NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]
ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT ALPHA
ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT ALPHA, CHLOROPLASTIC
Acetyl-CoA carboxylase carboxyltransferase subunit alpha
Component of the acetyl coenzyme A carboxylase (ACC) complex. First, biotin carboxylase catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the carboxyltransferase to acetyl-CoA to form malonyl-CoA.
Acetyl-CoA carboxylase is a heterohexamer composed of biotin carboxyl carrier protein (AccB), biotin carboxylase (AccC) and two subunits each of ACCase subunit alpha (AccA) and ACCase subunit beta (AccD).
ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA, CHLOROPLASTIC
Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
Acetyl-CoA carboxylase carboxyltransferase subunit beta
Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl-CoA.
Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction.
4'-phosphopantetheinyl transferase domain
Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.
Belongs to the P-Pant transferase superfamily. AcpS family.
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.
Belongs to the class I fructose-bisphosphate aldolase family.
Schiff-base intermediate with dihydroxyacetone-P
Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.
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.
Dehydroquinate synthase-like - alpha domain
3-DEHYDROQUINATE SYNTHASE, CHLOROPLASTIC
Bifunctional 3-dehydroquinate synthase/phosphatase
Binds 1 divalent metal cation per subunit. Can use either Co(2+) or Zn(2+).
In the N-terminal section; belongs to the sugar phosphate cyclases superfamily. Dehydroquinate synthase family.
In the C-terminal section; belongs to the GppA/Ppx family.
P-loop containing nucleotide triphosphate hydrolases
P-loop containing nucleoside triphosphate hydrolases
Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.
Catalyzes a trans-dehydration via an enolate intermediate.
Belongs to the type-II 3-dehydroquinase family.
Belongs to the class-II aminoacyl-tRNA synthetase family. AsnA subfamily.
the h+- or na+-translocating f-type, v-type and a-type atpase (f-atpase) superfamily
ATP synthase subunit a, sodium ion specific
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.
The ATPase of P.modestum is of special interest because it uses sodium ions instead of protons as the physiological coupling ion.
ATP synthase alpha/beta chain, C-terminal domain
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C-terminal domain of alpha and beta subunits of F1 ATP synthase
N-terminal domain of alpha and beta subunits of F1 ATP synthase
Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit.
Belongs to the ATPase alpha/beta chains family.
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 140-269
ATP synthase subunit alpha, sodium ion specific
Na(+)-translocating ATPase subunit alpha
Produces ATP from ADP in the presence of a sodium ion gradient across the membrane. The alpha chain is a regulatory subunit.
F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c.
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.
ATP synthase subunit beta, sodium ion specific
Produces ATP from ADP in the presence of a sodium ion gradient across the membrane. The beta chain is the catalytic subunit.
N-terminal domain of the delta subunit of the F1F0-ATP synthase
ATP SYNTHASE SUBUNIT DELTA, CHLOROPLASTIC
F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation.
This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction.
F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane proton channel. F(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). F(0) has three main subunits: a(1), b(2) and c(10-14). The alpha and beta chains form an alternating ring which encloses part of the gamma chain. F(1) is attached to F(0) by a central stalk formed by the gamma and epsilon chains, while a peripheral stalk is formed by the delta and b chains.
Belongs to the ATPase delta chain family.
ATP synthase subunit delta, sodium ion specific
The ATPase of I.tartaricus is of special interest because it uses sodium ions instead of protons as the physiological coupling ion.
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-118
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.
Belongs to the ATPase epsilon chain family.
ATP synthase epsilon chain, sodium ion specific
F-ATPase epsilon subunit, sodium ion specific
Na(+)-translocating ATPase subunit epsilon
Produces ATP from ADP in the presence of a sodium gradient across the membrane.
Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0).
F1F0 ATP synthase subunit B, membrane domain
ATP synthase subunit b, sodium ion specific
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 (By similarity).
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 (By similarity).
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.
