Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions.
Belongs to the complex I 23 kDa subunit family.
NDH-1 is composed of 15 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex.
NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.
Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues.
Belongs to the metal hydrolase YfiT family.
Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis.
Belongs to the universal ribosomal protein uL15 family.
Part of the 50S ribosomal subunit. Contacts proteins L4, L21 and L35.
Belongs to the type II topoisomerase GyrB family.
Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate.
Belongs to the transglycosylase MltG family.
Functions as a peptidoglycan terminase that cleaves nascent peptidoglycan strands endolytically to terminate their elongation.
Component in a DNA repair pathway. Removal of UV LIGHT damaged nucleotides. Recognizes pyrimidine dimers and cleave a phosphodiester bond immediately 5' to the lesion.
Belongs to the anaerobic coproporphyrinogen-III oxidase family. HemW subfamily.
Probably acts as a heme chaperone, transferring heme to an unknown acceptor. Binds one molecule of heme per monomer, possibly covalently. Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Belongs to the GTP-binding SRP family. SRP54 subfamily.
Composed of three domains: the N-terminal N domain, which is responsible for interactions with the ribosome, the central G domain, which binds GTP, and the C-terminal M domain, which binds the RNA and the signal sequence of the RNC.
Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY.
Part of the signal recognition particle protein translocation system, which is composed of SRP and FtsY.
Belongs to the BPG-independent phosphoglycerate mutase family. A-PGAM subfamily.
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate.
Belongs to the helicase family. UvrD subfamily.
Belongs to the class-I aminoacyl-tRNA synthetase family. GluQ subfamily.
Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon.
Belongs to the universal ribosomal protein uL18 family.
Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 23S rRNA (By similarity). Contacts protein L27 and the 5S rRNA.
This is one of the proteins that binds and mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.
Belongs to the NAD(P)-dependent epimerase/dehydratase family. dTDP-glucose dehydratase subfamily.
Glycosylated. Contains tightly bound reducing sugars (six per polypeptide chain) and fatty acids (covalently bound and located in the N-terminal region) (By similarity).
Shape maintenance, possible protection from noxious enzymes or exogenous and unsettling DNA, and may mediate homotypic cell-cell contacts.
The hydrophilic C-terminal region rich in aromatic AA could be engaged in interactions with nucleic acids, and the bound fatty acids and the N-terminal region could serve to anchor the layer to the outer membrane of D.radiodurans. HPI layer contain about 30% beta structure and virtually no alpha helix (By similarity).
Belongs to the methyltransferase superfamily. Tam family.
Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate.
Belongs to the universal ribosomal protein uL4 family.
Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.
One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).
Part of the 50S ribosomal subunit. Contacts proteins L15 and L34.
This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.
Belongs to the universal ribosomal protein uL14 family.
Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.
In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8 (By similarity). Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19.
Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis.
The covalent binding to the substrate causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein.
Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. LysJ subfamily.
Binds 1 pyridoxal phosphate per subunit.
Catalyzes the transfer of the amino group of L-glutamate to [LysW]-aminoadipate 6-semialdehyde, generating [LysW]-gamma-L-lysine.
Belongs to the GTP cyclohydrolase I type 2/NIF3 family.
Zinc phosphodiesterase, which displays some tRNA 3'-processing endonuclease activity. Probably involved in tRNA maturation, by removing a 3'-trailer from precursor tRNA (By similarity).
Belongs to the NAGSA dehydrogenase family. Type 1 subfamily. LysY sub-subfamily.
Catalyzes the NADPH-dependent reduction of [LysW]-aminoadipate 6-phosphate to yield [LysW]-aminoadipate 6-semialdehyde.
May bind long-chain fatty acids, such as palmitate, and may play a role in lipid transport or fatty acid metabolism.
On the 2D-gel the determined pI of this protein is: 4.65, its MW is: 32 kDa.
Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family.
Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S.
Homotetramer. Forms heterodimers with either ThiH or ThiS.
Required for maturation of 30S ribosomal subunits.
Binds to several small RNAs that accumulate during recovery from UV irradiation (PubMed:17392270). Contributes to the resistance of D.radiodurans to ultraviolet irradiation (PubMed:10766734).
Forms oligomers upon binding DrY RNA, The multimers are of an average size of 700 kDa and are composed of around 12 molecules of Rsr-DrY RNA.
The MIDAS-like motif in the VWFA-like domain binds divalent metal cations.
The horseshoe-shaped TROVE domain is built with 7 helical HEAT-like repeats, and is closed by the VWFA-like domain giving rise to a ring-shaped monomer. Single-stranded RNA is bound in the positively charged central cavity.
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IB subfamily.
Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids.
Cells lacking this gene show a normal growth rate, do not exhibit a decrease in the efficiency of natural transformation, but display a reduced capacity to survive ionizing radiation when exposed at doses superior to 2.5 kGy and exhibit increased sensitivity to mitomycin C.
Homooligomer composed of 8 to 10 subunits; probably arranged in a ring-structure.
Induced to high levels following extreme ionizing radiation exposure. Also highly induced in response to desiccation stress.
ssDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Plays a role in DNA repair and genome reconstitution, in a RecA-independent process, since DdrA is essential for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation in an environment lacking nutrients. In vitro, binds to the 3'-ends of single-stranded DNA, protecting them from nuclease degradation. Thus, DdrA is part of a DNA end-protection system that helps to preserve genome integrity following irradiation or desiccation. Does not display DNA strand annealing activity, unlike eukaryotic Rad52 protein homologs.
Belongs to the dihydroorotate dehydrogenase family. Type 2 subfamily.
Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor.
Belongs to the MurCDEF family. MurE subfamily.
Carboxylation is probably crucial for Mg(2+) binding and, consequently, for the gamma-phosphate positioning of ATP.
Catalyzes the addition of an amino acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.
Belongs to the binding-protein-dependent transport system permease family.
ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner.
Homohexamer. Organized in a ring with a central cavity.
Belongs to the ABC transporter superfamily.
Probably part of an ABC transporter complex. Responsible for energy coupling to the transport system (By similarity).
Belongs to the Maf family. YhdE subfamily.
Nucleoside triphosphate pyrophosphatase that hydrolyzes dTTP and UTP. May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids.
Allosterically activated by fructose 1,6-bisphosphate (FBP).
Belongs to the LDH/MDH superfamily. LDH family.
Catalyzes the conversion of lactate to pyruvate.
Belongs to the binding-protein-dependent transport system permease family. CysTW subfamily.
Belongs to the 3-hydroxyacyl-CoA dehydrogenase family.
Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication; it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box): 5'-TTATC[CA]A[CA]A-3'. DnaA binds to ATP and to acidic phospholipids (By similarity).
Belongs to the FPP/GGPP synthase family.
Belongs to the methyltransferase superfamily.
Specifically methylates the cytosine at position 2499 (m5C2499) of 23S rRNA.
Belongs to the ABC transporter superfamily. UvrA family.
Forms a heterotetramer with UvrB during the search for lesions.
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate.
Belongs to the bacterial ribosomal protein bL32 family.
Forms a cluster with L17 and L22, and with L22, a pair of 'tweezers' that hold together all the domains of the 23S rRNA. Interacts with the antibiotic troleandomycin which blocks the peptide exit tunnel.
Part of the 50S ribosomal subunit. Contacts proteins L17 and L22.
Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage (By similarity). Probably involved in base excision repair (PubMed:19303848).
Following severe irradiation (7 kGy of gamma irradiation) genomic DNA is fragmented. DNA is progressively degraded for the first 1.5 hours after IR, in a step promoted by RecA and counterbalanced by DNA Pol I and Pol III, followed by massive DNA synthesis and genome reassembly in the next hour. Optimal priming of DNA synthesis requires both RecA and RadA, Pol III initiates DNA synthesis while both Pol I and Pol III are required for its contination. In the absence of RecA the majority of the chromosome is still reconstituted, via either single-strand annealing or non-homologous end joining (PubMed:19303848).
Reduced DNA synthesis rate even in the absence of ionizing radiation (IR) (PubMed:19303848). Cells lacking this gene have a reduced capacity to survive IR (from 90% survival to <10(-7)), DNA repair following IR is slow (PubMed:20451472, PubMed:19303848). Single recA mutants rarely reconstitutes the whole genome following IR, and their DNA is not degraded post-IR (PubMed:19303848). A double recA-ddrB disruption shows no signs of DNA repair 24 hours after IR (PubMed:20451472). Double recA-radA deletion mutants have a more severe effect than either mutation alone after IR (PubMed:19303848).
Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved.
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane.
Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source.
Belongs to the glycosyltransferase 28 family. MurG subfamily.
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II).
Belongs to the succinate/malate CoA ligase alpha subunit family.
Heterotetramer of two alpha and two beta subunits.
Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit.
IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the synthesis of IGP and AICAR. The resulting ammonia molecule is channeled to the active site of HisF (By similarity).
Hydrolase that can act as a nucleoside triphosphatase and a dinucleoside polyphosphate pyrophosphatase. The best substrates are 8-oxo-dGTP and 8-oxo-GTP. Other substrates include Ap4A, dGTP and GTP. May be involved in protection from damage caused by radiation.
Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily.
Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a 'posttransfer' editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.
The C-terminal coiled-coil domain is crucial for aminoacylation activity.
ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site.
Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family.
Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate.
Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes.
Belongs to the cytidylate kinase family. Type 1 subfamily.
Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits. The heterotrimers can form oligomers, although 1 heterotrimer is thought to be able to translocate proteins. Interacts with the ribosome. Interacts with SecDF, and other proteins may be involved. Interacts with SecA.
Lacks conserved residue(s) required for the propagation of feature annotation.
The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently.
Has a dual activity phosphatase/phosphodiesterase in vitro, with a preference to phosphoenolpyruvate (PEP) and 2',3'-cAMP, respectively. Can also use 2',3'-cGMP, 2',3'-cCMP and various model substrates such as p-nitrophenyl phosphate (pNPP), bis-p-nitrophenyl phosphate (bis-pNPP) and p-nitrophenyl thymidine monophosphate (pNP-TMP).
Mn(2+) is the preferable metal for phosphatase activity. Phosphodiesterase activity is observed in the presence of Co(2+), Mn(2+) or Fe(2+).
Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes.
Belongs to the iron/manganese superoxide dismutase family.
Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
Belongs to the methyltransferase superfamily. PrmA family.
Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily.
Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process cysteine.
Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension.
Belongs to the ribose 5-phosphate isomerase family.
Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate.
Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit.
Heterodimer of a catalytic subunit (MsrP) and a heme-binding subunit (MsrQ).
