NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]
Putative 3-methyladenine DNA glycosylase
Belongs to the DNA glycosylase MPG family.
Carrier of the growing fatty acid chain in fatty acid biosynthesis.
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.
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.
Acetylated. Deacetylation by the SIR2-homolog deacetylase activates the enzyme.
Belongs to the ATP-dependent AMP-binding enzyme family.
N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
Composite domain of metallo-dependent hydrolases
Belongs to the metallo-dependent hydrolases superfamily. Adenine deaminase family.
Leucine Aminopeptidase, subunit E, domain 1
Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides.
Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.
Belongs to the purine/pyrimidine phosphoribosyltransferase family.
5-enolpyruvylshikimate-3-phosphate phospholyase
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 chorismate synthase family.
Key component of the proton channel; it plays a direct role in the translocation of protons 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(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.
ATP synthase alpha/beta chain, C-terminal domain
P-loop containing nucleotide triphosphate hydrolases
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
P-loop containing nucleoside triphosphate hydrolases
Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit.
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.
F0F1 ATP synthase delta/epsilon subunit, N-terminal
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
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).
ATP synthase, gamma subunit, helix hairpin domain
Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex.
Belongs to the ATPase gamma chain family.
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.
PROTEIN-GLUTAMATE METHYLESTERASE/PROTEIN-GLUTAMINE GLUTAMINASE
Involved in chemotaxis. Part of a chemotaxis signal transduction system that modulates chemotaxis in response to various stimuli. Catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins or MCP) by CheR. Also mediates the irreversible deamidation of specific glutamine residues to glutamic acid.
Contains a C-terminal catalytic domain, and an N-terminal region which modulates catalytic activity.
Phosphorylated by CheA. Phosphorylation of the N-terminal regulatory domain activates the methylesterase activity.
CHEMORECEPTOR GLUTAMINE DEAMIDASE CHED-RELATED
CNF1/YfiH-like putative cysteine hydrolases
Probable chemoreceptor glutamine deamidase CheD
Probably deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs), playing an important role in chemotaxis.
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).
Homohexamer. The oligomerization is ATP-dependent (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).
ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT, MITOCHONDRIAL
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.
ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS1, CHLOROPLASTIC
Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation.
Binds to the N-terminal domain of the chaperone ClpA.
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.
BIFUNCTIONAL COENZYME A SYNTHASE-RELATED
Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A.
Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis.
A monovalent cation. Ammonium or potassium.
Belongs to the type III pantothenate kinase family.
PROTOHEME IX FARNESYLTRANSFERASE, MITOCHONDRIAL
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.
Carbon 2 of the heme B porphyrin ring is defined according to the Fischer nomenclature.
Belongs to the UbiA prenyltransferase family. Protoheme IX farnesyltransferase subfamily.
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.
4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate.
Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown in E.coli that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction.
Glutathione synthetase ATP-binding domain-like
Binds 2 magnesium or manganese ions per subunit.
Belongs to the D-alanine--D-alanine ligase family.
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily.
Schiff-base intermediate with acetaldehyde
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.
DNA polymerase involved in damage-induced mutagenesis and translesion synthesis (TLS). It is not the major replicative DNA polymerase.
Belongs to the DNA polymerase type-C family. DnaE2 subfamily.
Heat shock protein DnaJ, cysteine-rich domain
Urease metallochaperone UreE, N-terminal domain
Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, DnaK-independent fashion. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins.
The J domain is necessary and sufficient to stimulate DnaK ATPase activity. Zinc center 1 plays an important role in the autonomous, DnaK-independent chaperone activity of DnaJ. Zinc center 2 is essential for interaction with DnaK and for DnaJ activity.
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
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.
Elongation Factor G (Translational Gtpase), domain 3
RIBOSOME-RELEASING FACTOR 2, MITOCHONDRIAL
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.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily.
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
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.
Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-Tu/EF-1A subfamily.
Necessary for normal cell division and for the maintenance of normal septation.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family.
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.
