The complete genome sequence of Thermodesulfovibrio yellowstonii strain ATCC 51303 / DSM 11347 / YP87.
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]
ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT ALPHA
ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT ALPHA, CHLOROPLASTIC
Acetyl-CoA carboxylase carboxyltransferase subunit alpha
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.
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).
4'-phosphopantetheinyl transferase domain
Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.
Belongs to the P-Pant transferase superfamily. AcpS family.
Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.
3-phosphoshikimate 1-carboxyvinyltransferase
5-enolpyruvylshikimate-3-phosphate synthase
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.
Dehydroquinate synthase-like - alpha domain
3-DEHYDROQUINATE SYNTHASE, CHLOROPLASTIC
Catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ).
Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+).
Belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family.
Involved in the third step of the chorismate pathway, which leads to the biosynthesis of aromatic amino acids. Catalyzes the cis-dehydration of 3-dehydroquinate (DHQ) and introduces the first double bond of the aromatic ring to yield 3-dehydroshikimate.
Belongs to the type-I 3-dehydroquinase family.
Leucine Dehydrogenase, chain A, domain 1
BIFUNCTIONAL 3-DEHYDROQUINATE DEHYDRATASE/SHIKIMATE DEHYDROGENASE, CHLOROPLASTIC
Aminoacid dehydrogenase-like, N-terminal domain
Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA).
Belongs to the shikimate dehydrogenase family.
P-loop containing nucleotide triphosphate hydrolases
P-loop containing nucleoside triphosphate hydrolases
Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.
ATP synthase alpha/beta chain, C-terminal domain
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C-terminal domain of alpha and beta subunits of F1 ATP synthase
N-terminal domain of alpha and beta subunits of F1 ATP synthase
Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit.
F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a(1), b(2) and c(9-12). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. CF(1) is attached to CF(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains.
Belongs to the ATPase alpha/beta chains family.
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits.
N-terminal domain of the delta subunit of the F1F0-ATP synthase
ATP SYNTHASE SUBUNIT DELTA, CHLOROPLASTIC
F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation.
This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction.
F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains.
Belongs to the ATPase delta chain family.
ATP synthase delta/epsilon subunit, C-terminal domain
F0F1 ATP synthase delta/epsilon subunit, N-terminal
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
Epsilon subunit of F1F0-ATP synthase C-terminal domain
Epsilon subunit of F1F0-ATP synthase N-terminal domain
Produces ATP from ADP in the presence of a proton gradient across the membrane.
F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c.
Belongs to the ATPase epsilon chain family.
Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0).
Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits.
Reversibly protonated during proton transport
Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism.
Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine.
Belongs to the radical SAM superfamily. Biotin synthase family.
ATP-dependent dethiobiotin synthetase BioD
Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA, also called 7,8-diammoniononanoate) to form a ureido ring.
Belongs to the dethiobiotin synthetase family.
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE
Putative 8-amino-7-oxononanoate synthase
Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide.
Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. BioF subfamily.
Catalyzes the transformation of pimelate into pimeloyl-CoA with concomitant hydrolysis of ATP to AMP.
CRISPR-associated endonuclease Cas1, C-terminal domain
CRISPR-associated endonuclease Cas1, N-terminal domain
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette.
Homodimer, forms a heterotetramer with a Cas2 homodimer.
Belongs to the CRISPR-associated endonuclease Cas1 family.
CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2 3
CRISPR-associated endoribonuclease Cas2 1
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease. Involved in the integration of spacer DNA into the CRISPR cassette.
Homodimer, forms a heterotetramer with a Cas1 homodimer.
Belongs to the CRISPR-associated endoribonuclease Cas2 protein family.
CRISPR-associated endoribonuclease Cas2 2
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.
Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL.
TCP-1-like chaperonin intermediate domain
60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL
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.
Forms a cylinder of 14 subunits composed of two heptameric rings stacked back-to-back. Interacts with the co-chaperonin GroES.
Belongs to the chaperonin (HSP60) family.
ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
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.
ClpX chaperone, C4-type zinc finger domain
ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL
ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED
Glucocorticoid receptor-like (DNA-binding domain)
ATP-dependent Clp protease ATP-binding subunit ClpX
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.
Pantetheine-phosphate adenylyltransferase
Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.
Catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation.
Belongs to the CobB/CobQ family. CobQ subfamily.
ADENOSYLCOBINAMIDE-GDP RIBAZOLETRANSFERASE
Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate.
3'-PHOSPHOADENOSINE-5'-PHOSPHOSULFATE SYNTHASE
BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHASE
ATP adenosine-5'-phosphosulfate 3'-phosphotransferase
Catalyzes the synthesis of activated sulfate.
4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE
Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).
Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB.
METHYLTETRAHYDROFOLATE:HOMOCYSTEINE METHYLTRANSFERASE RELATED
Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.
Belongs to the uroporphyrinogen decarboxylase family.
Glutathione synthetase ATP-binding domain-like
Binds 2 magnesium or manganese ions per subunit.
Belongs to the D-alanine--D-alanine ligase 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 polypeptide deformylase family.
GTPase that plays an essential role in the late steps of ribosome biogenesis.
Associates with the 50S ribosomal subunit.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family.
Deoxyguanosinetriphosphate triphosphohydrolase-like protein
Belongs to the dGTPase family. Type 2 subfamily.
CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA
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.
Heat shock protein 70kD (HSP70), C-terminal subdomain
Heat shock protein 70kD (HSP70), peptide-binding domain
Belongs to the heat shock protein 70 family.
5' to 3' exonuclease, C-terminal subdomain
CHROMOSOME TRANSMISSION FIDELITY FACTOR 18
DNA ligase/mRNA capping enzyme, catalytic domain
Polydeoxyribonucleotide synthase [NAD(+)]
DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA.
Belongs to the NAD-dependent DNA ligase family. LigA subfamily.
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.
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.
Gly-cisPro motif, important for rejection of L-amino acids
1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, CHLOROPLASTIC
1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
1-deoxyxylulose-5-phosphate reductoisomerase
2-C-methyl-D-erythritol 4-phosphate synthase
Catalyzes the NADPH-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
ELONGATION FACTOR P (EF-P) FAMILY PROTEIN
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 elongation factor P family.
DNA helicase RuvA subunit, C-terminal domain
Elongation factor Ts, dimerisation domain
Elongation factor Ts (EF-Ts), dimerisation domain
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.
Involved in Mg(2+) ion dislocation from EF-Tu
Assembles around the rod to form the L-ring and probably protects the motor/basal body from shearing forces during rotation.
The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod.
METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL
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.
C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC
C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED
Catalyzes the oxidation of 5,10-methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate.
Belongs to the tetrahydrofolate dehydrogenase/cyclohydrolase family.
Domain 2, N(10)-formyltetrahydrofolate synthetase
Formyltetrahydrofolate synthetase, domain 3
Belongs to the formate--tetrahydrofolate ligase family.
GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT A
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.
GLUTAMYL-TRNA GLN AMIDOTRANSFERASE SUBUNIT B MITOCHONDRIAL AND PROKARYOTIC PET112-RELATED
GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT B, MITOCHONDRIAL
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
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 GatB/GatE family. GatB subfamily.
Glu-tRNAGln amidotransferase C subunit, N-terminal domain
GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT C, MITOCHONDRIAL
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
Tetrahydrobiopterin biosynthesis enzymes-like
Belongs to the GTP cyclohydrolase I family.
GRANULE-BOUND STARCH SYNTHASE 1, CHLOROPLASTIC/AMYLOPLASTIC
STARCH SYNTHASE 1, CHLOROPLASTIC/AMYLOPLASTIC
UDP-Glycosyltransferase/glycogen phosphorylase
Synthesizes alpha-1,4-glucan chains using ADP-glucose.
Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.
GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE-RELATED
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 bacterial/plant glucose-1-phosphate adenylyltransferase family.
Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Alpha-D-phosphohexomutase, C-terminal domain
PHOSPHOGLUCOSAMINE MUTASE FAMILY PROTEIN
Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate.
Belongs to the phosphohexose mutase family.
UDP-N-acetylglucosamine pyrophosphorylase
N-acetylglucosamine-1-phosphate uridyltransferase
Glucosamine-1-phosphate N-acetyltransferase
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 N-terminal section; belongs to the N-acetylglucosamine-1-phosphate uridyltransferase family.
In the C-terminal section; belongs to the transferase hexapeptide repeat family.
SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL
Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
Plays an important role in substrate specificity
SEDOHEPTULOSE 7-PHOSPHATE ISOMERASE / DNAA INITIATOR-ASSOCIATING FACTOR FOR REPLICATION INITIATION
Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate.
The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate.
Belongs to the SIS family. GmhA subfamily.
Transcription elongation factor, GreA/GreB, C-terminal domain
Transcription elongation factor, GreA/GreB, N-terminal domain
GreA transcript cleavage protein, N-terminal domain
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.
GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE 1, CHLOROPLASTIC-RELATED
Glutamate-1-semialdehyde aminotransferase
Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. HemL subfamily.
Catalyzes the reduction of hydroxylamine to form NH(3) and H(2)O.
Glutamyl-tRNA reductase, N-terminal domain
Glutamyl tRNA-reductase catalytic, N-terminal domain
Glutamyl tRNA-reductase dimerization domain
Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA).
Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization.
During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA.
Belongs to the glutamyl-tRNA reductase family.
ATP PHOSPHORIBOSYLTRANSFERASE ATP-PRTASE
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.
Belongs to the ATP phosphoribosyltransferase family. Long subfamily.
1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO)METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISHF
IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF/H IGP SYNTHASE SUBUNIT HISF/H
Imidazole glycerol phosphate synthase subunit HisF
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.
IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE HIS7
Belongs to the imidazoleglycerol-phosphate dehydratase family.
Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
HEAT-INDUCIBLE TRANSCRIPTION REPRESSOR HRCA
Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons.
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.
ATP-DEPENDENT PROTEASE ATPASE SUBUNIT HSLU
ATPase subunit of a proteasome-like degradation complex; this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis.
A double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer. The assembly of the HslU/HslV complex is dependent on binding of ATP.
Belongs to the ClpX chaperone family. HslU subfamily.
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery.
Allosterically activated by HslU binding.
Belongs to the peptidase T1B family. HslV subfamily.
Metalloproteases ('zincins'), catalytic domain
Translation initiation factor IF- 2, domain 3
TRANSLATION INITIATION FACTOR IF-2, MITOCHONDRIAL
TRANSLATION INITIATION FACTOR IF-2-RELATED
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 TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. IF-2 subfamily.
KETOL-ACID REDUCTOISOMERASE, MITOCHONDRIAL
6-phosphogluconate dehydrogenase C-terminal domain-like
Alpha-keto-beta-hydroxylacyl reductoisomerase
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.
Belongs to the ketol-acid reductoisomerase family.
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.
Binds 1 [2Fe-2S] cluster per subunit. This cluster acts as a Lewis acid cofactor.
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE, CHLOROPLASTIC
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase
Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol.
Belongs to the GHMP kinase family. IspE subfamily.
4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE
4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE (FERREDOXIN), CHLOROPLASTIC
Inosine monophosphate dehydrogenase (IMPDH)
Nitrite and sulphite reductase 4Fe-4S domain-like
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase
Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate.
INOSINE TRIPHOSPHATE PYROPHOSPHATASE/HAM1 PROTEIN
non-canonical purine NTP pyrophosphatase, RdgB/HAM1 family
Non-canonical purine NTP pyrophosphatase
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.
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. Some bacteria have evolved a zinc-coordinating structure that stabilizes the LID domain.
CYTIDYLATE KINASE/PANTOATE-BETA-ALANINE LIGASE
Belongs to the cytidylate kinase family. Type 1 subfamily.
3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE, MITOCHONDRIAL
CMP-2-keto-3-deoxyoctulosonic acid synthase
Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.
3-ISOPROPYLMALATE DEHYDRATASE LARGE SUBUNIT 2
3-isopropylmalate dehydratase large subunit
Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate.
Belongs to the aconitase/IPM isomerase family. LeuC type 2 subfamily.
3-ISOPROPYLMALATE DEHYDRATASE SMALL SUBUNIT 1-RELATED
3-ISOPROPYLMALATE DEHYDRATASE SMALL SUBUNIT 2-RELATED-RELATED
3-isopropylmalate dehydratase small subunit
Belongs to the LeuD family. LeuD type 2 subfamily.