Part of the MsrPQ system that repairs oxidized cell envelope proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated cell envelope proteins from methionine oxidation. MsrQ provides electrons for reduction to the reductase catalytic subunit MsrP, using the quinone pool of the respiratory chain.
Belongs to the universal ribosomal protein uS10 family.
Involved in the binding of tRNA to the ribosomes.
Belongs to the class-I aminoacyl-tRNA synthetase family.
Belongs to the 5-formyltetrahydrofolate cyclo-ligase family.
Divalent metal cations. Prefers magnesium or manganese.
On the 2D-gel the determined pI of this unknown protein is: 4.23, its MW is: 31.5 kDa.
Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily.
Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP).
Belongs to the RNA methyltransferase RlmH family.
Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA.
Belongs to the short-chain dehydrogenases/reductases (SDR) family.
Catalyzes the NADPH-dependent reduction of beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, the first reductive step in the elongation cycle of fatty acid biosynthesis.
Belongs to the universal ribosomal protein uL23 family.
One of the early assembly protein (By similarity) it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Forms the main docking site for trigger factor binding to the ribosome (PubMed:16091460, PubMed:16271892).
Part of the 50S ribosomal subunit. Contacts protein L29 and trigger factor when it is bound to the ribosome (PubMed:16091460, PubMed:16271892).
Belongs to the universal ribosomal protein uS14 family.
Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.
Part of the 30S ribosomal subunit. Contacts proteins S3 and S10.
Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG family.
Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.
Belongs to the bacterial ribosomal protein bL27 family.
Binds the 5S and 23S rRNAs and also the tRNA in the P site.
Part of the 50S ribosomal subunit. Contacts protein L18.
Belongs to the glycosyl hydrolase 13 family.
IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins.
ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner.
Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. YchF/OLA1 subfamily.
Belongs to the RNA polymerase beta' chain family.
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription.
Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).
Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily.
Belongs to the protein-tyrosine phosphatase family.
Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 2B subfamily.
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.
Belongs to the chorismate synthase family.
Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system.
Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily.
Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily.
One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex.
Belongs to the bacterial ribosomal protein bL20 family.
Binds directly to 23S rRNA, probably serving to organize its structure.
Part of the 50S ribosomal subunit. Contacts proteins L13 and L21.
Belongs to the MnmG family. TrmFO subfamily.
Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs.
Belongs to the complex I 20 kDa subunit family.
NDH-1 is composed of 15 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex.
NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be a menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.
Belongs to the radical SAM superfamily. MqnC family.
Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Radical SAM enzyme that catalyzes the cyclization of dehypoxanthine futalosine (DHFL) into cyclic dehypoxanthine futalosine (CDHFL), a step in the biosynthesis of menaquinone (MK, vitamin K2).
Belongs to the HPF/YfiA ribosome-associated protein family. Long HPF subfamily.
Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth.
Involved in chromosome partition. Localize to both poles of the predivisional cell following completion of DNA replication. Binds to the DNA origin of replication (By similarity).
Belongs to the universal ribosomal protein uS9 family.
Belongs to the helicase family. DnaB subfamily.
Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity.
Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD).
Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA.
Belongs to the AIR carboxylase family. Class I subfamily.
Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR).
Belongs to the nucleobase:cation symporter-2 (NCS2) (TC 2.A.40) family. Azg-like subfamily.
Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+).
Binds 1 thiamine pyrophosphate per subunit.
Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate.
Belongs to the glycosyl hydrolase 13 family. GlgB subfamily.
Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position.
Belongs to the thiolase-like superfamily. Thiolase family.
Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another.
Belongs to the MqnA/MqnD family. MqnD subfamily.
Catalyzes the conversion of cyclic dehypoxanthine futalosine (cyclic DHFL) into 1,4-dihydroxy-6-naphthoate, a step in the biosynthesis of menaquinone (MK, vitamin K2).
Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides.
Belongs to the bacterial ribosomal protein bS6 family.
Binds together with bS18 to 16S ribosomal RNA.
Monomer. Part of the FGAM synthase complex composed of 1 PurL, 1 PurQ and 2 PurS subunits.
Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL.
Belongs to the carbohydrate kinase PfkB family.
Belongs to the complex I 24 kDa subunit family.
Belongs to the metallophosphoesterase superfamily.
Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven.
Belongs to the type-II 3-dehydroquinase family.
Catalyzes a trans-dehydration via an enolate intermediate.
Belongs to the lyase 1 family. Argininosuccinate lyase subfamily.
Binds 1 Mn(2+) or Fe(2+) ion per subunit.
Belongs to the histidinol dehydrogenase family.
Catalyzes the sequential NAD-dependent oxidations of L-histidinol to L-histidinaldehyde and then to L-histidine.
Homohexamer. The oligomerization is ATP-dependent (By similarity).
Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE. Acts before DnaK, in the processing of protein aggregates. Protein binding stimulates the ATPase activity; ATP hydrolysis unfolds the denatured protein aggregates, which probably helps expose new hydrophobic binding sites on the surface of ClpB-bound aggregates, contributing to the solubilization and refolding of denatured protein aggregates by DnaK (By similarity).
The Clp repeat (R) domain probably functions as a substrate-discriminating domain, recruiting aggregated proteins to the ClpB hexamer and/or stabilizing bound proteins. The NBD2 domain is responsible for oligomerization, whereas the NBD1 domain stabilizes the hexamer probably in an ATP-dependent manner. The movement of the coiled-coil domain is essential for ClpB ability to rescue proteins from an aggregated state, probably by pulling apart large aggregated proteins, which are bound between the coiled-coils motifs of adjacent ClpB subunits in the functional hexamer (By similarity).
Belongs to the LysR transcriptional regulatory family.
Belongs to the universal ribosomal protein uL5 family.
Forms a bridge to the 30S subunit in the 70S ribosome (By similarity). Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 (CTC) subcomplex. Is known to contact the 5S rRNA, 23S rRNA and the P site tRNA.
This is one of the proteins that bind and probably mediate the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement (By similarity). Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.
Catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to formate and tetrahydrofolate (FH4).
A 50S ribosomal subunit assembly protein with GTPase activity, required for 50S subunit assembly at low temperatures, may also play a role in translation. Binds GTP and analogs. Binds the 70S ribosome between the 30S and 50S subunits, in a similar position as ribosome-bound EF-G; it contacts a number of ribosomal proteins, both rRNAs and the A-site tRNA.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. BipA subfamily.
Belongs to the 2-oxoacid dehydrogenase family.
Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family.
Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+).
Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ).
Belongs to the bacterial ribosomal protein bL19 family.
Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L14.
This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site (By similarity). Binds the 23S rRNA.
Belongs to the purine nucleoside phosphorylase YfiH/LACC1 family.
Purine nucleoside enzyme that catalyzes the phosphorolysis of adenosine and inosine nucleosides, yielding D-ribose 1-phosphate and the respective free bases, adenine and hypoxanthine. Also catalyzes the phosphorolysis of S-methyl-5'-thioadenosine into adenine and S-methyl-5-thio-alpha-D-ribose 1-phosphate. Also has adenosine deaminase activity.
Belongs to the methyltransferase superfamily. RsmI family.
Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA.
Part of the FGAM synthase complex composed of 1 PurL, 1 PurQ and 2 PurS subunits.
Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.
Inhibited by zinc, calcium or copper ions.
Belongs to the AB hydrolase superfamily. MetX family.
Transfers an acetyl group from acetyl-CoA to L-homoserine, forming acetyl-L-homoserine.
Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine.
In the C-terminal section; belongs to the purine/pyrimidine phosphoribosyltransferase family.
Belongs to the gamma-glutamyl phosphate reductase family.
Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5-carboxylate.
Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds the extracellular potassium ions and delivers the ions to the membrane domain of KdpB through an intramembrane tunnel.
The system is composed of three essential subunits: KdpA, KdpB and KdpC.
Binds 4 Mg(2+) or Mn(2+) ions per subunit.
Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate.
Belongs to the LytR/CpsA/Psr (LCP) family.
Belongs to the universal ribosomal protein uS8 family.
One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit.
Part of the 30S ribosomal subunit. Contacts proteins S5 and S12.
Belongs to the aldehyde dehydrogenase family.
Belongs to the PEP-utilizing enzyme family.
Catalyzes the phosphorylation of pyruvate to phosphoenolpyruvate.
The N-terminal domain contains the ATP/Pi binding site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate binding site.
The reaction takes place in three steps, mediated by a phosphocarrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain (By similarity).
Belongs to the Orn/Lys/Arg decarboxylase class-II family. LysA subfamily.
Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.
Catalyzes the transfer of the enolpyruvyl moiety of phosphoenolpyruvate (PEP) to the 5-hydroxyl of shikimate-3-phosphate (S3P) to produce enolpyruvyl shikimate-3-phosphate and inorganic phosphate.
Belongs to the glycosyl hydrolase 26 family.
Catalyzes the conversion of urocanate to 4-imidazolone-5-propionate.
Belongs to the LDH/MDH superfamily. MDH type 2 family.
Catalyzes the reversible oxidation of malate to oxaloacetate.
Belongs to the succinate/malate CoA ligase beta subunit family.
Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit.
Belongs to the bacterial ribosomal protein bS20 family.
Citrate synthase is found in nearly all cells capable of oxidative metabolism.
Might regulate the synthesis and function of enzymes involved in later enzymatic steps of Krebs cycle. Loss in activity results in sporulation defect (By similarity).
Belongs to the type IB topoisomerase family.
Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.
Belongs to the universal ribosomal protein uS3 family.
Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.
Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14.
Belongs to the 3-oxoacid CoA-transferase subunit B family.
Activated by a monovalent cation that binds near, but not in, the active site. The most likely occupant of the site in vivo is potassium. Ion binding induces a conformational change that may alter substrate affinity.
Belongs to the carbohydrate kinase PfkB family. Ribokinase subfamily.
Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.
Requires a divalent cation, most likely magnesium in vivo, as an electrophilic catalyst to aid phosphoryl group transfer. It is the chelate of the metal and the nucleotide that is the actual substrate.
Binds 2 divalent metal cations per subunit.
Belongs to the TsuA/YedE (TC 9.B.102) family.
Belongs to the NAGSA dehydrogenase family. Type 2 subfamily.
Catalyzes the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde.
Belongs to the ABC transporter superfamily. Ycf16 family.
Belongs to the imidazoleglycerol-phosphate dehydratase family.
Belongs to the sulfate adenylyltransferase family.
Belongs to the RNA polymerase subunit omega family.
Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits (By similarity).
The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription (By similarity).