Fractions of enolase are present in both the cytoplasm and on the cell surface. The export of enolase possibly depends on the covalent binding to the substrate; once secreted, it remains attached to the cell surface.
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.
FLAGELLAR P-RING PERIPLASMIC PROTEIN FLGI
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.
Acts as an anti-CsrA protein, binds CsrA and prevents it from repressing translation of its target genes, one of which is flagellin. Binds to flagellin and participates in the assembly of the flagellum.
Interacts with translational regulator CsrA and flagellin(s).
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.
Leucine Dehydrogenase, chain A, domain 1
C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC
C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED
Aminoacid dehydrogenase-like, N-terminal domain
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.
N-terminal domain of MutM-like DNA repair proteins
DNA-(apurinic or apyrimidinic site) lyase MutM
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.
Proton donor; for beta-elimination activity
Proton donor; for delta-elimination activity
MUTAGENESIS OF ASP-24; ASP-28; ASP-162; GLU-166; HIS-261 AND ARG-348
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 1-433 IN COMPLEX WITH IRON
X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) OF 1-433
MUTAGENESIS OF ASP-24; GLN-84; ASN-196 AND GLU-203
MFS general substrate transporter like domains
Iron transpoter that exports Fe(2+) from the cell. Also binds to Co(2+) and Ni(2+). May act as a multivalent divalent metal transporter (PubMed:26608034). The transporter is composed of 12 transmembrane (TM) helices organized into N-terminal (TM1-6) and C-terminal (TM7-12) domains. The substrate-binding site is formed at the interface of the two domains and is alternately accessible from either side of the membrane. The transport cycle is viewed as a series of ligand-induced conformational changes that include open outward and open inward states (PubMed:26461048, PubMed:30082682).
The cofactor facilitates a conformational change critical to the transport cycle. The binding of Ca2+ from extracellular fluid activates the transporter by triggering a conformational change that enables the transition from the open outward to open inward states.
Belongs to the ferroportin (FP) (TC 2.A.100) family.
Slows down the kinetics of iron transport, while not affecting the iron binding ability. Complete loss of calcium binding.
Slows down the kinetics of iron transport, while not affecting the iron binding ability.
Reduces transport activity. Complete loss of calcium binding.
Complete loss of iron binding. Completely abolishes the transport ability.
ATP-DEPENDENT ZINC METALLOPROTEASE YME1L1
ATP-dependent zinc metalloprotease FtsH 1
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 central section; belongs to the AAA ATPase family.
In the C-terminal section; belongs to the peptidase M41 family.
ATP-DEPENDENT ZINC METALLOPROTEASE YME1L-RELATED
ATP-dependent zinc metalloprotease FtsH 2
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.
Converts GTP to 7,8-dihydroneopterin triphosphate.
Belongs to the GTP cyclohydrolase IV family.
ATP-dependent carboxylate-amine ligase which exhibits weak glutamate--cysteine ligase activity.
Belongs to the glutamate--cysteine ligase type 2 family. YbdK subfamily.
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
GLYCINE DEHYDROGENASE (DECARBOXYLATING), MITOCHONDRIAL
Glycine dehydrogenase (aminomethyl-transferring)
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.
The glycine cleavage system is composed of four proteins: P, T, L and H.
Aminomethyltransferase beta-barrel domains
Aminomethyltransferase beta-barrel domain
The glycine cleavage system catalyzes the degradation of glycine.
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.
Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Thiolesterase that catalyzes the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid.
Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family.
Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn-glycerol 3-phosphate.
Inhibited by fructose 1,6-bisphosphate (FBP).
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
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate.
Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily.
Head domain of nucleotide exchange factor GrpE
Coiled-coil domain of nucleotide exchange factor GrpE
Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ; upon interaction with the DnaJ-bound protein, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable complex. GrpE releases ADP from DnaK; ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding.
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.
Adenine nucleotide alpha hydrolases-like
GMP synthetase C-terminal dimerisation domain
Catalyzes the synthesis of GMP from XMP.
Catalyzes the ferrous insertion into protoporphyrin IX.
IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
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.
Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily.