ATP synthase gamma chain, sodium ion specific
F-ATPase gamma subunit, sodium ion specific
ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL
Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits.
Reversibly protonated during proton transport
ATP synthase subunit c, sodium ion specific
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 sodium 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 sodium translocation.
Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of 11 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits.
F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane sodium 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(11). 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.
Reversibly binds sodium during transport
Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits (Probable).
F-type ATPases have 2 components, F(1) - the catalytic core - and F(0) - the membrane sodium 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 (By similarity).
the mg(2+)/ca(2+) uniporter (mcu) family
ATP synthase protein I, sodium ion specific
A possible function for this protein is to guide the assembly of the membrane sector of the ATPase enzyme complex.
Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism.
Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3 cysteines and 1 arginine.
Belongs to the radical SAM superfamily. Biotin synthase family.
TRANS-ACONITATE 2-METHYLTRANSFERASE-RELATED
S-adenosyl-L-methionine-dependent methyltransferases
Malonyl-[acyl-carrier protein] O-methyltransferase 1
Converts the free carboxyl group of a malonyl-thioester to its methyl ester by transfer of a methyl group from S-adenosyl-L-methionine (SAM). It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway.
Belongs to the methyltransferase superfamily.
Malonyl-[acyl-carrier protein] O-methyltransferase 2
ATP-dependent dethiobiotin synthetase BioD
Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA, also called 7,8-diammoniononanoate) to form a ureido ring.
Belongs to the dethiobiotin synthetase family.
Carbamoyl-phosphate synthase small subunit, N-terminal domain
CARBAMOYL-PHOSPHATE SYNTHASE ARGININE-SPECIFIC SMALL CHAIN
Carbamoyl phosphate synthetase, small subunit N-terminal domain
Carbamoyl-phosphate synthase small chain
Carbamoyl-phosphate synthetase glutamine chain
Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate.
Carbamoyl-phosphate synthetase, large subunit oligomerisation domain
Carbamoyl phosphate synthetase, large subunit connection domain
Glutathione synthetase ATP-binding domain-like
Carbamoyl-phosphate synthase large chain
Carbamoyl-phosphate synthetase ammonia chain
Binds 4 Mg(2+) or Mn(2+) ions per subunit.
CRISPR-associated endonuclease Cas1, C-terminal domain
CRISPR-associated endonuclease Cas1, N-terminal domain
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette.
Homodimer, forms a heterotetramer with a Cas2 homodimer.
Belongs to the CRISPR-associated endonuclease Cas1 family.
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease. Involved in the integration of spacer DNA into the CRISPR cassette.
Homodimer, forms a heterotetramer with a Cas1 homodimer.
Belongs to the CRISPR-associated endoribonuclease Cas2 protein family.
Catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of cobyrinate, using either L-glutamine or ammonia as the nitrogen source.
Comprises of two domains. The C-terminal domain contains the binding site for glutamine and catalyzes the hydrolysis of this substrate to glutamate and ammonia. The N-terminal domain is anticipated to bind ATP and cobyrinate and catalyzes the ultimate synthesis of the diamide product. The ammonia produced via the glutaminase domain is probably translocated to the adjacent domain via a molecular tunnel, where it reacts with an activated intermediate.
The a and c carboxylates of cobyrinate are activated for nucleophilic attack via formation of a phosphorylated intermediate by ATP. CbiA catalyzes first the amidation of the c-carboxylate, and then that of the a-carboxylate.
Increases nucleophilicity of active site Cys
COBALT-PRECORRIN-5B C(1)-METHYLTRANSFERASE
Catalyzes the methylation of C-1 in cobalt-precorrin-5B to form cobalt-precorrin-6A.
The complete chromosome of Sebaldella termitidis ATCC 33386.
Energy-coupling factor transporter probable substrate-capture protein CbiM
Part of the energy-coupling factor (ECF) transporter complex CbiMNOQ involved in cobalt import.