Redox regulated molecular chaperone. Protects both thermally unfolding and oxidatively damaged proteins from irreversible aggregation. Plays an important role in the bacterial defense system toward oxidative stress.
Under oxidizing conditions two disulfide bonds are formed involving the reactive cysteines. Under reducing conditions zinc is bound to the reactive cysteines and the protein is inactive.
Belongs to the phosphohexose mutase family.
Belongs to the FAD-dependent oxidoreductase 2 family. FRD/SDH subfamily.
A Gly-cisPro motif from one monomer fits into the active site of the other monomer to allow specific chiral rejection of L-amino acids.
An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality.
Belongs to the ketol-acid reductoisomerase family.
Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate.
Associates with the 50S ribosomal subunit.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family.
GTPase that plays an essential role in the late steps of ribosome biogenesis.
2 residues (Tyr-66 and Arg-69) present in a large hydrophobic pocket are probably involved in substrate specificity. They are important for desuccinylation activity, but dispensable for deacetylation activity.
Belongs to the sirtuin family. Class III subfamily.
NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form.
Belongs to the UPF0073 (Hly-III) family.
Belongs to the methyltransferase superfamily. RsmH family.
Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA.
Belongs to the glycosyl hydrolase 13 family. TreS subfamily.
Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family.
Catalyzes the 2'-O methylation of guanosine at position 18 in tRNA.
Belongs to the universal ribosomal protein uL3 family.
One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
Part of the 50S ribosomal subunit. Forms a cluster with proteins L14 and L19. Also contacts proteins L13 and L17.
Belongs to the bacterial ribosomal protein bS16 family.
Belongs to the 4-toluene sulfonate uptake permease (TSUP) (TC 2.A.102) family.
Belongs to the radical SAM superfamily. Lipoyl synthase family.
Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives.
Belongs to the truncated hemoglobin family. Group II subfamily.
Belongs to the AAA ATPase family. RarA/MGS1/WRNIP1 subfamily.
Belongs to the DNA mismatch repair MutL/HexB family.
This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a 'molecular matchmaker', a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex.
Binds 2 heme c groups covalently per subunit.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily.
Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.
Binds 1 [4Fe-4S] cluster per subunit. The cluster is chelated by three Cys residues, the fourth Fe has a free coordination site that may bind a sulfur atom transferred from the persulfide of IscS.
Catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). The sulfur atoms are provided by the cysteine/cysteine desulfurase (IscS) system.
The thiolation reaction likely consists of two steps: a first activation step by ATP to form an adenylated intermediate of the target base of tRNA, and a second nucleophilic substitution step of the sulfur (S) atom supplied by the hydrosulfide attached to the Fe-S cluster.
Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA.
Belongs to the carbon-nitrogen hydrolase superfamily.
Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor.
Functions in the biosynthesis of branched-chain amino acids. Catalyzes the dehydration of (2R,3R)-2,3-dihydroxy-3-methylpentanoate (2,3-dihydroxy-3-methylvalerate) into 2-oxo-3-methylpentanoate (2-oxo-3-methylvalerate) and of (2R)-2,3-dihydroxy-3-methylbutanoate (2,3-dihydroxyisovalerate) into 2-oxo-3-methylbutanoate (2-oxoisovalerate), the penultimate precursor to L-isoleucine and L-valine, respectively.
Belongs to the metallo-dependent hydrolases superfamily. NagA family.
Binds 1 divalent metal cation per subunit.
Belongs to the acyl-CoA dehydrogenase family.
Belongs to the phosphopentomutase family.
Phosphotransfer between the C1 and C5 carbon atoms of pentose.
Belongs to the DNA polymerase type-C family. DnaE subfamily.
DNA polymerase III contains a core (composed of alpha, epsilon and theta chains) that associates with a tau subunit. This core dimerizes to form the PolIII' complex. PolIII' associates with the gamma complex (composed of gamma, delta, delta', psi and chi chains) and with the beta chain to form the complete DNA polymerase III complex (By similarity).
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative DNA synthesis in bacteria as well as the bulk of DNA synthesis/repair after ionizing radiation (IR) (PubMed:19303848). The alpha chain is the catalytic subunit (PubMed:19303848). Following severe irradiation (7 kGy of gamma irradiation) genomic DNA is fragmented. DNA is progressively degraded for the first 1.5 hours after IR, in a step promoted by RecA and counterbalanced by DNA Pol I and Pol III, followed by massive DNA synthesis and genome reassembly in the next hour. Optimal priming of DNA synthesis requires both RecA and RadA, Pol III initiates DNA synthesis while both Pol I and Pol III are required for its contination (PubMed:19303848). This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).
Belongs to the dGTPase family. Type 2 subfamily.
Binds 1 dipyrromethane group covalently.
Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.
The porphobilinogen subunits are added to the dipyrromethane group.
Binds 2 Zn(2+) ions per subunit. One is catalytic and the other provides a structural contribution.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. FeoB GTPase (TC 9.A.8) family.
Probable transporter of a GTP-driven Fe(2+) uptake system.
Belongs to the LeuD family. LeuD type 2 subfamily.
Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate.
Binds 1 pyruvoyl group covalently per subunit.
Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine.
Heterooctamer of four alpha and four beta subunits.
Is synthesized initially as an inactive proenzyme, which is activated by self-cleavage at a specific serine bond to produce a beta-subunit with a hydroxyl group at its C-terminus and an alpha-subunit with a pyruvoyl group at its N-terminus.
Belongs to the class-II pyridine nucleotide-disulfide oxidoreductase family.
Catalyzes the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate (cPMP).
Belongs to the ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family.
Part of the ABC transporter complex PstSACB involved in phosphate import. Responsible for energy coupling to the transport system.
The complex is composed of two ATP-binding proteins (PstB), two transmembrane proteins (PstC and PstA) and a solute-binding protein (PstS).
Belongs to the zinc-containing alcohol dehydrogenase family.
Catalyzes the NAD(+)-dependent oxidation of L-threonine to 2-amino-3-ketobutyrate.
Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily.
Binds the 23S rRNA and interacts with the tRNA in the E site.
Part of the 50S ribosomal subunit. Contacts protein L9.
Belongs to the peptidase M20A family. LysK subfamily.
Binds 2 Zn(2+) or Co(2+) ions per subunit.
Catalyzes the release of L-lysine from [LysW]-gamma-L-lysine.
Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.
Belongs to the metallophosphoesterase superfamily. YfcE family.
Belongs to the heat shock protein 70 family.
By stress conditions e.g. heat shock (By similarity).
Belongs to the bacterial solute-binding protein 1 family.
Probably part of a binding-protein-dependent transport system.
Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).
Belongs to the SIMIBI class G3E GTPase family. ArgK/MeaB subfamily.
Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate.
Involved in the maturation of [NiFe] hydrogenases. Required for nickel insertion into the metal center of the hydrogenase.
Belongs to the metallo-dependent hydrolases superfamily. Phosphotriesterase family.
Catalyzes the ferrous insertion into protoporphyrin IX.
Belongs to the short-chain dehydrogenases/reductases (SDR) family. FabI subfamily.
Acetyl-CoA carboxylase is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and the two subunits of carboxyl transferase in a 2:2 complex.
This protein is a component of the acetyl coenzyme A carboxylase complex; first, biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA.
Cell division protein that is involved in the assembly of the Z ring. May serve as a membrane anchor for the Z ring.
A transposase that is part of insertion sequence (IS) element ISDra2, it is necessary and sufficient for both transposon excision and insertion of ISDra2. This protein alone can be provided in trans and allows transposition of an empty IS element (tnpA or tnpA-tnpB replaced by a selectable marker) (PubMed:16359337, PubMed:20090938). ISDra2 binds subterminal imperfect palindromes at the left (LE) and right (RE) ends of the element and cleaves only the 'top strand' which is circularized and subsequently reinserted into the DNA target. This is called a 'peel and paste' mechanism and increases the copy number of the IS (Probable) (PubMed:20890269). Transposition is linked to DNA replication in the absence of irradiation, with maximal activity when the 'top strand' is on the replication lagging strand, and occurs preferentially on the lagging strand (PubMed:20691900). The IS element inserts 3' of the target sequence 5'-TTGAT-3'; target duplication has not been observed (PubMed:14676423, PubMed:16359337, PubMed:20090938, PubMed:20691900).
Belongs to the IS200/IS605 insertion sequence (IS) element family, formerly called IS8301 (PubMed:14676423, PubMed:20090938). This element is subject to strain polymorphism; in the ATCC 13939 / R1 strain genome sequenced by White there are 7 complete and 1 incomplete IS200/IS605 elements (PubMed:10567266). Another R1 strain has only 1 copy of this element (PubMed:14676423, PubMed:20090938). Another group found 2 copies of this element in untreated R1 strains (PubMed:16359337, PubMed:10567266, PubMed:14676423, PubMed:20090938).
Both the excision and insertion steps are inhibited by TnpB.
Mg(2+), Mn(2+) and Cd(2+) support DNA cleavage whereas Ca(2+) and Zn(2+) do not.
The helix containing the catalytic Tyr-132 (residues 127-133) is highly mobile. Recognition of the 5-base sequence immediately preceding the cleavage site is mediated by base-pairing to an imperfect palindrome, by sandwiching the fifth nucleotide between Tyr-30 and Trp-107 and hydrogen bonding to His-32, and by main chain atoms of Leu-106 and Trp-107.
Transposition of this element is induced approximately 100-fold by 10 kGy gamma irradiation and approximately 50-fold by 600 J/m(2) of UV irradiation, both of which damage DNA. It rarely transposes without irradiation (PubMed:16359337). Both excision and insertion of ISDra2 are increased by irradiation, transposition occurs in irradiated cells, probably triggered by single-stranded DNA formed during genome reassembly, and is not due to specific induction of TnpA expression (PubMed:20090938).
When tested in an R1 strain with only a single IS200 element (DR_1651 and DR_1652), required for transposition of the IS element; single tnpA or double tnpA-tnpB deletions leads to loss of transposition.
An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes.
The PRC barrel domain binds ribosomal protein uS19.
Belongs to the universal ribosomal protein uS15 family.
Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.
Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA.
Belongs to the protein kinase superfamily. RIO-type Ser/Thr kinase family.
Component of a complex that catalyzes the oxidation of glycolate to glyoxylate.
Belongs to the complex I subunit 1 family.
NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone.
Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). Is slightly more efficient at aminoacylating tRNA(Asn) over tRNA(Asp).
Belongs to the class-II aminoacyl-tRNA synthetase family. Type 2 subfamily.
Belongs to the adenylosuccinate synthetase family.
Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP.