Heat shock protein 90, C-terminal domain
Histidine kinase-like ATPase, C-terminal domain
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Molecular chaperone. Has ATPase activity.
Belongs to the heat shock protein 90 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.
Belongs to the metallo-dependent hydrolases superfamily. HutI family.
Catalyzes the conversion of urocanate to 4-imidazolone-5-propionate.
Isopentenyl diphosphate:dimethylallyl diphosphate isomerase
Type 2 isopentenyl diphosphate isomerase
Involved in the biosynthesis of isoprenoids. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).
Belongs to the IPP isomerase type 2 family.
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.
This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control.
Heterodimer of an alpha and a beta chain.
Belongs to the bacterial histone-like protein family.
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.
2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 1-RELATED
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
2-dehydro-3-deoxyphosphooctonate aldolase
3-deoxy-D-manno-octulosonic acid 8-phosphate synthase
Phospho-2-dehydro-3-deoxyoctonate aldolase
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.
Guanylate Kinase phosphate binding domain
Essential for recycling GMP and indirectly, cGMP.
Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis.
Belongs to the thymidylate kinase family.
LOW AFFINITY POTASSIUM TRANSPORT SYSTEM PROTEIN KUP
Probable potassium transport system protein Kup
Transport of potassium into the cell. Likely operates as a K(+):H(+) symporter.
Belongs to the HAK/KUP transporter (TC 2.A.72) family.
TRANSLATION FACTOR GUF1 HOMOLOG, CHLOROPLASTIC
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 TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. LepA subfamily.
PHOSPHATIDYLGLYCEROL--PROLIPOPROTEIN DIACYLGLYCERYL TRANSFERASE
PROLIPOPROTEIN DIACYLGLYCERYL TRANSFERASE
Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins.
LIPOYLTRANSFERASE 2, MITOCHONDRIAL-RELATED
Octanoyl-[acyl-carrier-protein]-protein N-octanoyltransferase
Catalyzes the transfer of endogenously produced octanoic acid from octanoyl-acyl-carrier-protein onto the lipoyl domains of lipoate-dependent enzymes. Lipoyl-ACP can also act as a substrate although octanoyl-ACP is likely to be the physiological substrate.
In the reaction, the free carboxyl group of octanoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes.
Catalyzes the phospholipid dependent N-acylation of the N-terminal cysteine of apolipoprotein, the last step in lipoprotein maturation.
Belongs to the CN hydrolase family. Apolipoprotein N-acyltransferase subfamily.
ABC TRANSPORTER ATP-BINDING PROTEIN MG467-RELATED
LIPOPROTEIN-RELEASING SYSTEM ATP-BINDING PROTEIN LOLD
Part of the ABC transporter complex LolCDE involved in the translocation of mature outer membrane-directed lipoproteins, from the inner membrane to the periplasmic chaperone, LolA. Responsible for the formation of the LolA-lipoprotein complex in an ATP-dependent manner.
The complex is composed of two ATP-binding proteins (LolD) and two transmembrane proteins (LolC and LolE).
Belongs to the ABC transporter superfamily. Lipoprotein translocase (TC 3.A.1.125) family.
ATP DEPENDENT LON PROTEASE FAMILY MEMBER
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.
CO dehydrogenase flavoprotein, C-terminal domain
Catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes.
In the transfer reaction, the free carboxyl group of lipoic acid is attached via an amide linkage to the epsilon-amino group of a specific lysine residue of lipoyl domains of lipoate-dependent enzymes.
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.
TETRAACYLDISACCHARIDE 4'-KINASE, MITOCHONDRIAL-RELATED
Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA).
MEMBRANE COMPONENT OF TRANSPORTER-RELATED
Macrolide export ATP-binding/permease protein MacB
Non-canonical ABC transporter that contains transmembrane domains (TMD), which form a pore in the inner membrane, and an ATP-binding domain (NBD), which is responsible for energy generation. Confers resistance against macrolides.
Belongs to the ABC transporter superfamily. Macrolide exporter (TC 3.A.1.122) family.