Forms an energy-coupling factor (ECF) transporter complex composed of an ATP-binding protein (A component, CbiO), a transmembrane protein (T component, CbiQ) and 2 possible substrate-capture proteins (S components, CbiM and CbiN) of unknown stoichimetry.
10 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL
Together with the chaperonin GroEL, plays an essential role in assisting protein folding. The GroEL-GroES system forms a nano-cage that allows encapsulation of the non-native substrate proteins and provides a physical environment optimized to promote and accelerate protein folding. GroES binds to the apical surface of the GroEL ring, thereby capping the opening of the GroEL channel.
Heptamer of 7 subunits arranged in a ring. Interacts with the chaperonin GroEL.
Genes encoding heat shock proteins 10 and 60 from Fusobacterium nucleatum ATCC 10953.
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.
NICOTINAMIDE-NUCLEOTIDE AMIDOHYDROLASE PNCC
Molybdenum cofactor biosynthesis proteins
Covalent carrier of the coenzyme of citrate lyase.
Oligomer with a subunit composition of (alpha,beta,gamma)6.
O-(phosphoribosyl dephospho-coenzyme A)serine
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
Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.
Fourteen ClpP subunits assemble into 2 heptameric rings which stack back to back to give a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes.
ClpX chaperone, C4-type zinc finger domain
ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL
ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED
Glucocorticoid receptor-like (DNA-binding domain)
ATP-dependent Clp protease ATP-binding subunit ClpX
ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP.
Component of the ClpX-ClpP complex. Forms a hexameric ring that, in the presence of ATP, binds to fourteen ClpP subunits assembled into a disk-like structure with a central cavity, resembling the structure of eukaryotic proteasomes.
Pantetheine-phosphate adenylyltransferase
Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.
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.
ADENOSYLCOBINAMIDE-GDP RIBAZOLETRANSFERASE
Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate.
NICOTINATE-NUCLEOTIDE--DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)
Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).
MUTAGENESIS OF 472-ARG--HIS-477; 1048-ARG--HIS-1053 AND ARG-1079
X-RAY CRYSTALLOGRAPHY (3.09 ANGSTROMS) IN COMPLEX WITH CRRNA AND TARGET SSRNA
STRUCTURE BY ELECTRON MICROSCOPY (3.2 ANGSTROMS) IN COMPLEX WITH CRRNA
CRISPR-associated endoribonuclease Cas13a
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements (spacer sequences) and target invading nucleic acids. Unlike many single-component effectors, this CRISPR-Cas system targets RNA (PubMed:27669025). CRISPR clusters are transcribed from pre-CRISPR RNA (crRNA) and processed into crRNA by this protein (PubMed:27669025, PubMed:28475872, PubMed:28757251). pre-crRNA processing yields a 5'-OH and probably a 2',3'-cyclic phosphate (PubMed:27669025). Also cleaves pre-crRNA from several other type VI-A CRISPR systems (PubMed:28475872). Cleaves linear target ssRNA in a crRNA-dependent fashion, preferentially before U residues (PubMed:27669025, PubMed:28475872). Cleavage of target ssRNA is about 80-fold faster than pre-crRNA processing and uses a different active site (PubMed:27669025). Binding a viable target RNA target activates this protein for non-specific RNA degradation in vitro (called collateral RNA degradation) (PubMed:27669025, PubMed:28475872, PubMed:28757251). Activation occurs with 10 fM target RNA (PubMed:28475872). crRNA maturation is not essential for activation of RNA degradation, but lack of mature crRNA (due to mutagenesis) decreases activation levels (PubMed:28475872). This system has a 3' protospacer flanking site in the target RNA (PFS), which is C and unavailable to base pair with crRNA (PFS is equivalent to PAM, the protospacer adjacent motif) (PubMed:28757251).
Pre-crRNA processing is metal independent, while crRNA-guided target RNA cleavage is dependent on divalent metal (i.e. inhibited by EDTA) (PubMed:27669025).