Belongs to the transthyretin family. 5-hydroxyisourate hydrolase subfamily.
Catalyzes the hydrolysis of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU).
HIU hydrolysis also occurs spontaneously, but more slowly.
Belongs to the complex I 49 kDa subunit family.
Belongs to the endoribonuclease YbeY family.
Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.
Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.
Belongs to the radical SAM superfamily. MqnE family.
Radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3-[(1-carboxyvinyl)oxy]benzoate, leading to aminodeoxyfutalosine (AFL), a key intermediate in the formation of menaquinone (MK, vitamin K2) from chorismate.
Belongs to the bacterial ribosomal protein bL33 family.
Part of the 50S ribosomal subunit. Contacts protein L35.
Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily.
Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature.
Converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of heme B porphyrin ring with a hydroxyethyl farnesyl side group.
Belongs to the flavin oxidoreductase frp family.
Belongs to the carotenoid/retinoid oxidoreductase family.
Acetylated. Deacetylation by the SIR2-homolog deacetylase activates the enzyme.
Belongs to the ATP-dependent AMP-binding enzyme family.
Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA.
Belongs to the universal ribosomal protein uL11 family.
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.
One or more lysine residues are methylated.
Part of the ribosomal stalk of the 50S ribosomal subunit. Interacts with L10 and the large rRNA to form the base of the stalk. L10 forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex (By similarity). Contacts the CTC protein (RL25).
Belongs to the class II aldolase/RraA-like family.
Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions (By similarity).
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily.
Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back-translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner.
Belongs to the transaldolase family. Type 3B subfamily.
Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway.
Homohexameric ring arranged as a trimer of dimers.
Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation.
Belongs to the isocitrate and isopropylmalate dehydrogenases family. LeuB type 1 subfamily.
Binds 1 Mg(2+) or Mn(2+) ion per subunit.
Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2-oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate.
The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.
Belongs to the tryptophan 2,3-dioxygenase family.
Heme-dependent dioxygenase that catalyzes the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring and converts L-tryptophan to N-formyl-L-kynurenine. Catalyzes the oxidative cleavage of the indole moiety.
Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate.
In the C-terminal section; belongs to the PRA-PH family.
In the N-terminal section; belongs to the PRA-CH family.
Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily.
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
Belongs to the protein N5-glutamine methyltransferase family. PrmC subfamily.
Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif.
Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes.
Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.
Belongs to the ATPase alpha/beta chains family.
Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit (By similarity).
Inhibited by fructose 1,6-bisphosphate (FBP).
Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate.
Catalyzes the ATP-dependent phosphorylation of fructose-l-phosphate to fructose-l,6-bisphosphate.
Belongs to the 4-hydroxybenzoyl-CoA thioesterase family.
Belongs to the radical SAM superfamily. RlmN family.
Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.
Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs.
Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily.
Tetramer of two alpha and two beta subunits.
Belongs to the site-specific recombinase resolvase family.
Cells lacking this gene show a normal growth rate, do not exhibit a decrease in the efficiency of natural transformation, but display a reduced capacity to survive ionizing radiation when exposed at doses superior to 2.5 kGy. DNA repair following irradiations is slower. Cannot be complemented by ssb. A double recA-ddrB disruption shows no signs of DNA repair 24 hours after irradiation.
Contains a novel ssDNA-binding fold, which is structurally and topologically distinct from the OB-fold universally found in standard SSB proteins. The disordered C-terminus of DdrB may mediate interactions with other proteins important for DNA damage recovery (By similarity).
Homopentamer arranged in a ring-structure; DNA binds between subunits and along the top of the ring. The pentamers self-associate to coat ssDNA in higher-ordered structures; oligomerization facilitates the assembly of extended nucleoprotein complexes. Self-assembly does not however require ssDNA-binding. Interacts with SSB.
ssDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Plays a role in DNA repair and genome reconstitution in a RecA-independent process. Required for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. Binds ssDNA but not dsDNA. Stimulates annealing of complementary ssDNA. Does not complement an ssb disruption.
Belongs to the complex I 75 kDa subunit family.
NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.
Belongs to the ATP phosphoribosyltransferase family. Short subfamily.
Catalyzes the condensation of ATP and 5-phosphoribose 1-diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of HisG enzymatic activity (By similarity).
Heteromultimer composed of HisG and HisZ subunits.
Lacks the C-terminal regulatory region which is replaced by HisZ.
Belongs to the bacterial solute-binding protein 5 family.
Participates in transcription elongation, termination and antitermination.
Belongs to the class-II aminoacyl-tRNA synthetase family.
Catalyzes the attachment of glycine to tRNA(Gly).
Belongs to the universal ribosomal protein uL1 family.
Binds directly to 23S rRNA. Forms the L1 stalk. Unlike the case in the Thermus thermophilus 70S ribosome, this protein is not seen to block the exit path of the E site tRNA. It is clear that the protein in the structure is flexible however, so this is probably due to its position in these crystals.
Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.
Required for maturation of urease via the functional incorporation of the urease nickel metallocenter.
UreD, UreF and UreG form a complex that acts as a GTP-hydrolysis-dependent molecular chaperone, activating the urease apoprotein by helping to assemble the nickel containing metallocenter of UreC. The UreE protein probably delivers the nickel.
Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A).
Belongs to the acetylglutamate kinase family. ArgB subfamily.
Catalyzes the ATP-dependent phosphorylation of N-acetyl-L-glutamate.
Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.
The active site is a redox-active disulfide bond.
Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain.
Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs.
Belongs to the universal ribosomal protein uL30 family.
Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA).
Belongs to the metallo-dependent hydrolases superfamily. HutI family.
Catalyzes the hydrolytic cleavage of the carbon-nitrogen bond in imidazolone-5-propanoate to yield N-formimidoyl-L-glutamate. It is the third step in the universal histidine degradation pathway.
Binds 1 Mg(2+) ion per subunit. May bind a second metal ion at a regulatory site, or after substrate binding.
Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family.
Specifically methylates the N7 position of a guanine in 16S rRNA.
This protein specifically catalyzes the removal of signal peptides from prolipoproteins.
Interacts with UvrB in an incision complex.
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision.
The N-terminal domain determines nucleotide recognition and specific binding, while the C-terminal domain determines the specific binding to the target protein.
Transfers a GMP moiety from GTP to Mo-molybdopterin (Mo-MPT) cofactor (Moco or molybdenum cofactor) to form Mo-molybdopterin guanine dinucleotide (Mo-MGD) cofactor.
Plays a role in the regulation of phosphate uptake.
Belongs to the MqnA/MqnD family. MqnA subfamily.
Catalyzes the dehydration of chorismate into 3-[(1-carboxyvinyl)oxy]benzoate, a step in the biosynthesis of menaquinone (MK, vitamin K2).
Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln).
Belongs to the autoinducer-2 exporter (AI-2E) (TC 2.A.86) family.
Catalyzes the insertion of molybdate into adenylated molybdopterin with the concomitant release of AMP.
Belongs to the CPA3 antiporters (TC 2.A.63) subunit E family.
Belongs to the anthranilate synthase component I family.
Heterotetramer consisting of two non-identical subunits: a beta subunit (TrpG) and a large alpha subunit (TrpE).
Part of a heterotetrameric complex that catalyzes the two-step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine-binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia.
Catalyzes the cleavage of L-kynurenine (L-Kyn) and L-3-hydroxykynurenine (L-3OHKyn) into anthranilic acid (AA) and 3-hydroxyanthranilic acid (3-OHAA), respectively.
Belongs to the binding-protein-dependent transport system permease family. MalFG subfamily.
Part of the ABC transporter complex MalEFGK involved in maltose/maltodextrin import. Probably responsible for the translocation of the substrate across the membrane.
Belongs to the DsbB family. BdbC subfamily.
Required for disulfide bond formation in some proteins.
Has three domains with a flexible linker between the domains II and III and assumes an 'L' shape. Domain III is highly mobile and contacts RuvB.
Homotetramer. Forms an RuvA(8)-RuvB(12)-Holliday junction (HJ) complex. HJ DNA is sandwiched between 2 RuvA tetramers; dsDNA enters through RuvA and exits via RuvB. An RuvB hexamer assembles on each DNA strand where it exits the tetramer. Each RuvB hexamer is contacted by two RuvA subunits (via domain III) on 2 adjacent RuvB subunits; this complex drives branch migration. In the full resolvosome a probable DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms which resolves the HJ.
The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair, while the RuvA-RuvB complex plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR). RuvA specifically binds to HJ cruciform DNA, conferring on it an open structure. The RuvB hexamer acts as an ATP-dependent pump, pulling dsDNA into and through the RuvAB complex. HJ branch migration allows RuvC to scan DNA until it finds its consensus sequence, where it cleaves and resolves the cruciform DNA.
Catalyzes the synthesis of GMP from XMP.
Binds HJ DNA independently of homologous core or consensus sequence; Mn(2+) is not essential for binding but improves it, while >1.0 mM Mg(2+) inhibit binding. Also binds Y-junction DNA less well. Requires a homologous core to cleave DNA (PubMed:35744678). Another study shows divalent cations (Mn(2+), Mg(2+) and Ca(2+), tested up to 5.0 mM) improve DNA binding considerably over binding in their absence (PubMed:36000732).
D.radiodurans metalloenzymes exhibit a strong preference for Mn(2+) rather than Mg(2+).
Homodimer which binds Holliday junction (HJ) DNA (PubMed:35744678). The HJ becomes 2-fold symmetrical on binding to RuvC with unstacked arms; it has a different conformation from HJ DNA in complex with RuvA. In the full resolvosome a probable DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms which resolves the HJ.
In vitro only Mn(2+) supports endonuclease activity; Mg(2+) inhibits binding to HJ DNA (PubMed:35744678). Another study shows Mn(2+) is the preferred cofactor but Mg(2+) does support cleavage (PubMed:36000732). Binds 2 Mn(2+) ion per subunit (By similarity).
Only heterozygous strains can be obtained, suggesting this gene is essential.
The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair (PubMed:36000732). Endonuclease that resolves HJ intermediates (PubMed:35744678, PubMed:36000732). Cleaves cruciform DNA by making single-stranded nicks across the HJ at symmetrical positions within the homologous arms, probably yielding a 5'-phosphate and a 3'-hydroxyl group; requires a central core of homology in the junction (PubMed:35744678, PubMed:36000732). The consensus cleavage sequence is 5'-(G/C)TC(C/G)-3' (a different site than E.coli); cleavage occurs on the 3'-side of the TC dinucleotide at the point of strand exchange (PubMed:36000732). Also resolves nicked HJ intermediates, replication forks and Y-junction DNA in vitro (PubMed:36000732). HJ branch migration catalyzed by RuvA-RuvB allows RuvC to scan DNA until it finds its consensus sequence, where it cleaves and resolves the cruciform DNA (By similarity).
Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family. TrmL subfamily.
Could methylate the ribose at the nucleotide 34 wobble position in tRNA.
Catalyzes two sequential steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine. In the second step the latter compound is decarboxylated to form 4'-phosphopantotheine.
Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine.
In the C-terminal section; belongs to the PPC synthetase family.
In the N-terminal section; belongs to the HFCD (homo-oligomeric flavin containing Cys decarboxylase) superfamily.
Belongs to the bacterial ribosomal protein bL28 family.
Belongs to the anthranilate phosphoribosyltransferase family.
Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA).
Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair.
An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control.
Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family.
Catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin.
Belongs to the GatB/GatE family. GatB subfamily.
Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. ArgD subfamily.
May also have succinyldiaminopimelate aminotransferase activity, thus carrying out the corresponding step in lysine biosynthesis.
The glycine cleavage system catalyzes the degradation of glycine. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.
The glycine cleavage system is composed of four proteins: P, T, L and H.
Appears to contribute to D.radiodurans capacity to survive exposure to ionizing radiation (PubMed:15454524). Likely functions as a DNA damage-induced nucleoid-associated protein (NAP) that contributes to the enhanced level of nucleoid compaction after irradiation by bridging DNA duplexes, thereby limiting the dispersion of the fragmented genome immediately after irradiation to facilitate subsequent DNA repair. In vitro, binds both ssDNA and dsDNA, and is able to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases (PubMed:35801857, PubMed:28542368).
Cells lacking this gene show a normal growth rate, do not exhibit a decrease in the efficiency of natural transformation, and is as resistant to ionizing radiation as wild-type. However, deletion of the ddrC gene decreases the ionizing radiation resistance of the ddrB mutant strain or the recA mutant strain, and appears to increase that of the pprA mutant strain. Moreover, cells lacking both ddrC and ddrD exhibit a slight (two-fold) increase in sensitivity to ionizing radiation, but this phenotype is apparent only at the highest applied doses (PubMed:15454524). The ddrC deletion mutant is 10 times more ssensitive to high doses of UV radiation than wild-type cells, and the ddrC deletion significantly increases UV-sensitivity of uvrA or uvsE deletion mutant strains (PubMed:28542368).
Induced to high levels following extreme ionizing radiation exposure (PubMed:15454524, PubMed:28542368). Is induced after gamma-irradiation in an IrrE/DdrO dependent manner (PubMed:28542368). Also highly induced in response to desiccation stress (PubMed:15454524).
Is composed of two domains, an unusual N-terminal wHTH motif and a more classical four-helix bundle at its C-terminus, which is domain swapped in the DdrC homodimer. The domain swapping creates an asymmetric dimer exhibiting two distinct DNA binding surfaces corresponding to a high- and a low-affinity DNA binding site.
Was originally predicted on the opposite strand.
Belongs to the universal ribosomal protein uS2 family.
Belongs to the V-ATPase F subunit family.
Belongs to the bacterial ribosomal protein bL34 family.
Part of the 50S ribosomal subunit. Contacts protein L4.
An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family.
Belongs to the OMP decarboxylase family. Type 2 subfamily.
Belongs to the MsrB Met sulfoxide reductase family.
Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis: the synthesis of N-acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate.
Heterotetramer of two alpha and two beta chains.
Some bacteria possess a monofunctional ArgJ, i.e. capable of catalyzing only the fifth step of the arginine biosynthetic pathway.
Belongs to the aconitase/IPM isomerase family. LeuC type 2 subfamily.
Belongs to the universal ribosomal protein uS19 family.
Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.
Belongs to the P-Pant transferase superfamily. AcpS family.
Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.
Binds and transfers iron-sulfur (Fe-S) clusters to target apoproteins. Can hydrolyze ATP.
In the C-terminal section; belongs to the Mrp/NBP35 ATP-binding proteins family.
In the N-terminal section; belongs to the MIP18 family.
Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus.
E2 component of the 2-oxoglutarate dehydrogenase (OGDH) complex which catalyzes the second step in the conversion of 2-oxoglutarate to succinyl-CoA and CO(2).
Belongs to the pyridoxal phosphate-binding protein YggS/PROSC family.
Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis.
Belongs to the universal ribosomal protein uL2 family.
One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).
Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome (By similarity).
IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit (By similarity).
Belongs to the leucine-binding protein family.
Belongs to the 3-oxoacid CoA-transferase subunit A family.
Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs.
Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth.
Mycophenolic acid (MPA) is a non-competitive inhibitor that prevents formation of the closed enzyme conformation by binding to the same site as the amobile flap. In contrast, mizoribine monophosphate (MZP) is a competitive inhibitor that induces the closed conformation. MPA is a potent inhibitor of mammalian IMPDHs but a poor inhibitor of the bacterial enzymes. MZP is a more potent inhibitor of bacterial IMPDH.
Tetramer of two alpha and two beta chains.
The alpha subunit is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate.
Belongs to the PHP hydrolase family. HisK subfamily.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. PrfC subfamily.
Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP.
Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.
Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrR subfamily.
Regulates the transcription of the pyrimidine nucleotide (pyr) operon in response to exogenous pyrimidines.
Belongs to the glycosyltransferase 4 family. MraY subfamily.
Catalyzes the initial step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan: transfers peptidoglycan precursor phospho-MurNAc-pentapeptide from UDP-MurNAc-pentapeptide onto the lipid carrier undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide, known as lipid I.
Belongs to the glutamine synthetase family.
Belongs to the bacterial solute-binding protein ModA family.
Catalyzes the condensation of para-aminobenzoate (pABA) with 6-hydroxymethyl-7,8-dihydropterin diphosphate (DHPt-PP) to form 7,8-dihydropteroate (H2Pte), the immediate precursor of folate derivatives.
Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family.
Involved in the biosynthesis of ADP-glucose, a building block required for the elongation reactions to produce glycogen. Catalyzes the reaction between ATP and alpha-D-glucose 1-phosphate (G1P) to produce pyrophosphate and ADP-Glc.
Belongs to the methylenetetrahydrofolate reductase family.
Belongs to the threonine synthase family.
Belongs to the globin family. Two-domain flavohemoproteins subfamily.
Consists of two distinct domains; an N-terminal heme-containing oxygen-binding domain and a C-terminal reductase domain with binding sites for FAD and NAD(P)H.
In the C-terminal section; belongs to the flavoprotein pyridine nucleotide cytochrome reductase family.
Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily.
Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).
Belongs to the V-ATPase E subunit family.
Produces ATP from ADP in the presence of a proton gradient across the membrane.
Involved in DNA repair and RecF pathway recombination.
Contains an N-terminal PQQ binding domain and a C-terminal disorganized low-complexity (LC) hydrophilic region.
Mutant is sensitive to gamma radiation and hypersensitive to desiccation. It shows delayed DNA double-strand break repair and delayed recovery of desiccated nucleoid.
Plays an important role in resistance to desiccation and radiation, maybe by protecting genome integrity under extreme conditions.
Belongs to the glutamate 5-kinase family.
Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate.
Composed of three structural domains: an N-terminal zinc-peptidase domain, a central helix-turn-helix motif, and a C-terminal GAF-type domain.
It is uncertain whether Met-1 or Val-41 is the initiator.
Mutant is sensitive to ionizing radiation, UV light and mitomycin C.
Plays a central regulatory role in DNA repair and protection pathways in response to radiation stress (PubMed:12804570, PubMed:22051194). Acts as a site-specific metalloprotease that cleaves and inactivates the repressor protein DdrO, resulting in induced expression of genes required for DNA repair and cell survival after exposure to radiation (By similarity). Regulates the expression of dozens of proteins from different pathways, including the important DNA repair proteins RecA and PprA (PubMed:12399492, PubMed:12804570, PubMed:22051194). Binds to the promoters of recA and pprA (PubMed:22051194).
Belongs to the GHMP kinase family. IspE subfamily.
Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol.
Belongs to the Nudix hydrolase family. PCD1 subfamily.
Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell.
4'-phosphopantetheine is transferred from CoA to a specific serine of apo-ACP by AcpS. This modification is essential for activity because fatty acids are bound in thioester linkage to the sulfhydryl of the prosthetic group.
Belongs to the acyl carrier protein (ACP) family.
Carrier of the growing fatty acid chain in fatty acid biosynthesis.
Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate.
Appears to contribute to D.radiodurans capacity to survive exposure to ionizing radiation. May play a role in DNA repair and genome reconstitution.
Cells lacking this gene show a normal growth rate, do not exhibit a decrease in the efficiency of natural transformation, and is as resistant to ionizing radiation as wild-type. However, deletion of the ddrC gene decreases the ionizing radiation resistance of the recA mutant strain, and appears to increase that of the pprA mutant strain. Moreover, cells lacking both ddrC and ddrD exhibit a slight (two-fold) increase in sensitivity to ionizing radiation, but this phenotype is apparent only at the highest applied doses.
Belongs to the Dus family. DusA subfamily.
Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs.
Homodimer. Heterotetramer of two MnmE and two MnmG subunits.
NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34.
Uptake of L-lactate across the membrane. Can also transport D-lactate and glycolate.
Homododecamer. The 12 subunits form a hollow sphere into which the mineral iron core of up to 500 Fe(3+) can be deposited (By similarity).
Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity).
Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP).
Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the 'tag peptide' encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation.
Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).
Catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO(3)- to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).
Belongs to the ABC-3 integral membrane protein family.
Cells lacking this gene show a reduced growth rate, do not exhibit a decrease in the efficiency of natural transformation, but are much more sensitive to ionizing radiation than the wild-type strain.
Phosphorylated by RqkA in vitro. Phosphorylated primarily at Thr-88, and to a little extent at Ser-128 and Thr-160.
Phosphorylation increases DNA binding affinity.
The PprA protein combined with an immunofluorescence technique can be used to visualize radiation-induced DNA strand breaks in mammalian cultured cells, allowing the evaluation of DNA damage responses. This detection method could also be applicable to genotoxic tests in the environmental and pharmaceutical fields.
dsDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Plays a role in DNA repair and genome reconstitution, and is necessary for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. In vitro, binds to double-stranded DNA carrying strand breaks and stimulates the DNA end-joining reaction catalyzed by DNA ligases. Thus, PprA plays a critical role in a non-homologous end-joining (NHEJ) pathway for the repair of radiation-induced DNA double-strands breaks. Cannot bind to dsDNA without strand breaks or single-stranded DNA.