NAD-DEPENDENT MALIC ENZYME, MITOCHONDRIAL
Divalent metal cations. Prefers magnesium or manganese.
Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
MALATE DEHYDROGENASE 2, MITOCHONDRIAL-RELATED
Catalyzes the reversible oxidation of malate to oxaloacetate.
Belongs to the LDH/MDH superfamily. MDH type 2 family.
X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH MAGNESIUM
4-(2'-carboxyphenyl)-4-oxybutyric acid synthase
Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:24872444). Does not show N-succinylamino acid racemase (NSAR) activity with N-succinyl-L-phenylglycine as substrate (PubMed:24872444).
kcat is 17 sec(-1) with SHCHC as substrate.
Belongs to the mandelate racemase/muconate lactonizing enzyme family. MenC type 1 subfamily.
2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE-1-CARBOXYLATE SYNTHASE
Thiamin diphosphate-binding fold (THDP-binding)
Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).
Binds 1 thiamine pyrophosphate per subunit.
Belongs to the TPP enzyme family. MenD subfamily.
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.
ligand shared between two neighboring subunits
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.
Adenine nucleotide alpha hydrolases-like domains
MITOCHONDRIAL TRNA-SPECIFIC 2-THIOURIDYLASE 1
TRNA 5-METHYLAMINOMETHYL-2-THIOURIDYLATE -METHYLTRANSFERASE
Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34.
TRNA MODIFICATION GTPASE GTPBP3, MITOCHONDRIAL
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.
Homodimer. Heterotetramer of two MnmE and two MnmG subunits.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family.
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.
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.
LARGE-CONDUCTANCE MECHANOSENSITIVE CHANNEL
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.
Biosynthetic peptidoglycan transglycosylase-like
BIOSYNTHETIC PEPTIDOGLYCAN TRANSGLYCOSYLASE
MONOFUNCTIONAL BIOSYNTHETIC PEPTIDOGLYCAN TRANSGLYCOSYLASE
Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors.
Belongs to the glycosyltransferase 51 family.
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-acetylenolpyruvoylglucosamine reductase, C-terminal domain
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
FAD-binding/transporter-associated domain-like
Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain
UDP-N-ACETYLMURAMATE--L-ALANINE LIGASE-RELATED
MurD-like peptide ligases, catalytic domain
MurD-like peptide ligases, peptide-binding domain
UDP-N-acetylmuramoyl-L-alanine synthetase
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase
Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).
UDP-N-ACETYLGLUCOSAMINE--N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE 1
UDP-Glycosyltransferase/glycogen phosphorylase
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.
A novel assay monitering infection of luminescent E. coli by Bdellovibrio bacteriovorus 109J reveals a role for methyl accepting chemotaxis proteins in predation.
Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane.
Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.
Nucleoside diphosphate kinase-like domain
NUCLEOSIDE DIPHOSPHATE KINASE DDB_G0292928-RELATED
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.
NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
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.
2 residues (Tyr-58 and Arg-61) present in a large hydrophobic pocket are probably involved in substrate specificity. They are important for desuccinylation activity, but dispensable for deacetylation activity.
This protein might be subject to alternative promoter usage and might also encode a protein with a 13 residue-longer N-terminus.
Belongs to the sirtuin family. Class III subfamily.
VITAMIN B12-DEPENDENT RIBONUCLEOTIDE REDUCTASE
Ribonucleoside-diphosphate reductase NrdJ
Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and/or for immediate growth after restoration of oxygen (By similarity).
5'-deoxyadenosylcobalamine (coenzyme B12).
Belongs to the ribonucleoside diphosphate reductase class-2 family.
Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes.
BIFUNCTIONAL DTTP/UTP PYROPHOSPHATASE/METHYLTRANSFERASE PROTEIN-RELATED
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.
Belongs to the Maf family. YhdE subfamily.
Nucleoside triphosphate pyrophosphatase that hydrolyzes 7-methyl-GTP (m(7)GTP). May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids.