Target RNA acts as an activator for non-specific ssRNA cleavage; the target RNA and complementary crRNA must both be at least 20 nucleotides long to activate the HEPN-like catalytic pocket for RNase activity (PubMed:28757251).
Crystals show the 3'-end of target RNA interacting with an adjacent protein molecule, and mutagenesis of those amino acid residues decreases target RNA cleavage, but it is not clear if this is physiological (PubMed:28757251).
The X-ray structure in complex with crRNA and target RNA shows a crRNA-recognition lobe (REC, residues 1-360) which anchors the crRNA repeat and a nuclease lobe (NUC, residues 361-1159) which binds the spacer crRNA-target RNA duplex and cleaves target RNA (PubMed:28757251). The target ssRNase active sites are within the 2 HEPN-like folds, which interact in vivo to form the functional active site (PubMed:26593719, PubMed:28757251). The N-terminal region and HEPN-like fold 2 play a role in pre-crRNA processing (PubMed:28475872). Binding of target RNA to the Cas13a-crRNA complex induces conformational changes that include bringing the 2 HEPN-like domains together to form the target cleavage active site, widening the channel that binds the crRNA-target RNA duplex, facilitating contact between the NUC lobe and the RNA duplex, and altering the conformation of the crRNA (PubMed:28757251).
Can be used to detect low levels of cellular transcripts, which might be useful to create sequence-specific RNA-targeting tools (PubMed:27669025).
Part of a type VI-A uridine-prefering CRISPR-Cas system.
Belongs to the CRISPR-associated endoribonuclease Cas13a family.
Binds 3'-end of target RNA, in adjacent protein
Binds 3' nucleotide of the target RNA PFS
No cleavage of target RNA, retains pre-crRNA cleavage. Still no effect on pre-crRNA cleavage; when associated with 1048-A--A-1053.
Dramatically decreased cleavage of target RNA.
No cleavage of target RNA, retains pre-crRNA cleavage. Still no effect on pre-crRNA cleavage; when associated with 427-A--A-477.
Complete loss of pre-crRNA cleavage, retains target RNA cleavage. Decreased ability to activate non-specific RNA degradation when tested with a 6-spacer CRISPR array.
Barely detectable pre-crRNA cleavage, retains target RNA cleavage.
MUTAGENESIS OF ARG-597; HIS-602; ARG-1278 AND HIS-1283
X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) WITH AND WITHOUT CRRNA
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements (spacers) and target invading nucleic acids. Unlike many single-component effectors, this CRISPR-Cas system targets RNA (PubMed:27256883, PubMed:28086085). CRISPR clusters are transcribed from pre-CRISPR RNA (crRNA) and processed into crRNA (optimally 28 nucleotides in this system) by this protein (PubMed:27256883, PubMed:27669025, PubMed:28475872, PubMed:28086085). This protein processes pre-crRNA at a 'non-typical' site 1 nucleotide upstream of the pre-crRNA stem-loop; it cleaves pre-crRNA from L.buccalis and L.wadei in a similar fashion, whereas the enzymes from the latter 2 bacteria cleave their own pre-crRNA 3 nt further upstream (PubMed:28475872). When the appropriate target sequences are cloned into the CRISPR array, confers immunity to ssRNA(+) enterobacteria phage MS2 (PubMed:27256883). Cleaves linear target ssRNA in a crRNA-dependent fashion, preferentially before U residues; has no activity on partially dsRNA, ssDNA or dsDNA (PubMed:27256883). RNA secondary structure surrounding the target influence the cleavage site and efficiency; unlike other CRISPR-Cas effectors Cas13a cleaves outside of the crRNA binding site (PubMed:27256883). In the presence of a viable RNA target other RNAs are also degraded (called collateral RNA degradation), suggesting this type of CRISPR-Cas might also prevent viral spread by inducing programmed cell death or dormancy (PubMed:27256883). This system has a 3' protospacer flanking site (PFS), it does not cleave when the 3' PFS is G (PFS is equivalent to PAM, the protospacer adjacent motif) (PubMed:27256883). Mutations of its active site residues results in an RNA-programmed RNA-binding protein (PubMed:27256883).
ssRNA target cleavage requires Mg(2+), weak target cleavage is seen with Mn(2+) and Ca(2+).
