. They contribute to the formation of Salmonella-induced filaments (Sifs) in infected epithelial cells and to replication in macrophages [
].SopD is a type III virulence effector protein whose structure consists of 38% α-helix and 26% β-strand [
].