Leucyl/phenylalanyl-tRNA-protein transferase, C-terminal domain
Leucyl/phenylalanyl-tRNA-protein transferase, N-terminal domain
LEUCYL/PHENYLALANYL-TRNA--PROTEIN TRANSFERASE
Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine.
Udp N-acetylglucosamine O-acyltransferase, C-terminal domain
ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE, MITOCHONDRIAL-RELATED
Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.
Belongs to the transferase hexapeptide repeat family. LpxA subfamily.
UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE 1, MITOCHONDRIAL-RELATED
UDP-3-O-acyl-N-acetylglucosamine deacetylase
UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase
Catalyzes the hydrolysis of UDP-3-O-myristoyl-N-acetylglucosamine to form UDP-3-O-myristoylglucosamine and acetate, the committed step in lipid A biosynthesis.
This protein specifically catalyzes the removal of signal peptides from prolipoproteins.
5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE
Cobalamin-independent methionine synthase
Methionine synthase, vitamin-B12 independent isozyme
Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation.
Belongs to the vitamin-B12 independent methionine synthase family.
Dimethylallyl diphosphate:tRNA dimethylallyltransferase
Isopentenyl-diphosphate:tRNA isopentenyltransferase
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).
Methylthiotransferase, N-terminal domain
CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 1
MITOCHONDRIAL TRNA METHYLTHIOTRANSFERASE CDK5RAP1
radical SAM methylthiotransferase, MiaB/RimO family
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB
Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine.
Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Belongs to the methylthiotransferase family. MiaB subfamily.
GidA associated domain, C-terminal subdomain
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
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.
Homodimer. Heterotetramer of two MnmE and two MnmG subunits.
MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN 1
MOLYBDOPTERIN COFACTOR SYNTHESIS PROTEIN A
Molybdenum cofactor biosynthesis protein A
Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate.
Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine and 1 [4Fe-4S] cluster coordinated with 3 cysteines and the GTP-derived substrate.
Belongs to the radical SAM superfamily. MoaA family.
PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE HOMOLOG
UDP-MurNAc-pentapeptide phosphotransferase
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 glycosyltransferase 4 family. MraY subfamily.
AMIDOHYDRO-REL DOMAIN-CONTAINING PROTEIN
Composite domain of metallo-dependent hydrolases
5-methylthioadenosine/S-adenosylhomocysteine deaminase
Catalyzes the deamination of 5-methylthioadenosine and S-adenosyl-L-homocysteine into 5-methylthioinosine and S-inosyl-L-homocysteine, respectively. Is also able to deaminate adenosine.
Belongs to the metallo-dependent hydrolases superfamily. MTA/SAH deaminase family.
Probable S-methyl-5'-thioinosine phosphorylase
Catalyzes the reversible phosphorylation of S-methyl-5'-thioinosine (MTI) to hypoxanthine and 5-methylthioribose-1-phosphate. Involved in the breakdown of S-methyl-5'-thioadenosine (MTA), a major by-product of polyamine biosynthesis. Catabolism of (MTA) occurs via deamination to MTI and phosphorolysis to hypoxanthine.
Although this enzyme belongs to the family of MTA phosphorylases based on sequence homology, it has been shown that conserved amino acid substitutions in the substrate binding pocket convert the substrate specificity of this enzyme from 6-aminopurines to 6-oxopurines.
Belongs to the PNP/MTAP phosphorylase family. MTAP subfamily.
translation initiation factor eif-2b, domain 1
S-methyl-5-thioribose-1-phosphate isomerase
Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).
Belongs to the eIF-2B alpha/beta/delta subunits family. MtnA subfamily.
UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE
UDP-N-acetylglucosamine enolpyruvyl transferase
Cell wall formation. Adds enolpyruvyl to UDP-N-acetylglucosamine.
Belongs to the EPSP synthase family. MurA subfamily.
2-(S-cysteinyl)pyruvic acid O-phosphothioketal
UDP-N-ACETYLGLUCOSAMINE--N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE 1
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase
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 glycosyltransferase 28 family. MurG subfamily.
Histidine kinase-like ATPase, C-terminal domain
MutL, C-terminal domain, dimerisation subdomain
MutL, C-terminal domain, regulatory subdomain
DNA MISMATCH REPAIR PROTEIN MLH, PMS, MUTL
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
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.