RNase activity on target is decreased by EDTA (PubMed:27256883). Target RNA acts as an activator for non-specific ssRNA degradation (PubMed:27256883).
The target ssRNase active sites are within the 2 HEPN-like folds which interact in vivo (PubMed:26593719, PubMed:27256883, PubMed:28086085). The X-ray structure in complex with crRNA shows a crRNA-recognition lobe (REC, residues 1-498) which makes most of the contacts with crRNA and is essential for pre-crRNA cleavage, and a nuclease lobe (NUC, residues 499-1389) which also makes a few contacts with the crRNA repeat and is responsible for target ssRNA cleavage (PubMed:28086085). Binding of crRNA induces conformational changes that probably stabilize crRNA-binding and facilitate target ssRNA recognition (PubMed:28086085). Mutagenesis of the crRNA and this protein show the stem loop and 3'-direct repeat of the crRNA are essential for target ssRNase while the 5'-end of the crRNA and its bulge-containing stem are essential for pre-crRNA cleavage (PubMed:28086085).
Can be reprogrammed to target specific mRNAs in an E.coli system, which might be useful to create specific RNA-targeting tools (PubMed:27256883).
Wild-type cleavage of target RNA and pre-crRNA processing.
No cleavage of target RNA, no change in pre-crRNA processing.
No cleavage of target ssRNA, no change in pre-crRNA processing.
No longer protects against infection by MS2 phage, loss of ssRNase activity.
No cleavage of target RNA, decreased pre-crRNA processing.
No longer protects against infection by MS2 phage, loss of ssRNase activity, still binds both crRNA and target ssRNA.
Wild-type cleavage of target RNA, decreased pre-crRNA processing.
CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. Unlike many single-component effectors, this CRISPR-Cas system targets RNA (PubMed:28475872). CRISPR clusters are transcribed from pre-CRISPR RNA (crRNA) and processed into crRNA by this protein (PubMed:28475872). Cleaves linear target ssRNA in a pre-crRNA-dependent fashion, preferentially before U residues (PubMed:28475872). Binding a viable target RNA target activates this protein for non-specific RNA degradation in vitro (called collateral RNA degradation), which is fairly sensitive as it requires picomolar levels of viable target RNA (PubMed:28475872, PubMed:28408723).
Pre-crRNA processing is metal independent, while crRNA-guided target RNA cleavage is dependent on divalent metal.
Target RNA acts as an activator for non-specific ssRNA degradation (PubMed:28475872, PubMed:28408723).
The target ssRNase active sites are probably within the 2 HEPN-like folds, and the 2 folds interact in vivo.
Can be used to detect RNA or DNA with atomolar sensitivity and single-base mismatch specificity when combined with isothermal amplification, allowing detection of virus, bacterial pathogens, to genotype DNA and to identify mutations in cell-free DNA. Additionally the reagents can be lyophilized and reconstituted on paper for field work (PubMed:28408723).
Binds 2 magnesium or manganese ions per subunit.
Belongs to the D-alanine--D-alanine ligase family.
Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.
Belongs to the polypeptide deformylase family.
GTPase that plays an essential role in the late steps of ribosome biogenesis.
Associates with the 50S ribosomal subunit.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family.
5' to 3' exonuclease, C-terminal subdomain
DNA integrity scanning protein, DisA, N-terminal domain
Participates in a DNA-damage check-point. DisA forms globular foci that rapidly scan along the chromosomes searching for lesions.