Belongs to the Maf family. YceF 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:ubiquinone oxidoreductase, 30kDa subunit
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 2, MITOCHONDRIAL
NADH-UBIQUINONE OXIDOREDUCTASE 49 KDA SUBUNIT
NDH-1 is composed of 13 different subunits. Subunits NuoB, CD, E, F, and G constitute the peripheral sector of the complex.
In the N-terminal section; belongs to the complex I 30 kDa subunit family.
In the C-terminal section; belongs to the complex I 49 kDa subunit 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.
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 1 family.
NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 8, MITOCHONDRIAL
NADH DEHYDROGENASE UBIQUINONE IRON-SULFUR PROTEIN 8, MITOCHONDRIAL
Belongs to the complex I 23 kDa subunit family.
NADH-UBIQUINONE OXIDOREDUCTASE SUBUNIT ND4L
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.
3-METHYL-2-OXOBUTANOATE HYDROXYMETHYLTRANSFERASE
Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is transferred onto alpha-ketoisovalerate to form ketopantoate.
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 pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine.
Binds 1 pyruvoyl group covalently per subunit.
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.
Schiff-base intermediate with substrate; via pyruvic acid
PYRUVATE, PHOSPHATE DIKINASE REGULATORY PROTEIN 1, CHLOROPLASTIC
Putative pyruvate, phosphate dikinase regulatory protein
Bifunctional serine/threonine kinase and phosphorylase involved in the regulation of the pyruvate, phosphate dikinase (PPDK) by catalyzing its phosphorylation/dephosphorylation.
Belongs to the pyruvate, phosphate/water dikinase regulatory protein family. PDRP subfamily.
Pyridoxine/pyridoxamine 5'-phosphate oxidase
Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).
Belongs to the pyridoxamine 5'-phosphate oxidase 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.
Phosphoglycerate kinase, N-terminal domain
PHOSPHOGLYCERATE KINASE 1, CHLOROPLASTIC-RELATED
Belongs to the phosphoglycerate kinase family.
PHOSPHONATES IMPORT ATP-BINDING PROTEIN PHNC
Part of the ABC transporter complex PhnCDE involved in phosphonates import. Responsible for energy coupling to the transport system.
The complex is composed of two ATP-binding proteins (PhnC), two transmembrane proteins (PhnE) and a solute-binding protein (PhnD).
Belongs to the ABC transporter superfamily. Phosphonates importer (TC 3.A.1.9.1) family.
Transcriptional coactivator/pterin dehydratase
PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE
Putative pterin-4-alpha-carbinolamine dehydratase
4-alpha-hydroxy-tetrahydropterin dehydratase
Belongs to the pterin-4-alpha-carbinolamine dehydratase family.
DNA-dependent ATPase and 5'-3' DNA helicase that efficiently unwinds G-quadruplex (G4) DNA structures. May be involved in resolving commom issues that arise during DNA replication, recombination, and repair.
Belongs to the helicase family. PIF1 subfamily.
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.
Phosphate import ATP-binding protein PstB
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 ABC transporter superfamily. Phosphate importer (TC 3.A.1.7) family.
The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.
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.
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.
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 reversible phosphorylation of UMP to UDP.
Allosterically activated by GTP. Inhibited by UTP.
Involved in allosteric activation by GTP
Catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)).
NADPH-DEPENDENT 7-CYANO-7-DEAZAGUANINE REDUCTASE
Tetrahydrobiopterin biosynthesis enzymes-like
Catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1).
Belongs to the GTP cyclohydrolase I family. QueF type 1 subfamily.
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.
MITOCHONDRIAL DNA REPAIR PROTEIN RECA HOMOLOG-RELATED
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.
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.
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.
An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. 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 S19.
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.
39S RIBOSOMAL PROTEIN L10, MITOCHONDRIAL
Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors.
Part of the ribosomal stalk of the 50S ribosomal subunit. The N-terminus interacts with L11 and the large rRNA to form the base of the stalk. The C-terminus forms an elongated spine to which L12 dimers bind in a sequential fashion forming a multimeric L10(L12)X complex.