Belongs to the methylmalonyl-CoA epimerase family.
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.
Belongs to the SAICAR synthetase family.
Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.
Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes.
D.radiodurans possesses an atypical cell envelope comprising an inner membrane, a large periplasmic space with a thick peptidoglycan (PG) layer, and an outer membrane (OM) covered by a surface layer (S-layer).
Deletion causes substantial alterations in cell envelope structure, and a significant defect in resistance to solvent and shear stresses. Mutants shed exterior layers of the cellular envelope (PubMed:16946272). Deletion mutants show a significant decrease of the UV resistance, especially under desiccation conditions (PubMed:26909071). Deletions mutants show large disruptions in the OM, but the S-layer is unchanged compared to wild-type cells (PubMed:35943982).
Homotrimer (PubMed:35577074, PubMed:35943982). Part of a heterooligomeric complex resulting in the main assembly named S-layer deinoxanthin-binding complex (SDBC) which is composed of six different subunits, namely SlpA, DR_2310, DR_0505, DR_A0283, DR_A0282, and DR_A0281 (PubMed:32071085).
Plays an important role in the structural organization and integrity of the cell envelope, bridging the outer membrane to the peptidoglyan layer (PubMed:16946272, PubMed:26074883, PubMed:35943982). Is a highly abundant molecule in the D.radiodurans cell envelope but is not a fundamental component of the S-layer (PubMed:35943982). Binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium, and could be part of the first lane of defense against UV radiation, especially under desiccation (PubMed:26909071). Appears to be a nonselective channel (PubMed:32071085). Is able to transport charged amino acids such as Lys, Arg and Glu; the large dimension of the pore points toward the physiological importance of the SDBC complex in assisting and allowing the exchange of substances, including nutrients, with the surrounding environment (PubMed:35577074).
The structure is characterized by a pore region with a massive beta-barrel organization which is embedded in the outer membrane and shows some protrusions into the S-layer, a stalk region consisting of a trimeric coiled coil, and a collar region at the base of the stalk (PubMed:35577074). More precisely, SlpA exhibits a tripartite organization, with its C-terminal part forming a homotrimeric 30-stranded OM beta-barrel (OMBB), its central part forming a long trimeric coiled coil that can traverse the large periplasmic space, and the extreme N-terminal part forming an SLH domain trimer that can interact with the PG layer (PubMed:35943982).
Was originally thought to be a major constituent of the S-layer. However, structural and deletion mutant studies showed that SlpA is an outer membrane protein and is not an integral part of the S-layer (PubMed:35943982).
A lyase-type mechanism (elimination/hydration) is suggested for the cleavage of the lactyl ether bond of MurNAc 6-phosphate, with the formation of an alpha,beta-unsaturated aldehyde intermediate with (E)-stereochemistry, followed by the syn addition of water to give product.
Belongs to the GCKR-like family. MurNAc-6-P etherase subfamily.
Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6-phosphate and D-lactate.
Belongs to the GHMP kinase family. Homoserine kinase subfamily.
Catalyzes the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate.
Belongs to the V-ATPase 116 kDa subunit family.
Belongs to the universal ribosomal protein uL29 family.
Binds the 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.
Part of the 50S ribosomal subunit. Contacts protein L23 and trigger factor when it is complexed with the ribosome (PubMed:16091460, PubMed:16271892).
Belongs to the bacterial solute-binding protein 3 family.
Belongs to the aspartate-semialdehyde dehydrogenase family.
Catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (L-ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate.
Belongs to the glucose-1-phosphate thymidylyltransferase family.
Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis.
Part of the binding-protein-dependent transport system for molybdenum; probably responsible for the translocation of the substrate across the membrane.
Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available.
Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin.
Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.
Synthesizes alpha-1,4-glucan chains using ADP-glucose.
Belongs to the Nudix hydrolase family. NudC subfamily.
Divalent metal cations. Mg(2+) or Mn(2+).
mRNA decapping enzyme that specifically removes the nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by hydrolyzing the diphosphate linkage to produce nicotinamide mononucleotide (NMN) and 5' monophosphate mRNA. The NAD-cap is present at the 5'-end of some mRNAs and stabilizes RNA against 5'-processing. Has preference for mRNAs with a 5'-end purine. Catalyzes the hydrolysis of a broad range of dinucleotide pyrophosphates.
Belongs to the V-ATPase D subunit family.
Belongs to the trans-sulfuration enzymes family.
Belongs to the purine/pyrimidine phosphoribosyltransferase family.
Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family.
tRNA nucleotidyltransferase involved in the synthesis of the tRNA CCA terminus. Adds the terminal adenosine residue to tRNA.
Constitutively expressed, highly up-regulated following ionizing radiation for at least 12 hours (at protein level).
Essential, it cannot be knocked out. As SSB levels are depleted growth slows, tolerance to ionizing radiation and UV light decreases rapidly. Cannot be complemented by ddrB.
Homodimer. Binds ssDNA. Interacts with DdrB.
Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism (By similarity). Essential for ionizing radiation resistance. Stimulates the 5'-3' DNA helicase activity of RecD-like helicase. Stimulates RecA protein-promoted DNA three-strand exchange reactions in vitro with both D.radiodurans and E.coli-derived RecA. Complements an ssb deletion in E.coli, but does not complement a ddrb disruption in D.radiodurans.
Belongs to the bacterial ribosomal protein bL9 family.
Part of the 50S ribosomal subunit. Contacts protein L31.
Belongs to the RecD family. RecD-like subfamily.
DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-dependent 5'-3' DNA helicase. Appears to move along DNA in single base steps, powered by hydrolysis of 1 molecule of ATP. Has low processivity; short (20 bp) substrates with 5'-overhangs or forked ends are the best substrates, is much less efficient on 52 or 76 bp substrates with 5'- overhangs. The presence of single-stranded DNA-binding protein (SSB) increases unwinding 4-5 fold. Has no activity on blunt DNA or DNA with 3'-overhangs. Requires at least 10 bases of 5'-ssDNA for helicase activity.
There are no RecB or RecC orthologs in this organism.
Belongs to the thiolase-like superfamily. FabH family.
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.
The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH.
Belongs to the pseudouridine synthase TruB family. Type 1 subfamily.
Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.
Belongs to the universal ribosomal protein uS7 family.
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA.
Part of the 30S ribosomal subunit. Contacts proteins S9 and S11.
To bacterial alkanal monooxygenase alpha and beta chains.
Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). Also edits incorrectly charged L-seryl-tRNA(Thr).
Belongs to the bacterial ribosomal protein bL12 family.
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation (Probable).
Homodimer. Part of the ribosomal stalk of the 50S ribosomal subunit. Forms a multimeric L10(L12)X complex, where L10 forms an elongated spine to which 2 to 4 L12 dimers bind in a sequential fashion. Binds GTP-bound translation factors (Probable).
Belongs to the pseudouridine-5'-phosphate glycosidase family.
Catalyzes the reversible cleavage of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil. Functions biologically in the cleavage direction, as part of a pseudouridine degradation pathway.
Belongs to the methyl-accepting chemotaxis (MCP) protein family.
Flavin prenyltransferase that catalyzes the synthesis of the prenylated FMN cofactor (prenyl-FMN) for 4-hydroxy-3-polyprenylbenzoic acid decarboxylase UbiD. The prenyltransferase is metal-independent and links a dimethylallyl moiety from dimethylallyl monophosphate (DMAP) to the flavin N5 and C6 atoms of FMN.
Catalyzes the cleavage of 5-oxoproline to form L-glutamate coupled to the hydrolysis of ATP to ADP and inorganic phosphate.
Forms a complex composed of PxpA, PxpB and PxpC.
Belongs to the HpcH/HpaI aldolase family. Citrate lyase beta subunit-like subfamily.
May play a role in fatty acid biosynthesis.
This organism lacks the other subunits that are necessary for ATP-independent citrate lyase activity. Even though this protein has clear similarity to citrate lyase beta subunit, it is expected to have a somewhat different enzyme activity.
Catalyzes the NADP(+) dependent oxidation of succinate semialdehyde to succinate.
Belongs to the glycogen phosphorylase family.
Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln).
Belongs to the amidase family. GatA subfamily.
Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family.
Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP.
Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily.
Belongs to the universal ribosomal protein uL16 family.
Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center.
Part of the 50S ribosomal subunit. Contacts the CTC protein (RL25).
Belongs to the major facilitator superfamily. Set transporter family.
Involved in the efflux of sugars. The physiological role may be the detoxification of non-metabolizable sugar analogs (By similarity).
Belongs to the class-II fumarase/aspartase family. Fumarase subfamily.
Involved in the TCA cycle. Catalyzes the stereospecific interconversion of fumarate to L-malate.
There are 2 substrate-binding sites: the catalytic A site, and the non-catalytic B site that may play a role in the transfer of substrate or product between the active site and the solvent. Alternatively, the B site may bind allosteric effectors.
Belongs to the universal ribosomal protein uS13 family.
Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.
Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome.
In the C-terminal section; belongs to the phosphate acetyltransferase and butyryltransferase family.
In the N-terminal section; belongs to the CobB/CobQ family.
The N-terminal region seems to be important for proper quaternary structure. The C-terminal region contains the substrate-binding site (By similarity).
Belongs to the universal stress protein A family.
Belongs to the universal ribosomal protein uS11 family.
Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.
Part of the 30S ribosomal subunit. Interacts with proteins S7 and S18. Binds to IF-3.
DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
Belongs to the EPSP synthase family. MurA subfamily.
Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine.
Belongs to the polypeptide deformylase family.
Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.
Belongs to the uroporphyrinogen-III synthase family.
Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III.
Belongs to the proline dehydrogenase family.
Converts proline to delta-1-pyrroline-5-carboxylate.
Belongs to the transketolase family. DXPS subfamily.
Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP).
Belongs to the pseudouridine synthase RsuA family.
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation.
Belongs to the AfsR/DnrI/RedD regulatory family.
Belongs to the universal ribosomal protein uL6 family.
It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity). This protein binds to the 23S rRNA, and is important in its secondary structure.
Could be involved in insertion of integral membrane proteins into the membrane.
Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme.
Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A.
Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein.
A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.
Belongs to the topoisomerase GyrA/ParC subunit family.
Belongs to the type II topoisomerase GyrA/ParC subunit family.
Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.
Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.
Affinity for substrate L-arginine is increased by TrpRS II.
Belongs to the NOS family. Bacterial NOS oxygenase subfamily.