Has also diadenylate cyclase activity, catalyzing the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP). c-di-AMP likely acts as a signaling molecule that may couple DNA integrity with a cellular process.
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.
Sequencing of the dnaK heat shock operon of Fusobacterium nucleatum subsp. polymorphum ATCC 10953.
Heat shock protein 70kD (HSP70), C-terminal subdomain
Heat shock protein 70kD (HSP70), peptide-binding domain
Belongs to the heat shock protein 70 family.
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.
DNA polymerase, Y-family, little finger domain
DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBER
Lesion bypass DNA polymerase (Y-family), little finger domain
Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.
Belongs to the DNA polymerase type-Y family.
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.
1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, CHLOROPLASTIC
1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
1-deoxyxylulose-5-phosphate reductoisomerase
2-C-methyl-D-erythritol 4-phosphate synthase
Catalyzes the NADPH-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
1-D-DEOXYXYLULOSE 5-PHOSPHATE SYNTHASE-RELATED
1-DEOXY-D-XYLULOSE-5-PHOSPHATE SYNTHASE, CHLOROPLASTIC
Thiamin diphosphate-binding fold (THDP-binding)
Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP).
Binds 1 thiamine pyrophosphate per subunit.
Belongs to the transketolase family. DXPS subfamily.
ENERGY-COUPLING FACTOR TRANSPORTER ATP-BINDING PROTEIN ECFA1
ATP-binding (A) component of a common energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates.
Forms a stable energy-coupling factor (ECF) transporter complex composed of 2 membrane-embedded substrate-binding proteins (S component), 2 ATP-binding proteins (A component) and 2 transmembrane proteins (T component).
Belongs to the ABC transporter superfamily. Energy-coupling factor EcfA family.
ENERGY-COUPLING FACTOR TRANSPORTER ATP-BINDING PROTEIN ECFA2
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.
Prokaryotic type KH domain (KH-domain type II)
An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism.
Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Era GTPase family.
Ethanolamine ammonia-lyase light chain (EutC)
Ethanolamine ammonia-lyase light chain (EutC), N-terminal domain
ETHANOLAMINE AMMONIA-LYASE SMALL SUBUNIT
Catalyzes the deamination of various vicinal amino-alcohols to oxo compounds. Allows this organism to utilize ethanolamine as the sole source of nitrogen and carbon in the presence of external vitamin B12.
Binds between the large and small subunits.
The basic unit is a heterodimer which dimerizes to form tetramers. The heterotetramers trimerize; 6 large subunits form a core ring with 6 small subunits projecting outwards.
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.
D-fructose-1,6-bisphosphate 1-phosphohydrolase class 3
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III, CHLOROPLASTIC
Beta-ketoacyl-[acyl-carrier-protein] synthase III
3-oxoacyl-[acyl-carrier-protein] synthase 3
3-oxoacyl-[acyl-carrier-protein] synthase III
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched-chain and/or straight-chain of fatty acids.
The last Arg residue of the ACP-binding site is essential for the weak association between ACP/AcpP and FabH.
Belongs to the thiolase-like superfamily. FabH family.
(3R)-HYDROXYMYRISTOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
3-HYDROXYACYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
Thioesterase/thiol ester dehydrase-isomerase
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ
Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs.
Belongs to the thioester dehydratase family. FabZ subfamily.
SPERMIDINE/PUTRESCINE IMPORT ATP-BINDING PROTEIN POTA
Fe(3+) ions import ATP-binding protein FbpC
Part of the ABC transporter complex FbpABC involved in Fe(3+) ions import. Responsible for energy coupling to the transport system.
The complex is composed of two ATP-binding proteins (FbpC), two transmembrane proteins (FbpB) and a solute-binding protein (FbpA).
Belongs to the ABC transporter superfamily. Fe(3+) ion importer (TC 3.A.1.10) family.
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.