Belongs to the universal ribosomal protein uL10 family.
Ribosomal protein L11, C-terminal domain
Ribosomal protein L11/L12, N-terminal domain
39S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.
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.
One or more lysine residues are methylated.
Belongs to the universal ribosomal protein uL11 family.
39S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL
This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.
Belongs to the universal ribosomal protein uL13 family.
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 L18, MITOCHONDRIAL
This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, 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 and 23S rRNAs.
Belongs to the universal ribosomal protein uL18 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.
Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.
Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.
Belongs to the universal ribosomal protein uL1 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.
50S RIBOSOMAL PROTEIN L22, CHLOROPLASTIC
CHLOROPLAST 50S RIBOSOMAL PROTEIN L22-RELATED
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).
The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.
Belongs to the universal ribosomal protein uL22 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.
39S RIBOSOMAL PROTEIN L24, MITOCHONDRIAL
One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.
One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.
Belongs to the universal ribosomal protein uL24 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.
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.
Ribosomal protein L30, ferredoxin-like fold domain
39S RIBOSOMAL PROTEIN L30, MITOCHONDRIAL
Belongs to the universal ribosomal protein uL30 family.
50S RIBOSOMAL PROTEIN L31, CHLOROPLASTIC
Belongs to the bacterial ribosomal protein bL31 family. Type B subfamily.
Belongs to the bacterial ribosomal protein bL32 family.
Belongs to the bacterial ribosomal protein bL35 family.
50S RIBOSOMAL PROTEIN L3-1, CHLOROPLASTIC
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.
Belongs to the universal ribosomal protein uL3 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 is 1 of the proteins that binds and probably mediates 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. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.
Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA and the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome.
Belongs to the universal ribosomal protein uL5 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.
39S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL
Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation.
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.
Belongs to the bacterial ribosomal protein bL12 family.
Belongs to the bacterial ribosomal protein bL9 family.
S-adenosyl-L-methionine-dependent methyltransferases
Ribosomal RNA large subunit methyltransferase E
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE 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.
Dual-specificity RNA methyltransferase RlmN
23S rRNA (adenine(2503)-C(2))-methyltransferase
Ribosomal RNA large subunit methyltransferase N
tRNA (adenine(37)-C(2))-methyltransferase
Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity.
Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.
Belongs to the radical SAM superfamily. RlmN family.
Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism.
Ribonuclease H-like superfamily/Ribonuclease H
Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding.
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.
Endoribonuclease that initiates mRNA decay.
DNA-directed RNA polymerase, insert domain
C-terminal domain of RNA polymerase alpha subunit
Insert subdomain of RNA polymerase alpha subunit
DNA-directed RNA polymerase subunit alpha
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
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.
Belongs to the RNA polymerase alpha chain family.
DNA-directed RNA polymerase, beta subunit, external 1 domain
DNA-directed RNA polymerase, subunit 2, domain 6
RNA polymerase alpha subunit dimerisation domain
DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA
beta and beta-prime subunits of DNA dependent RNA-polymerase
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 beta'
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.
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.
37S RIBOSOMAL PROTEIN S10, MITOCHONDRIAL
Involved in the binding of tRNA to the ribosomes.
Belongs to the universal ribosomal protein uS10 family.
40S RIBOSOMAL PROTEIN S14/30S RIBOSOMAL PROTEIN S11
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.
Belongs to the universal ribosomal protein uS11 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.
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.
28S RIBOSOMAL PROTEIN S18C, MITOCHONDRIAL
Binds as a heterodimer with protein S6 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 S6.
Belongs to the bacterial ribosomal protein bS18 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.
30S RIBOSOMAL PROTEIN S20, CHLOROPLASTIC
Belongs to the bacterial ribosomal protein bS20 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.
With S4 and S12 plays an important role in translational accuracy.
Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.
Part of the 30S ribosomal subunit. Contacts proteins S4 and S8.
The N-terminal domain interacts with the head of the 30S subunit; the C-terminal domain interacts with the body and contacts protein S4. The interaction surface between S4 and S5 is involved in control of translational fidelity.
