The medium (M) genome segment of Hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins [], Gn and Gc (also known as G1 and G2, respectively) as a polyprotein precursor [, ]. Gn and Gc forms homotetramers at the surface of the virion, which attach the virion to host cell receptors including integrin beta3/ITGB3 and induce internalization, predominantly through clathrin-dependent endocytosis [, ]. This entry represents the polyprotein region which forms the Gc glycoprotein. It has been shown that the N-terminal region of glycoprotein Gc has the conserved CNP motif, suggested to be an integrin-binding motif []. Gc protein has a typical class II fusion protein fold consisting of a central β-sandwich domain (termed domain I) made of eight β-strands arranged in two antiparallel β-sheets, domain II which has an elongated shape with two subdomains (a central, opened β-barrel proximal to domain I and a distal β-sandwich 'tip'), and domain III, which has an Ig-like fold [, ].
This entry represents prokaryotic, primarily monofunctional, chorismate mutases of the AroQ class from high GC Gram-positive bacteria and archaea. In Corynebacterium and Pyrococcus, these are the apparently the sole chorismate mutase enzymes in their respective genomes. This is coupled with the presence in those genomes of the enzymes of the chorismate pathways both up- and downstream of chorismate mutase.The bifunctional members associated with this entry either have an N-terminal 3-dehydroquinate dehydratase domain or a C-terminal prephenate dehydratase domain associated with an amino acid-binding ACT domain.
Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria) []. This protein is cross-linked by a spore coat-associated transglutaminase.
This entry represents archaeal probable tRNA pseudouridine synthase B. It may be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.
This family consists of uncharacterised proteins found in firmicutes and high GC Gram-positive bacteria associated with human and animal guts. The function of this family is unknown.
This entry represents a protein region that is cleaved from a bunyavirus polyprotein to become the nonstructural protein NSm (encoded by the M segment). This region is flanked by glycoprotein Gn (also known as GP2) and glycoprotein Gc (also known as GP1), which plays a role in virion budding at Golgi tubes and in the subcellular location of Gc protein [].
The medium (M) genome segment of Hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins [], Gn and Gc (also known as G1 and G2, respectively) as a polyprotein precursor[, ]. Gn and Gc forms homotetramers at the surface of the virion, which attach the virion to host cell receptors including integrin beta3/ITGB3 and induce internalization, predominantly through clathrin-dependent endocytosis [, ]. This entry represents the Gn glycoprotein in which, the N-terminal two-thirds has been denoted as 'head' (Gn-H) interacts with Gc ectodomain. Release of Gn-H at acid pH induces a further conformational change of the Gc domain II tip which exposes non-polar side chains for insertion into the endosomal membrane [, ]. The C-terminal region of the Gn ectodomain is denoted as Gn base (Gn-B), which contributes the most to the intra-spike tetrameric contacts.
This family consists of uncharacterised proteins around 300 residues in length and is mainly found in various high GC Gram-positive bacteria, but also in several pathogenic and non-pathogenic enterobacteria (Salmonella, E. coli). The function of this family is not clear.
This family of proteins, often annotated as a putative IMP dehydrogenase, are related to IMP dehydrogenase and GMP reductase. Most species with a member of this family belong to the high GC Gram-positive bacteria.
This entry consists mostly of a standalone domain found in short uncharacterised proteins from various high GC Gram-positive bacteria, primarily Mycobacterium species. However, in some proteins, such as the Rv0943c protein from Mycobacterium tuberculosis H37Rv, this domain is found at the C terminus, following the FAD/NAD(P)-binding domain ().
This entry represents the Pus 10 family of tRNA pseudouridine synthases. Family members are responsible for the synthesis of pseudouridine from uracil-54 and uracil-55 in the psi GC loop of transfer RNAs []. The family appears to be distinct from the five commonly identified families of Psi synthases [].
All proteins in this entry for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the N-terminal region of DinG from some low GC Gram-positive bacteria.
This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see ). Sequence alignments suggest that these sequences perform the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade represents a subfamily that spans low GC Gram-positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium [, , ].