Belongs to the DNA mismatch repair MutL/HexB family.
DNA MISMATCH REPAIR PROTEIN MSH1, MITOCHONDRIAL
DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER
This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.
Belongs to the DNA mismatch repair MutS family.
Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate.
Belongs to the quinolinate synthase family. Type 2 subfamily.
ATP-DEPENDENT (S)-NAD(P)H-HYDRATE DEHYDRATASE
ATP-DEPENDENT (S)-NAD(P)H-HYDRATE DEHYDRATASE FAMILY MEMBER
Bifunctional NAD(P)H-hydrate repair enzyme Nnr
ADP-dependent (S)-NAD(P)H-hydrate dehydratase
Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration (By similarity).
In the N-terminal section; belongs to the NnrE/AIBP family.
In the C-terminal section; belongs to the NnrD/CARKD family.
NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form.
Belongs to the sirtuin family. Class U subfamily.
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 7, MITOCHONDRIAL
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.
NDH-1 is composed of 14 different subunits. Subunits NuoB, C, D, E, F, and G constitute the peripheral sector of the complex.
Belongs to the complex I 20 kDa subunit family.
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 2, MITOCHONDRIAL
NADH-UBIQUINONE OXIDOREDUCTASE 49 KDA SUBUNIT
Belongs to the complex I 49 kDa subunit family.
NADH-UBIQUINONE OXIDOREDUCTASE SUBUNIT ND4L
NDH-1 is composed of 14 different subunits. Subunits NuoA, H, J, K, L, M, N constitute the membrane sector of the complex.
Belongs to the complex I subunit 4L family.
Belongs to the complex I subunit 2 family.
ANTITERMINATION NUSB DOMAIN-CONTAINING PROTEIN
N UTILIZATION SUBSTANCE PROTEIN B-RELATED
Transcription antitermination protein NusB
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.
DEVELOPMENTALLY REGULATED GTP-BINDING PROTEIN-RELATED
MITOCHONDRIAL RIBOSOME-ASSOCIATED GTPASE 2
Obg GTP-binding protein N-terminal domain
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.
Pantoate-beta-alanine ligase, C-terminal domain
Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate.
The reaction proceeds by a bi uni uni bi ping pong mechanism.
Belongs to the pantothenate synthetase family.
Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate.
FATTY ACID/PHOSPHOLIPID SYNTHESIS PROTEIN PLSX
Isocitrate/Isopropylmalate dehydrogenase-like
Acyl-[acyl-carrier-protein]--phosphate acyltransferase
Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA.
Homodimer. Probably interacts with PlsY.
Associated with the membrane possibly through PlsY.
POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL
Eukaryotic type KH-domain (KH-domain type I)
Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction.
Belongs to the polyribonucleotide nucleotidyltransferase family.
MTRF1L RELEASE FACTOR GLUTAMINE METHYLTRANSFERASE
S-adenosyl-L-methionine-dependent methyltransferases
Release factor glutamine methyltransferase
Protein-glutamine N-methyltransferase PrmC
Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif.
Belongs to the protein N5-glutamine methyltransferase family. PrmC subfamily.
DELTA-1-PYRROLINE-5-CARBOXYLATE SYNTHASE
Glutamyl-gamma-semialdehyde dehydrogenase
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.
Belongs to the gamma-glutamyl phosphate reductase family.
The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.
TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3
TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED
Phosphoribosylformylglycinamidine cyclo-ligase
Phosphoribosyl-aminoimidazole synthetase
PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
Belongs to the SAICAR synthetase family.
BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN ATIC
BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH
Phosphoribosylaminoimidazolecarboxamide formyltransferase
The IMP cyclohydrolase activity resides in the N-terminal region.
Adenylosuccinate Synthetase, subunit A, domain 1
Adenylosuccinate Synthetase, subunit A, domain 2
Adenylosuccinate Synthetase, subunit A, domain 3
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 adenylosuccinate synthetase family.
DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL-RELATED
Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit
Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor.
Heterotetramer of 2 PyrK and 2 PyrD type B subunits.
Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily.
S-ADENOSYLMETHIONINE:TRNA RIBOSYLTRANSFERASE-ISOMERASE
Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA).
RIBOSOME-BINDING FACTOR A, CHLOROPLASTIC-RELATED
One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.
Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes.
Recombination protein O, C-terminal domain
Involved in DNA repair and RecF pathway recombination.
Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.
Methylated by PrmC. Methylation increases the termination efficiency of RF1.
Belongs to the prokaryotic/mitochondrial release factor family.
RNA-free RNase P that catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus.
RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO
Ribosomal protein S12 (aspartate-C(3))-methylthiotransferase
Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12.
Belongs to the methylthiotransferase family. RimO subfamily.
Ribosome maturation factor RimP, C-terminal domain
Required for maturation of 30S ribosomal subunits.
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE DMRL SYNTHASE LUMAZINE SYNTHASE
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.
54S RIBOSOMAL PROTEIN L38, MITOCHONDRIAL
Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.
Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L19. In the 70S ribosome, L14 and L19 interact and together make contacts with the 16S rRNA in bridges B5 and B8.
Belongs to the universal ribosomal protein uL14 family.
39S RIBOSOMAL PROTEIN L15, MITOCHONDRIAL
Belongs to the universal ribosomal protein uL15 family.
39S RIBOSOMAL PROTEIN L16, MITOCHONDRIAL
Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.
Belongs to the universal ribosomal protein uL16 family.
39S RIBOSOMAL PROTEIN L17, MITOCHONDRIAL
Part of the 50S ribosomal subunit. Contacts protein L32.
Belongs to the bacterial ribosomal protein bL17 family.
39S RIBOSOMAL PROTEIN L19, MITOCHONDRIAL
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.
Belongs to the bacterial ribosomal protein bL19 family.
50S RIBOSOMAL PROTEIN L20, CHLOROPLASTIC
Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.
Belongs to the bacterial ribosomal protein bL20 family.
39S RIBOSOMAL PROTEIN L21, MITOCHONDRIAL
This protein binds to 23S rRNA in the presence of protein L20.
Part of the 50S ribosomal subunit. Contacts protein L20.
Belongs to the bacterial ribosomal protein bL21 family.
RIBOSOMAL_L23EN DOMAIN-CONTAINING PROTEIN
One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.
Part of the 50S ribosomal subunit. Contacts protein L29, and trigger factor when it is bound to the ribosome.
Belongs to the universal ribosomal protein uL23 family.
RIBOSOMAL PROTEIN L25/GLN-TRNA SYNTHETASE, ANTI-CODON-BINDING DOMAIN-CONTAINING PROTEIN
This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.
Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Binds to the 5S rRNA independently of L5 and L18.
Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily.
39S RIBOSOMAL PROTEIN L27, MITOCHONDRIAL
Belongs to the bacterial ribosomal protein bL27 family.
50S RIBOSOMAL PROTEIN L29, CHLOROPLASTIC
60S RIBOSOMAL PROTEIN L35/50S RIBOSOMAL PROTEIN L29
Belongs to the universal ribosomal protein uL29 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.
Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome.
Belongs to the universal ribosomal protein uL2 family.
50S RIBOSOMAL PROTEIN L31, CHLOROPLASTIC
Belongs to the bacterial ribosomal protein bL31 family. Type A subfamily.
Belongs to the bacterial ribosomal protein bL32 family.
Belongs to the bacterial ribosomal protein bL35 family.
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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
Forms part of the polypeptide exit tunnel.
Belongs to the universal ribosomal protein uL4 family.
This protein binds to the 23S rRNA, and is important in its secondary structure. 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.
Belongs to the universal ribosomal protein uL6 family.
Belongs to the bacterial ribosomal protein bL9 family.
RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE H
23S rRNA (pseudouridine1915-N3)-methyltransferase
rRNA (pseudouridine-N3-)-methyltransferase RlmH
Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA.
Belongs to the RNA methyltransferase RlmH family.
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.
Homohexameric ring arranged as a trimer of dimers.
DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA
beta and beta-prime subunits of DNA dependent RNA-polymerase
DNA-directed RNA polymerase subunit beta'
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.
Belongs to the RNA polymerase beta' chain family.
DNA-directed RNA polymerase subunit omega
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.
Belongs to the RNA polymerase subunit omega family.
28S RIBOSOMAL PROTEIN S12, MITOCHONDRIAL
With S4 and S5 plays an important role in translational accuracy.