Belongs to the universal ribosomal protein uS5 family.
Binds together with S18 to 16S ribosomal RNA.
Belongs to the bacterial ribosomal protein bS6 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.
Ribosomal RNA adenine dimethylase-like, domain 2
Ribosomal RNA small subunit methyltransferase A
16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase
S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase
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 class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily.
S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASES SUPERFAMILY PROTEIN
Ribosomal RNA small subunit methyltransferase G 1
16S rRNA 7-methylguanosine methyltransferase 1
Specifically methylates the N7 position of guanine in position 527 of 16S rRNA.
Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family.
Ribosomal RNA small subunit methyltransferase G 2
16S rRNA 7-methylguanosine methyltransferase 2
Ribosomal RNA small subunit methyltransferase G 3
16S rRNA 7-methylguanosine methyltransferase 3
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.
RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE J
Specifically methylates the guanosine in position 1516 of 16S rRNA.
Belongs to the methyltransferase superfamily. RsmJ 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.
Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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.
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.
Formate/glycerate dehydrogenase catalytic domain-like
May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine.
Belongs to the adenosylhomocysteinase family.
the general secretory pathway (sec) family
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-YajC and YidC.
INACTIVE SELENIDE, WATER DIKINASE-LIKE PROTEIN-RELATED
Synthesizes selenophosphate from selenide and ATP.
Belongs to the selenophosphate synthase 1 family. Class I subfamily.
Rhodanese/Cell cycle control phosphatase
Involved in the post-transcriptional modification of the uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Catalyzes the conversion of 2-thiouridine (S2U-RNA) to 2-selenouridine (Se2U-RNA). Acts in a two-step process involving geranylation of 2-thiouridine (S2U) to S-geranyl-2-thiouridine (geS2U) and subsequent selenation of the latter derivative to 2-selenouridine (Se2U) in the tRNA chain.
SUGAR FERMENTATION STIMULATION PROTEIN A
Sugar fermentation stimulation protein homolog
STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3
Required for chromosome condensation and partitioning.
Contains large globular domains required for ATP hydrolysis at each terminus and a third globular domain forming a flexible SMC hinge near the middle of the molecule. These domains are separated by coiled-coil structures.
CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE
Catalyzes the condensation of L-serine with palmitoyl-CoA (hexadecanoyl-CoA) to produce 3-oxosphinganine.
Significantly inhibited by palmitoyl-CoA concentrations greater than 100 uM.
kcat is 0.03 sec(-1) (in the presence of 100 uM of palmitoyl-CoA).
Predominantly concentrated in a limited region near the inner membrane or organelle-like multilayered membrane structure.
Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
TMRNA-BINDING COMPONENT OF TRANS-TRANSLATION TAGGING COMPLEX
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.
The tmRNA-SmpB complex associates with stalled 70S ribosomes.
SUCCINATE--COA LIGASE [GDP-FORMING] SUBUNIT BETA, MITOCHONDRIAL
Succinate--CoA ligase [ADP-forming] subunit beta
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.
Heterotetramer of two alpha and two beta subunits.
Belongs to the succinate/malate CoA ligase beta subunit family.
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
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 class-II aminoacyl-tRNA synthetase family.
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 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.
PHENYLALANINE--TRNA LIGASE, MITOCHONDRIAL
Phenylalanine--tRNA ligase alpha subunit
Phenylalanyl-tRNA synthetase alpha subunit
Tetramer of two alpha and two beta subunits.
Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily.
Ferrodoxin-fold anticodon-binding domain
Phenylalanyl-trna Synthetase, Chain B, domain 3
PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47
Phenylalanyl-tRNA synthetase beta subunit
Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily.
DNA POLYMERASE SUBUNIT GAMMA-2, MITOCHONDRIAL
GLYCYL-TRNA SYNTHETASE/DNA POLYMERASE SUBUNIT GAMMA-2
Catalyzes the attachment of glycine to tRNA(Gly).
HISTIDINE--TRNA LIGASE, MITOCHONDRIAL-RELATED
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 class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily.