Catalyzes the production of nitric oxide. The complex between TrpRS II and nitric oxide synthase oxygenase catalyzes the regioselective nitration of tryptophan at the 4-position.
Homodimer. Forms a complex with trpS2; one homodimer of trpS2 binds one homodimer of nos.
Nitric oxide synthase activity is increased by trpS2.
This protein is similar to the oxygenase domain of eukaryotic nitric oxide synthases but lacks the reductase domain which, in eukaryotes, is responsible for transfer of electrons to the ferric heme during nitric oxide synthesis.
Belongs to the complex I subunit 4 family.
Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP-GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5-monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain.
In the C-terminal section; belongs to the transferase hexapeptide repeat family.
In the N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family.
Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.
Belongs to the SurE nucleotidase family.
Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates.
Contains two rhodanese domains with different primary structures but with near identical secondary structure conformations suggesting a common evolutionary origin. Only the C-terminal rhodanese domain contains the catalytic cysteine residue (By similarity).
Has oligopeptidase activity and degrades a variety of small bioactive peptides.
Contains one covalently linked tetrapyrrole chromophore. Lacks the cysteine conserved in plant phytochromes (at the position of Met-259) that binds chromophore. An engineered sequence used for X-ray crystallography forms a thioether link to biliverdin through Cys-24. The natural sequence can bind phycocyanobilin and phytochromobilin in vitro, but the identity of the natural chromophore is unknown.
In the N-terminal section; belongs to the phytochrome family.
Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
Belongs to the universal ribosomal protein uS4 family.
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.
Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity.
With S5 and S12 plays an important role in translational accuracy.
Binds to the N-terminal domain of the chaperone ClpA.
Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation.
Belongs to the metallo-dependent hydrolases superfamily. Allantoinase family.
Carboxylation allows a single lysine to coordinate two zinc ions.
Catalyzes the conversion of allantoin (5-ureidohydantoin) to allantoic acid by hydrolytic cleavage of the five-member hydantoin ring.
Belongs to the thioesterase PaaI family.
Belongs to the Cob(I)alamin adenosyltransferase family.
Belongs to the helicase family. RecQ subfamily.
Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction.
ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.
Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes.
Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily.
Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile).
IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)).
Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class I DHOase subfamily.
Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family.
Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34.
Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily.
Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons.
May be involved in recombinational repair of damaged DNA.
Belongs to the complex I subunit 6 family.
Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
Strongly inhibited by sodium azide and sodium cyanide, and slightly inhibited by 3-amino-1,2,4-triazole.
Belongs to the pyridoxamine 5'-phosphate oxidase family.
Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).
The IMP cyclohydrolase activity resides in the N-terminal region.
Essential for recycling GMP and indirectly, cGMP.
Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily.
Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).
Toxic component of a type II toxin-antitoxin (TA) system.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily.
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.
Belongs to the ETF alpha-subunit/FixB family.
Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.
Belongs to the Cu-Zn superoxide dismutase family.
Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
Lacks the last conserved histidine that binds copper.
Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle.
Belongs to the purine/pyrimidine phosphoribosyltransferase family. Xpt subfamily.
Converts the preformed base xanthine, a product of nucleic acid breakdown, to xanthosine 5'-monophosphate (XMP), so it can be reused for RNA or DNA synthesis.
Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection.
Mutants display an increased sensitivity to oxidative stress, and a slightly increased sensitivity to ionizing radiation and UV exposure.
The RecF protein is involved in DNA metabolism; it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP (By similarity).
May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO.
Removes 5-oxoproline from various penultimate amino acid residues except L-proline.
Belongs to the CorA metal ion transporter (MIT) (TC 1.A.35) family.
Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.
12 di-nuclear ferroxidase centers are located at the interfaces between subunits related by 2-fold symmetry axes.
Addition of Ca(2+) to dodecameric dps can result in the reduction of bound Fe(3+).
Dodecameric dps forms large aggregates upon binding to DNA.
Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe(2+) oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.
The 12 subunits form a hollow sphere into which the mineral iron core of up to 500 Fe(3+) can be deposited (By similarity). The homododecameric forms at higher concentration of salt, the homodimeric form under reducing, low-salt conditions. The assembly of the dodecamer is irreversible.
Bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides.
Heterooligomer composed of large and small subunits.
Functions as a ribosomal silencing factor. Interacts with ribosomal protein uL14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation.
Interacts with ribosomal protein uL14 (rplN).
Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).
Probably involved in ribonucleotide reductase function.
Belongs to the cytidine and deoxycytidylate deaminase family.
Belongs to the heme-copper respiratory oxidase family.
Belongs to the thymidylate kinase family.
Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis.
Belongs to the complex I subunit 2 family.
Belongs to the gluconeogenesis factor family.
Required for morphogenesis under gluconeogenic growth conditions.
Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.
Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34.
Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA.
Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily.
Catalyzes two reactions in de novo purine nucleotide biosynthesis. Catalyzes the breakdown of 5-aminoimidazole- (N-succinylocarboxamide) ribotide (SAICAR or 2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate) to 5-aminoimidazole-4-carboxamide ribotide (AICAR or 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide) and fumarate, and of adenylosuccinate (ADS or N(6)-(1,2-dicarboxyethyl)-AMP) to adenosine monophosphate (AMP) and fumarate.
Homotetramer. Residues from neighboring subunits contribute catalytic and substrate-binding residues to each active site (By similarity).
Has 3 domains, the large (RuvB-L) and small ATPase (RuvB-S) domains and the C-terminal head (RuvB-H) domain. The head domain binds DNA, while the ATPase domains jointly bind ATP, ADP or are empty depending on the state of the subunit in the translocation cycle. During a single DNA translocation step the structure of each domain remains the same, but their relative positions change.
Homohexamer. Forms an RuvA(8)-RuvB(12)-Holliday junction (HJ) complex. HJ DNA is sandwiched between 2 RuvA tetramers; dsDNA enters through RuvA and exits via RuvB. An RuvB hexamer assembles on each DNA strand where it exits the tetramer. Each RuvB hexamer is contacted by two RuvA subunits (via domain III) on 2 adjacent RuvB subunits; this complex drives branch migration. In the full resolvosome a probable DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms which resolves the HJ.
The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair, while the RuvA-RuvB complex plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR). RuvA specifically binds to HJ cruciform DNA, conferring on it an open structure. The RuvB hexamer acts as an ATP-dependent pump, pulling dsDNA into and through the RuvAB complex. RuvB forms 2 homohexamers on either side of HJ DNA bound by 1 or 2 RuvA tetramers; 4 subunits per hexamer contact DNA at a time. Coordinated motions by a converter formed by DNA-disengaged RuvB subunits stimulates ATP hydrolysis and nucleotide exchange. Immobilization of the converter enables RuvB to convert the ATP-contained energy into a lever motion, pulling 2 nucleotides of DNA out of the RuvA tetramer per ATP hydrolyzed, thus driving DNA branch migration. The RuvB motors rotate together with the DNA substrate, which together with the progressing nucleotide cycle form the mechanistic basis for DNA recombination by continuous HJ branch migration. Branch migration allows RuvC to scan DNA until it finds its consensus sequence, where it cleaves and resolves cruciform DNA.
Belongs to the bacterial ribosomal protein bS18 family.
Binds as a heterodimer with protein bS6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit.
Part of the 30S ribosomal subunit. Forms a tight heterodimer with protein bS6.
Belongs to the ABC transporter superfamily. Spermidine/putrescine importer (TC 3.A.1.11.1) family.
Part of the ABC transporter complex PotABCD involved in spermidine/putrescine import. Responsible for energy coupling to the transport system.
The complex is composed of two ATP-binding proteins (PotA), two transmembrane proteins (PotB and PotC) and a solute-binding protein (PotD).
Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit acts as a catalytic chaperone that increases the ATP-binding affinity of the ATP-hydrolyzing subunit KdpB by the formation of a transient KdpB/KdpC/ATP ternary complex.
Belongs to the FKBP-type PPIase family. Tig subfamily.
Binds to the 50S ribosomal subunit via interactions with ribosomal protein L23. Also interacts with 23S rRNA and proteins L24 and L29 when complexed with the ribosome (PubMed:16091460, PubMed:16271892).
Consists of 3 domains; the N-terminus binds the ribosome, the middle domain has PPIase activity, while the C-terminus has intrinsic chaperone activity on its own.
Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase (By similarity). Probably changes conformation upon binding to the ribosome (maybe in particular due to interaction with L24), exposing a hydrophobic crevice that is probably important for its chaperone activity (PubMed:16091460, PubMed:16271892).
Belongs to the 2H phosphoesterase superfamily. ThpR family.
Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester.
Belongs to the class-I DAHP synthase family.
Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP).
Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site.
In the C-terminal section; belongs to the helicase family. RecG subfamily.
In the N-terminal section; belongs to the UvrB family.
Belongs to the elongation factor P family.
Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.
Belongs to the metallo-dependent hydrolases superfamily. ATZ/TRZ family.
Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia.
Has no RNase activity in the presence of Mg(2+), Ca(2+) or Zn(2+).
Has robust sequence-specific RNase activity, acting as a 5'-3' exo/endonuclease on ssRNA substrates with minimally 3 consecutive adenine bases. Has no detectable nuclease activity on dsRNA, dsDNA or Holliday junction DNA.
Monomer; also forms low amounts of dimers.
Belongs to the enoyl-CoA hydratase/isomerase family.
Contains an active site 4-methylidene-imidazol-5-one (MIO), which is formed autocatalytically by cyclization and dehydration of residues Ala-Ser-Gly.
Belongs to the tRNA pseudouridine synthase TruA family.
Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.
Belongs to the bacterial ribosomal protein bL36 family.
Belongs to the drug/metabolite transporter (DMT) superfamily. Small multidrug resistance (SMR) (TC 2.A.7.1) family.
Autokinase activity is stimulated by DNA damage. Stimulated by PQQ and DNA ends in vitro.
Belongs to the protein kinase superfamily. Ser/Thr protein kinase family.
Contains an N-terminal catalytic kinase domain and a C-terminal PQQ binding domain.
Expression is induced in response to DNA damage.
Mutant exhibits higher sensitivity to different DNA-damaging agents. It shows altered phosphoprotein profile and impaired DSB repair. Deletion affects expression of genes involved in intermediary metabolism, stress response and growth under stressed conditions.
Plays an important role in radiation resistance and DNA double-strand break (DSB) repair. Involved in transcriptional regulation of genes important for bacterial stress response. Phosphorylates PprA in vitro.
Belongs to the Ca(2+):cation antiporter (CaCA) (TC 2.A.19) family.