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.
Belongs to the universal ribosomal protein uS12 family.
30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18
37S RIBOSOMAL PROTEIN SWS2, MITOCHONDRIAL
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.
Belongs to the universal ribosomal protein uS13 family.
28S RIBOSOMAL PROTEIN S14, MITOCHONDRIAL
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 universal ribosomal protein uS14 family. Zinc-binding uS14 subfamily.
37S RIBOSOMAL PROTEIN S28, MITOCHONDRIAL
RIBOSOMAL PROTEIN S15, BACTERIAL AND ORGANELLAR
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.
Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.
Part of the 30S ribosomal subunit. Forms a bridge to the 50S subunit in the 70S ribosome, contacting the 23S rRNA.
Belongs to the universal ribosomal protein uS15 family.
28S RIBOSOMAL PROTEIN S16, MITOCHONDRIAL
Belongs to the bacterial ribosomal protein bS16 family.
37S RIBOSOMAL PROTEIN S17, MITOCHONDRIAL
One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.
Belongs to the universal ribosomal protein uS17 family.
37S RIBOSOMAL PROTEIN S19, MITOCHONDRIAL
Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.
Belongs to the universal ribosomal protein uS19 family.
Belongs to the bacterial ribosomal protein bS21 family.
30S RIBOSOMAL PROTEIN S2 PROKARYOTIC AND ORGANELLAR
Belongs to the universal ribosomal protein uS2 family.
Prokaryotic type KH domain (KH-domain type II)
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 universal ribosomal protein uS3 family.
37S RIBOSOMAL PROTEIN NAM9, MITOCHONDRIAL
One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.
With S5 and S12 plays an important role in translational accuracy.
Part of the 30S ribosomal subunit. Contacts protein S5. The interaction surface between S4 and S5 is involved in control of translational fidelity.
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 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.
Belongs to the universal ribosomal protein uS7 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 universal ribosomal protein uS8 family.
Putative methyltransferase TM0872, insert domain
12S RRNA N4-METHYLCYTIDINE METHYLTRANSFERASE
16S rRNA (cytosine(1402)-N(4))-methyltransferase
Ribosomal RNA small subunit methyltransferase H
rRNA (cytosine-N(4)-)-methyltransferase RsmH
Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA.
Belongs to the methyltransferase superfamily. RsmH family.
Holliday junction branch migration complex subunit RuvA
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.
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.
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.
HOLLIDAY JUNCTION ATP-DEPENDENT DNA HELICASE RUVB
Holliday junction branch migration complex subunit RuvB
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.
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.
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.
Ribonuclease H-like superfamily/Ribonuclease H
CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC
The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair. Endonuclease that resolves HJ intermediates. Cleaves cruciform DNA by making single-stranded nicks across the HJ at symmetrical positions within the homologous arms, yielding a 5'-phosphate and a 3'-hydroxyl group; requires a central core of homology in the junction. The consensus cleavage sequence is 5'-(A/T)TT(C/G)-3'. Cleavage occurs on the 3'-side of the TT dinucleotide at the point of strand exchange. 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.
Homodimer which binds Holliday junction (HJ) DNA. 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.
Helical scaffold and wing domains of SecA
SECA INNER MEMBRANE COMPONENT OF SEC PROTEIN SECRETION SYSTEM
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.
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.
Multidrug efflux transporter AcrB transmembrane domain
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.
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.
Belongs to the SecD/SecF family. SecD 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.
Belongs to the SecD/SecF family. SecF subfamily.
S-adenosylmethionine decarboxylase domain
S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME
S-adenosylmethionine decarboxylase beta chain
S-adenosylmethionine decarboxylase alpha chain
Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine.
Binds 1 pyruvoyl group covalently per subunit.
Heterotetramer of two alpha and two beta chains arranged as a dimer of alpha/beta heterodimers.
Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl group blocking the N-terminus of the alpha chain.
Belongs to the prokaryotic AdoMetDC family. Type 1 subfamily.
Schiff-base intermediate with substrate; via pyruvic acid
Proton acceptor; for processing activity
Cysteine-tRNA ligase, C-terminal anti-codon recognition domain
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Belongs to the class-I aminoacyl-tRNA synthetase family.
Non-discriminating aspartyl-tRNA synthetase
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).