This entry represents essentially the full length, ~60 residues, of a two-gene paralogous family from Acidobacterium sp. MP5ACTX8. Sequences consist of an N-terminal signal sequence ending in a GC motif, suggestive of the lipoprotein signal sequence, followed immediately by a C-terminal domain sequence with characteristics PEP-CTERM-like sequences, including a PExP motif and a transmembrane helix. Both members occur next to the novel exosortase variant, XrtJ, which contains a novel C-terminal domain [].
Archaeal Pus10 is responsible for the synthesis of pseudouridine from uracil-54 and uracil-55 in the psi GC loop of transfer RNAs []. This entry also includes Pus10 homologues from eukaryotes. Human Pus10 homologue is a modulator of TRAIL-induced cell death and is required for the progression of the apoptotic signal through intrinsic mitochondrial cell death [, ]. Although eukaryotic Pus10 shares a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not resolved [].
This family of proteins restricted to the high GC Gram-positive bacteria includes GMP reductase from Mycobacterium smegmatis (GUAB1), which is involved in the purine-salvage pathway. This protein is composed of two domains: a catalytic domain with a TIM barrel structure and another that folds as a typical Bateman domain composed of two CBS domains (cystathionine-beta-synthase domain, CBS, ), which are essential for the NADPH-dependent conversion of GMP to IMP [].
Pseudouridine, the most common RNA modification, has been suggested to play a role in RNA stability, RNA folding/secondary structure, and translation efficiency and fidelity. Trub2 has been identified as a pseudouridine synthase that contributes to the conversion of uridine to pseudouridine (PSI) at position 390 in mitochondrial COXI (MT-CO1) mRNA and at position 697-699 in mitochondrial COXIII (MT-CO3) mRNA [, ]. Trub2 also catalyses pseudouridylation of some tRNAs, including synthesis of pseudouridine(55) from uracil-55, in the psi GC loop of a subset of tRNAs [].
HRTV is an insect-borne virus found in America that can infect humans. It belongs to the newly defined family Phenuiviridae, order Bunyavirales. HRTV contains three single-stranded RNA segments (L, M, and S). The M segment of the virus encodes a polyprotein precursor that is cleaved into two glycoproteins, Gn and Gc. Gc is a fusion protein facilitating virus entry into host cells []. G2 (also known as Gc) is necessary for optimal glycoprotein G1 (also found as Gn) expression and efficient production or viral-like particles and possibly for the cell infection, as G2 is determinant for cell fusion []. Phleboviral G2 fusion glycoprotein is both functionally and structurally analogous to the fusion glycoproteins of alphaviruses and flaviviruses, all of them recognize DC-SIGN receptor to enable viral attachment [].This domain is found at the C-terminal of several Phlebovirus glycoprotein G2 sequences. Two prefusion conformation structures of bunyavirus Gc from RVFV in the Phenuiviridae family []and Hantaan virus (HTNV) in the Hantaviridae family []have been solved.
This entry represents the pseudokinase domain found in membrane Guanylate Cyclase receptor guanylyl cyclase C (GC-C, also known as heat-stable enterotoxin receptor). This domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. GC-C binds and is activated by the intestinal hormones, guanylin (GN) and uroguanylin (UGN), which are secreted after salty meals to inhibit sodium absorption and induce the secretion of chloride, bicarbonate, and water. GN and UGN are also present in the kidney, where they induce increased salt and water secretion. This prevents the development of hypernatremia and hypervolemia after ingestion of high amounts of salt [, , ]. Membrane (or particulate) guanylate cyclases (GCs) consist of an extracellular ligand-binding domain, a single transmembrane region, and an intracellular tail that contains a PK-like domain, an amphiphatic region and a catalytic GC domain that catalyses the conversion of GTP into cGMP and pyrophosphate. Membrane GCs act as receptors that transduce an extracellular signal to the intracellular production of cGMP, which has been implicated in many processes including cell proliferation, phototransduction, and muscle contractility, through its downstream effectors such as PKG. The PK-like domain of GCs functions as a negative regulator of the catalytic GC domain and may also act as a docking site for interacting proteins such as GC-activating proteins [, , ].
Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated . By contract, Escherichia coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex.This entry also includes DhaKLM operon coactivator DhaQ from Streptococcus lactis. It forms a heterotetramer with DhaS and functions as a transcriptional regulator [].
HRTV is an insect-borne virus found in America that can infect humans. It belongs to the newly defined family Phenuiviridae, order Bunyavirales. HRTV contains three single-stranded RNA segments (L, M, and S). The M segment of the virus encodes a polyprotein precursor that is cleaved into two glycoproteins, Gn and Gc. Gc is a fusion protein facilitating virus entry into host cells []. G2 (also known as Gc) is necessary for optimal glycoprotein G1 (also found as Gn) expression and efficient production or viral-like particles and possibly for the cell infection, as G2 is determinant for cell fusion []. Phleboviral G2 fusion glycoprotein is both functionally and structurally analogous to the fusion glycoproteins of alphaviruses and flaviviruses, all of them recognize DC-SIGN receptor to enable viral attachment [].This domain consists of the N-terminal and middle domains, known as fusion domain, of several Phlebovirus glycoprotein G2 sequences.
Herpesviruses are dsDNA viruses with no RNA stage. This entry represents a conserved domain found in several Herpes viruses glycoproteins, including:Glycoprotein-D (gD or gIV), which is common to Human herpesvirus 1 (HHV-1) and Human herpesvirus 2 (HHV-2), as well as Equid herpesvirus 1, Bovine herpesvirus 1 and Meleagrid herpesvirus 1 (MeHV-1). Glycoprotein-D has been found on the viral envelope and the plasma membrane of infected cells. gD immunisation can produce an immune response to bovine herpes virus (BHV-1). This response is stronger than that of the other major glycoproteins gB (gI) and gC (gIII) in BHV-1 [, , , ].Glycoprotein G (gG), which is one of the seven external glycoproteins of Human herpesvirus 1 (HHV-1) and Human herpesvirus 2 (HHV-2) []. In the HHV-2 virus-infected cell, gG-2 iscleaved into a secreted amino-terminal portion (sgG-2) and a carboxy-terminal portion. The latter protein is further O-glycosylated, generating the cell membrane-associated mature gG-2 (mgG-2). The mgG-2 protein has widely been used as a prototype antigen for detection of type-specific antibodies against HHV-2 [].Glycoprotein GX (gX), which was initially identified in Suid herpesvirus 1 (Pseudorabies virus).
This entry describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Also included are enzymes with the common name of N-acylamino acid racemase (NAAAR, or the more general term, racemase / racemase family), which refers to the enzyme's industrial application as a racemase that catalyses the racemization of N-acylamino acids, and not to its biological function as o-succinylbenzoic acid synthetase []. NAAARs act on a broad range of N-acylamino acids rather than amino acids. Enantiopure amino acids are of industrial interest as chiral building blocks for antibiotics, herbicides, and drugs. Most members of this group of o-succinylbenzoate synthases are proteins from low GC Gram-positive bacteria and archaea. menC/NAAAR is a member of the enolase superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion [, ].
The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigmafactors, are required for the transcription of specific subsets of genes.With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors [].This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:and SigG:as well as SigB:), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []:Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus.Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis [, ]; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.This entry represents CobF precorrin-6A synthase (), a pathway-specific enzyme in the aerobic pathway. After precorrin-4 is methylated at C-11 by CobM to produce precorrin-5, the extruded acyl group is then removed in the subsequent step, which also sees a methyl group added at C-1 in a reaction catalysed by CobF. The product of this reaction is precorrin-6A, which is subsequently reduced by an NADH-dependent reductase to precorrin-6B []. This entry identifies CobF in high GC Gram-positive, alphaproteobacteria and pseudomonas-related species.
The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ].Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three α-helices and a pair of antiparallel β-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the β-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see ). Most DtxR-type metalloregulators bind as dimers to the DNA major groove.