LEUCINE--TRNA LIGASE, MITOCHONDRIAL-RELATED
Methionyl-tRNA synthetase (MetRS), Zn-domain
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 class-I aminoacyl-tRNA synthetase family. MetG type 1 subfamily.
BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
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).
Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension.
Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily.
Arginyl tRNA synthetase N-terminal domain
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain
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.
THREONINE--TRNA LIGASE, CHLOROPLASTIC/MITOCHONDRIAL 2
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).
Valyl-tRNA synthetase, C-terminal domain
Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
VALINE--TRNA LIGASE, CHLOROPLASTIC/MITOCHONDRIAL 2
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.
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.
The C-terminal coiled-coil domain is crucial for aminoacylation activity.
Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily.
Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).
Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 2 subfamily.
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.
Belongs to the tryptophan 2,3-dioxygenase family.
Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway.
Belongs to the transaldolase family. Type 3B subfamily.
the twin arginine targeting (tat) family
SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATA
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.
The Tat system comprises two distinct complexes: a TatABC complex, containing multiple copies of TatA, TatB and TatC subunits, and a separate TatA complex, containing only TatA subunits. Substrates initially bind to the TatABC complex, which probably triggers association of the separate TatA complex to form the active translocon.
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.
Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine.
The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a P-loop motif involved in ATP binding.
Belongs to the tRNA(Ile)-lysidine synthase family.
Part of the Tol-Pal system, which plays a role in outer membrane invagination during cell division and is important for maintaining outer membrane integrity.
The Tol-Pal system is composed of five core proteins: the inner membrane proteins TolA, TolQ and TolR, the periplasmic protein TolB and the outer membrane protein Pal. They form a network linking the inner and outer membranes and the peptidoglycan layer.
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P).
Belongs to the triosephosphate isomerase family.
RHODANESE-LIKE DOMAIN-CONTAINING PROTEIN 7-RELATED
THIOSULFATE SULFURTRANSFERASE/RHODANESE-LIKE DOMAIN-CONTAINING PROTEIN 2
Catalyzes oxygen-dependent 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs.
3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE/TRNA GUANINE-N 7 - -METHYLTRANSFERASE
tRNA (guanine(46)-N(7))-methyltransferase
Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA.
Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family.
Specifically methylates guanosine-37 in various tRNAs.
Belongs to the RNA methyltransferase TrmD family.
METHYLENETETRAHYDROFOLATE--TRNA-(URACIL-5-)-METHYLTRANSFERASE TRMFO
Folate-dependent tRNA (uracil-5-)-methyltransferase
Folate-dependent tRNA(M-5-U54)-methyltransferase
Catalyzes the folate-dependent formation of 5-methyl-uridine at position 54 (M-5-U54) in all tRNAs.
Belongs to the MnmG family. TrmFO subfamily.
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.
Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.
Belongs to the pseudouridine synthase TruB family. Type 1 subfamily.
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.
tRNA 2-thiocytidine biosynthesis protein TtcA
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.
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.
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.
Thymidylate synthase/dCMP hydroxymethylase domain
Thymidylate synthase/dCMP hydroxymethylase
Catalyzes the reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis.
Belongs to the thymidylate synthase family. Bacterial-type ThyA subfamily.
2-METHOXY-6-POLYPRENYL-1,4-BENZOQUINOL METHYLASE, MITOCHONDRIAL
Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase
Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2).
Belongs to the class I-like SAM-binding methyltransferase superfamily. MenG/UbiE family.
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. 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.
Interacts with UvrB in an incision complex.
TRANSLATIONAL ACTIVATOR OF CYTOCHROME C OXIDASE 1
DNA-binding regulatory protein, YebC/PmpR family
Probable transcriptional regulatory protein Bd1964
TRNA (URACIL(54)-C(5))-METHYLTRANSFERASE
Uncharacterized RNA methyltransferase Bd2056
Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.
Uncharacterized RNA methyltransferase Bd3828
Metalloproteases ('zincins'), catalytic domain
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.