Belongs to the class-II aminoacyl-tRNA synthetase family. Type 1 subfamily.
Glutamate-tRNA synthetase, class I, anticodon-binding domain 1
GLUTAMATE--TRNA LIGASE, MITOCHONDRIAL-RELATED
An anticodon-binding domain of class I aminoacyl-tRNA synthetases
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).
Belongs to the class-I aminoacyl-tRNA synthetase family. Glutamate--tRNA ligase type 1 subfamily.
GLYCINE--TRNA LIGASE, CHLOROPLASTIC/MITOCHONDRIAL 2
Tetramer of two alpha and two beta subunits.
Belongs to the class-II aminoacyl-tRNA synthetase family.
HISTIDINE--TRNA LIGASE, MITOCHONDRIAL-RELATED
MITOCHONDRIAL RIBOSOME PROTEIN L39/PROLYL-TRNA LIGASE FAMILY MEMBER
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). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.
Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain.
Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily.
Serine-tRNA synthetase, tRNA binding domain
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).
Homodimer. The tRNA molecule binds across the dimer.
Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding.
Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily.
Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway.
Belongs to the transaldolase family. Type 3B subfamily.
Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).
Homodimer. Within each dimer, one monomer is responsible for RNA recognition and catalysis, while the other monomer binds to the replacement base PreQ1.
Belongs to the queuine tRNA-ribosyltransferase family.
RNA binding; important for wobble base 34 recognition
PHOSPHOMETHYLPYRIMIDINE SYNTHASE, CHLOROPLASTIC
Hydroxymethylpyrimidine phosphate synthase
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.
Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
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.
TRIGGER FACTOR CHAPERONE AND PEPTIDYL-PROLYL CIS/TRANS ISOMERASE
TRIGGER FACTOR-LIKE PROTEIN TIG, CHLOROPLASTIC
Triger factor/SurA peptide-binding domain-like
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.
About half TF is bound to the ribosome near the polypeptide exit tunnel while the other half is free in the cytoplasm.
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.
Belongs to the FKBP-type PPIase family. Tig subfamily.
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P).
Belongs to the triosephosphate isomerase family.
Specifically methylates guanosine-37 in various tRNAs.
Belongs to the RNA methyltransferase TrmD family.
N-(5'-PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE
Pseudouridine synthase I, catalytic domain, C-terminal subdomain
Pseudouridine synthase I, catalytic domain, N-terminal subdomain
Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.
Belongs to the tRNA pseudouridine synthase TruA family.
TRNA N6-ADENOSINE THREONYLCARBAMOYLTRANSFERASE
TRNA N6-ADENOSINE THREONYLCARBAMOYLTRANSFERASE, MITOCHONDRIAL-RELATED
t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaD
tRNA threonylcarbamoyladenosine biosynthesis protein TsaD
Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction.
Prokaryotic ubiquitin-like protein UBact
May function as a protein modifier covalently attached to lysine residues of substrate proteins. This may serve to target the modified proteins for degradation by proteasomes.
Belongs to the ubiquitin-like protein UBact family.
Isoglutamyl lysine isopeptide (Glu-Lys) (interchain with K-? in acceptor proteins)
Catalyzes the dephosphorylation of undecaprenyl diphosphate (UPP). Confers resistance to bacitracin.
Bacitracin is thought to be involved in the inhibition of peptidoglycan synthesis by sequestering undecaprenyl diphosphate, thereby reducing the pool of lipid carrier available.
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage.
Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex.
The beta-hairpin motif is involved in DNA binding.
Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the recombining DNA molecules. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids.
Forms a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD.
Belongs to the 'phage' integrase family. XerC subfamily.
O-(3'-phospho-DNA)-tyrosine intermediate
Nucleoid-associated protein YbaB-like domain
Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection.
TRANSCRIPTIONAL REGULATORY PROTEIN YEBC-RELATED
DNA-binding regulatory protein, YebC/PmpR family
Probable transcriptional regulatory protein THEYE_A1868
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
UPF0173 METAL-DEPENDENT HYDROLASE MJ1163-RELATED
UPF0173 METAL-DEPENDENT HYDROLASE TM_1162
UPF0173 metal-dependent hydrolase THEYE_A0282
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 endoribonuclease YbeY family.