cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain of the bacitracin-resistance transporter. The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multi-enzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.
pfam09438, DUF2017, Domain of unknown function (DUF2017). This is an alpha-helical domain found in gene neighborhoods that contain genes encoding ubiquitin, cysteine synthases and JAB peptidases.
TIGR01263, 4-hydroxyphenylpyruvate_dioxygenase, 4-hydroxyphenylpyruvate dioxygenase. This protein oxidizes 4-hydroxyphenylpyruvate, a tyrosine and phenylalanine catabolite, to homogentisate. Homogentisate can undergo a further non-enzymatic oxidation and polymerization into brown pigments that protect some bacterial species from light. A similar process occurs spontaneously in blood and is hemolytic (see . In some bacterial species, this enzyme has been studied as a hemolysin. [Energy metabolism, Amino acids and amines].
pfam03767, Acid_phosphat_B, HAD superfamily, subfamily IIIB (Acid phosphatase). This family proteins includes acid phosphatases and a number of vegetative storage proteins.
cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
TIGR01136, Cysteine_synthase, cysteine synthase. This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the seed and score below the trusted cutoff. [Amino acid biosynthesis, Serine family].
cd01011, nicotinamidase, Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is also called pyrazinamidase, because in converts the tuberculosis drug pyrazinamide (PZA) into its active form pyrazinoic acid (POA).
pfam01936, NYN, NYN domain. These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.
cd07716, RNaseZ_short-form-like_MBL-fold, uncharacterized bacterial subgroup of Ribonuclease Z, short form; MBL-fold metallo-hydrolase domain. The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. Only the short form exists in bacteria. Members of this bacterial subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.
cd17074, Ubl_CysO_like, ubiquitin-like (Ubl) domain found in Mycobacterium tuberculosis CysO and similar proteins. CysO, also termed 9.5 kDa culture filtrate antigen cfp10A, together with CysM (Cysteine synthase M), forms a protein complex CysM-CysO that represents a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. The replacement of the acetyl group of O-acetylserine by CysO thiocarboxylate to generate a protein-bound cysteine is catalyzed by CysM in a pyridoxal 5?-phosphate (PLP)-dependent manner. The family also includes QbsE that functions as the sulfide donor for the biosynthesis of thioquinolobactin in Pseudomonas fluorescens. A JAMM motif protein QbsD catalyzes removal of the carboxy-terminal dipeptide from QbsE. Both CysO and QbsE are similar to prokaryotic sulfur carrier proteins such as ThiS and MoaD, containing the beta-grasp ubiquitin-like fold.
cd01276, PKCI_related, Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members.
pfam13769, Virulence_fact, Virulence factor. This domain is found in conserved virulence factors. It is often found in association with pfam02985 and pfam08712.
pfam09678, Caa3_CtaG, Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG). Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis.
pfam10648, Gmad2, Immunoglobulin-like domain of bacterial spore germination. This domain is found linked to the GerMN domain pfam10646 in some bacterial proteins. It is predicted to contain an immunoglobulin-like all-beta fold.
cd16282, metallo-hydrolase-like_MBL-fold, uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry.
COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription].
pfam01082, Cu2_monooxygen, Copper type II ascorbate-dependent monooxygenase, N-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.
TIGR02983, putative_RNA_polymerase_ECF-subfamily_sigma_factor, RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
cd03443, PaaI_thioesterase, PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not been determined. Sequence similarity between PaaI, E. coli medium chain acyl-CoA thioesterase II, and human thioesterase III suggests they all belong to the same thioesterase superfamily. The conserved fold present in these thioesterases is referred to as an asymmetric hot dog fold, similar to those of 4-hydroxybenzoyl-CoA thioesterase (4HBT) and the beta-hydroxydecanoyl-ACP dehydratases (FabA/FabZ).
cd05289, MDR_like_2, alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases. Members identified as zinc-dependent alcohol dehydrogenases and quinone oxidoreductase. QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction.
cd07432, PHP_HisPPase, Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.
pfam14539, DUF4442, Domain of unknown function (DUF4442). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 139 and 165 amino acids in length. There is a conserved PYF sequence motif. There is a single completely conserved residue N that may be functionally important.
cd04683, Nudix_Hydrolase_24, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.
TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like). [Unknown function, General].
pfam14013, MT0933_antitox, MT0933-like antitoxin protein. This family of proteins contains the MT0933 protein, which has been identified as an antitoxin to /protein MT0934. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 90 amino acids in length.
cd05371, HSD10-like_SDR_c, 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs. HSD10, also known as amyloid-peptide-binding alcohol dehydrogenase (ABAD), was previously identified as a L-3-hydroxyacyl-CoA dehydrogenase, HADH2. In fatty acid metabolism, HADH2 catalyzes the third step of beta-oxidation, the conversion of a hydroxyl to a keto group in the NAD-dependent oxidation of L-3-hydroxyacyl CoA. In addition to alcohol dehydrogenase and HADH2 activites, HSD10 has steroid dehydrogenase activity. Although the mechanism is unclear, HSD10 is implicated in the formation of amyloid beta-petide in the brain (which is linked to the development of Alzheimer's disease). Although HSD10 is normally concentrated in the mitochondria, in the presence of amyloid beta-peptide it translocates into the plasma membrane, where it's action may generate cytotoxic aldehydes and may lower estrogen levels through its use of 17-beta-estradiol as a substrate. HSD10 is a member of the SRD family, but differs from other SDRs by the presence of two insertions of unknown function. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.
TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other].
cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins.
cd13538, PBP2_ModA_like_1, Substrate binding domain of putative molybdate-binding protein;the type 2 periplasmic binding protein fold. This subfamily contains domains found in ModA proteins of putative ABC-type transporter. Molybdate transport system is comprised of a periplasmic binding protein, an integral membrane protein, and an energizer protein. These three proteins are coded by modA, modB, and modC genes, respectively. ModA proteins serve as initial receptors in the ABC transport of molybdate mostly in eubacteria and archaea. After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
TIGR00237, exodeoxyribonuclease_VII_large_subunit, exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits. [DNA metabolism, Degradation of DNA].
cd09170, PLDc_Nuc, Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Catalytic domain of an EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Nuc is an endonuclease cleaving both single- and double-stranded DNA. It is the smallest known member of the phospholipase D (PLD, EC 3.1.4.4) superfamily that includes a diverse group of proteins with various catalytic functions. Most members of this superfamily have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, Nuc only has one copy of the HKD motif per subunit but form a functionally active homodimer (it is most likely also active in solution as a multimeric protein), which has a single active site at the dimer interface containing the HKD motifs from both subunits. Due to the lack of a distinct domain for DNA binding, Nuc cuts DNA non-specifically. It utilizes a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit.
cd01908, YafJ, Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II glutamine amidotransferases including glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The YafJ fold is also somewhat similar to the Ntn (N-terminal nucleophile) hydrolase fold of the proteasomal alpha and beta subunits.
cd01118, ArsB_permease, Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump (ArsAB). The ArsAB complex is similar in many ways to ATP-binding cassette transporters, which have two groups of six transmembrane-spanning helical segments and two nucleotide-binding domains. The ArsB proteins belong to the ArsB/NhaD superfamily of permeases that translocate sodium, arsenate, sulfate, and organic anions across biological membranes in all three kingdoms of life.
cd04762, HTH_MerR-trunc, Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
pfam04138, GtrA, GtrA-like protein. Members of this family are predicted to be integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides. The GtrA family are a subset of this family. GtrA is predicted to be an integral membrane protein with 4 transmembrane spans. It is involved is in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation. Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane. Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyzes the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b). This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and monocytogenes strains. Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose.
pfam14030, DUF4245, Protein of unknown function (DUF4245). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 235 amino acids in length.
TIGR02141, modB_ABC, molybdate ABC transporter, permease protein. This model describes the permease protein, ModB, of the molybdate ABC transporter. This system has been characterized in E. coli, Staphylococcus carnosus, Rhodobacter capsulatus and Azotobacter vinlandii. Molybdate is chemically similar to sulfate, thiosulfate, and selenate. These related substrates, and sometimes molybdate itself, can be transported by the homologous sulfate receptor. Some apparent molybdenum transport operons include a permease related to this ModB, although less similar than some sulfate permease proteins and not included in this model. [Transport and binding proteins, Anions].
cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases. This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and 3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.