Ca(+)/H(+) antiporter that extrudes calcium in exchange for external protons.
Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH.
Allosterically activated by GTP, when glutamine is the substrate; GTP has no effect on the reaction when ammonia is the substrate. The allosteric effector GTP functions by stabilizing the protein conformation that binds the tetrahedral intermediate(s) formed during glutamine hydrolysis. Inhibited by the product CTP, via allosteric rather than competitive inhibition.
CTPSs have evolved a hybrid strategy for distinguishing between UTP and CTP. The overlapping regions of the product feedback inhibitory and substrate sites recognize a common feature in both compounds, the triphosphate moiety. To differentiate isosteric substrate and product pyrimidine rings, an additional pocket far from the expected kinase/ligase catalytic site, specifically recognizes the cytosine and ribose portions of the product inhibitor.
Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates.
Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.
In the C-terminal section; belongs to the HTP reductase family.
In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminase family.
Belongs to the aconitase/IPM isomerase family.
Involved in the catabolism of short chain fatty acids (SCFA) via the tricarboxylic acid (TCA)(acetyl degradation route) and probably the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the reversible isomerization of citrate to isocitrate via cis-aconitate. Could catalyze the hydration of 2-methyl-cis-aconitate to yield (2R,3S)-2-methylisocitrate. The apo form of AcnA functions as a RNA-binding regulatory protein.
Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.
Belongs to the SecD/SecF family. SecD subfamily.
Belongs to the SecD/SecF family. SecF subfamily.
Forms a complex with SecD. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved.
Forms a complex with SecF. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved.
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA.
Belongs to the polyribonucleotide nucleotidyltransferase family.
Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction.
Belongs to the PINc/VapC protein family.
Toxic component of a toxin-antitoxin (TA) system. An RNase.
Belongs to the argininosuccinate synthase family. Type 1 subfamily.
Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins.
In the C-terminal section; belongs to the peptidase M41 family.
In the central section; belongs to the AAA ATPase family.
Belongs to the CcmF/CycK/Ccl1/NrfE/CcsA family.
Belongs to the CPA3 antiporters (TC 2.A.63) subunit F family.
Belongs to the bacterial ribosomal protein bL35 family.
Part of the 50S ribosomal subunit. Contacts proteins L15 and L33.
Belongs to the universal ribosomal protein uL22 family.
Part of the 50S ribosomal subunit. Contacts protein L32.
The globular domain of the protein is located by the polypeptide exit tunnel on the outside of the subunit while an extended beta-hairpin forms part of the wall of the tunnel. Forms a pair of 'tweezers' with L32 that hold together two different domains of the 23S rRNA. Interacts with the tunnel-blocking modified macrolide azithromycin. Upon binding of the macrolide troleadomycin to the ribosome, the tip of the beta-hairpin is displaced, which severely restricts the tunnel. This and experiments in E.coli have led to the suggestion that it is part of the gating mechanism involved in translation arrest in the absence of the protein export system.
This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).
Belongs to the pyrroline-5-carboxylate reductase family.
Catalyzes the reduction of 1-pyrroline-5-carboxylate (PCA) to L-proline.
Belongs to the RNA methyltransferase TrmD family.
Specifically methylates guanosine-37 in various tRNAs.
H(+)-stimulated, divalent metal cation uptake system.
Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes. TatA could form the protein-conducting channel of the Tat system.
In the C-terminal section; belongs to the transposase 35 family.
In the N-terminal section; belongs to the transposase 2 family.
Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate.
Allosterically activated by ADP and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate.
Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade 'B1' sub-subfamily.
Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis.
Belongs to the RNA polymerase beta chain family.
Belongs to the bleomycin resistance protein family.
The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein.
Belongs to the universal ribosomal protein uL10 family.
Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL.
Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel.
Catalyzes the first step in the biosynthesis of NAD from nicotinic acid, the ATP-dependent synthesis of beta-nicotinate D-ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate.
Transiently phosphorylated on a His residue during the reaction cycle. Phosphorylation strongly increases the affinity for substrates and increases the rate of nicotinate D-ribonucleotide production. Dephosphorylation regenerates the low-affinity form of the enzyme, leading to product release.
Belongs to the GTP-binding SRP family. FtsY subfamily.
Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Acts as a receptor for the complex formed by the signal recognition particle (SRP) and the ribosome-nascent chain (RNC).
tRNA nucleotidyltransferase involved in the synthesis of the tRNA CCA terminus. Adds the two cytidine residues to tRNA.
In the C-terminal section; belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family.
Belongs to the dicarboxylate/amino acid:cation symporter (DAACS) (TC 2.A.23) family.
Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate across the membrane.
Belongs to the histone deacetylase family.
Component of the dihydroxyacetone kinase complex, which is responsible for the phosphoenolpyruvate (PEP)-dependent phosphorylation of dihydroxyacetone. DhaM serves as the phosphoryl donor. Is phosphorylated by phosphoenolpyruvate in an EI- and HPr-dependent reaction, and a phosphorelay system on histidine residues finally leads to phosphoryl transfer to DhaL and dihydroxyacetone.
Belongs to the class-II aminoacyl-tRNA synthetase family. HisZ subfamily.
Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine (By similarity).
This function is generally fulfilled by the C-terminal part of HisG, which is missing in some bacteria such as this one.
Belongs to the fluoride channel Fluc/FEX (TC 1.A.43) family.
Fluoride-specific ion channel. Important for reducing fluoride concentration in the cell, thus reducing its toxicity.
Na(+) is not transported, but it plays an essential structural role and its presence is essential for fluoride channel function.
Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly.
One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex.
Involved in urease metallocenter assembly. Binds nickel. Probably functions as a nickel donor during metallocenter assembly.
Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit.
Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell (By similarity).
Belongs to the bacterial ribosomal protein bL21 family.
Part of the 50S ribosomal subunit. Contacts proteins L15 and L20.
Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family.
Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA.
Belongs to the chaperonin (HSP60) family.
Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES.
Together with its co-chaperonin GroES, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding.
Belongs to the type-B carboxylesterase/lipase family.
Catalyzes the NADPH-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
Belongs to the metallo-dependent hydrolases superfamily. Urease alpha subunit family.
Carboxylation allows a single lysine to coordinate two nickel ions.
Heterohexamer of 3 UreC (alpha) and 3 UreAB (gamma/beta) subunits.
Belongs to the cysteine synthase/cystathionine beta-synthase family.
Belongs to the complex I 51 kDa subunit family.
NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain.
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism.
Consists of three domains, a large central CORE domain and two small peripheral domains, NMPbind and LID, which undergo movements during catalysis. The LID domain closes over the site of phosphoryl transfer upon ATP binding. Assembling and dissambling the active center during each catalytic cycle provides an effective means to prevent ATP hydrolysis.
Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.
Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.
Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family.
Belongs to the shaker potassium channel beta subunit family.
Belongs to the class I-like SAM-binding methyltransferase superfamily. MenG/UbiE family.
Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2).
Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit.
RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme.
A monovalent cation. Ammonium or potassium.
Belongs to the type III pantothenate kinase family.
Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis.
Catalyzes the attachment of tryptophan to tRNA(Trp).
Belongs to the FMN-dependent alpha-hydroxy acid dehydrogenase family.
Belongs to the multi antimicrobial extrusion (MATE) (TC 2.A.66.1) family.
Belongs to the chromate ion transporter (CHR) (TC 2.A.51) family.
Belongs to the complex I 30 kDa subunit family.
This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Belongs to the phenylacetyl-CoA ligase family.
Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA).
Belongs to the SIMIBI class G3E GTPase family. HypB/HupM subfamily.
Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily.
Part of the 50S ribosomal subunit. Contacts proteins L11 and L16, the A site tRNA, and the 5S and 23S rRNAs.
This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit. This protein has three domains. The N-terminal one is bound on the solvent face, the middle domain fills the space between the 5S rRNA and the L11 arm contacting the 23S rRNA while the C-terminal domain is on the edge of the intersubunit interface and contacts the A site. The protein conformation changes upon binding of a tRNA mimic to the A site, although the mimic does not interact directly with CTC itself, consistent with CTCs presumed role in moderating A site binding.
Belongs to the SIMIBI class G3E GTPase family. UreG subfamily.
Facilitates the functional incorporation of the urease nickel metallocenter. This process requires GTP hydrolysis, probably effectuated by UreG.
Homodimer. UreD, UreF and UreG form a complex that acts as a GTP-hydrolysis-dependent molecular chaperone, activating the urease apoprotein by helping to assemble the nickel containing metallocenter of UreC. The UreE protein probably delivers the nickel.
Belongs to the uroporphyrinogen decarboxylase family.
Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.
Belongs to the universal ribosomal protein uS17 family.
One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.
Belongs to the RNA polymerase alpha chain family.
Homodimer. The RNAP catalytic core consists of 2 alpha, 1 beta, 1 beta' and 1 omega subunit. When a sigma factor is associated with the core the holoenzyme is formed, which can initiate transcription.
The N-terminal domain is essential for RNAP assembly and basal transcription, whereas the C-terminal domain is involved in interaction with transcriptional regulators and with upstream promoter elements.
Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding.
Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IA subfamily.
Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm.
Belongs to the bacterial ribosomal protein bL17 family.
Part of the 50S ribosomal subunit. Contacts proteins L3 and L32.
Belongs to the D-alanine--D-alanine ligase family.
Binds 2 magnesium or manganese ions per subunit.
Belongs to the ABC transporter superfamily. Heme (hemin) importer (TC 3.A.1.14.5) family.
Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system.
The complex is composed of two ATP-binding proteins (HmuV), two transmembrane proteins (HmuU) and a solute-binding protein (HmuT).
Belongs to the bacterial diacylglycerol kinase family.
Mn(2+), Zn(2+), Cd(2+) and Co(2+) support activity to lesser extents.
Belongs to the universal ribosomal protein uS12 family.
Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.
Part of the 30S ribosomal subunit. Contacts proteins S8 and S17. May interact with IF1 in the 30S initiation complex.
With S4 and S5 plays an important role in translational accuracy.
Belongs to the uracil-DNA glycosylase (UDG) superfamily. Type 4 (UDGa) family.
Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily.
Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).
Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding.
Homodimer. The tRNA molecule binds across the dimer.
Belongs to the glucose-6-phosphate dehydrogenase family.
Catalyzes the oxidation of glucose 6-phosphate to 6-phosphogluconolactone.
The heme is bound between the two transmembrane subunits.
In the C-terminal section; belongs to the urease beta subunit family.
In the N-terminal section; belongs to the urease gamma subunit family.
Belongs to the GMC oxidoreductase family.