Domain 2, N(10)-formyltetrahydrofolate synthetase
Formyltetrahydrofolate synthetase, domain 3
Belongs to the formate--tetrahydrofolate ligase family.
ATP-DEPENDENT ZINC METALLOPROTEASE YME1L-RELATED
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 YME1L1
Catalyzes the reversible isomerization of glucose-6-phosphate to fructose-6-phosphate.
Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P).
Belongs to the GHMP kinase family. GalK subfamily.
GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
UDP-glucose--hexose-1-phosphate uridylyltransferase
Belongs to the galactose-1-phosphate uridylyltransferase type 2 family.
GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT A
Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln).
Belongs to the amidase family. GatA subfamily.
GLUTAMYL-TRNA GLN AMIDOTRANSFERASE SUBUNIT B MITOCHONDRIAL AND PROKARYOTIC PET112-RELATED
GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT B, MITOCHONDRIAL
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln).
Belongs to the GatB/GatE family. GatB subfamily.
Glu-tRNAGln amidotransferase C subunit, N-terminal domain
GLUTAMYL-TRNA(GLN) AMIDOTRANSFERASE SUBUNIT C, MITOCHONDRIAL
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
Tetrahydrobiopterin biosynthesis enzymes-like
Toroid-shaped homodecamer, composed of two pentamers of five dimers.
Belongs to the GTP cyclohydrolase I family.
GRANULE-BOUND STARCH SYNTHASE 1, CHLOROPLASTIC/AMYLOPLASTIC
STARCH SYNTHASE 1, CHLOROPLASTIC/AMYLOPLASTIC
UDP-Glycosyltransferase/glycogen phosphorylase
Synthesizes alpha-1,4-glucan chains using ADP-glucose.
Belongs to the glycosyltransferase 1 family. Bacterial/plant glycogen synthase subfamily.
1,4-alpha-D-glucan:1,4-alpha-D-glucan 6-glucosyl-transferase
Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position.
Belongs to the glycosyl hydrolase 13 family. GlgB subfamily.
GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE-RELATED
Involved in the biosynthesis of ADP-glucose, a building block required for the elongation reactions to produce glycogen. Catalyzes the reaction between ATP and alpha-D-glucose 1-phosphate (G1P) to produce pyrophosphate and ADP-Glc.
Belongs to the bacterial/plant glucose-1-phosphate adenylyltransferase family.
Cobalamin (vitamin B12)-dependent enzymes
Catalyzes the carbon skeleton rearrangement of L-glutamate to L-threo-3-methylaspartate ((2S,3S)-3-methylaspartate).
Heterotetramer composed of 2 epsilon subunits (GlmE) and 2 sigma subunits (GlmS). GlmE exists as a homodimer and GlmS as a monomer.
Belongs to the methylaspartate mutase GlmE subunit family.
Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3
Alpha-D-phosphohexomutase, C-terminal domain
PHOSPHOGLUCOSAMINE MUTASE FAMILY PROTEIN
Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate.
Belongs to the phosphohexose mutase family.
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE, ISOMERIZING
GLUTAMINE--FRUCTOSE-6-PHOSPHATE TRANSAMINASE (ISOMERIZING)
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Glutamine--fructose-6-phosphate aminotransferase [isomerizing]
L-glutamine--D-fructose-6-phosphate amidotransferase
Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source.
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.
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).
SEDOHEPTULOSE 7-PHOSPHATE ISOMERASE / DNAA INITIATOR-ASSOCIATING FACTOR FOR REPLICATION INITIATION
Catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate.
The reaction produces a racemic mixture of D-glycero-alpha-D-manno-heptose 7-phosphate and D-glycero-beta-D-manno-heptose 7-phosphate.
Belongs to the SIS family. GmhA subfamily.
Belongs to the methylaspartate mutase GlmS subunit family.
GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD(+)] 2, CHLOROPLASTIC
6-phosphogluconate dehydrogenase C-terminal domain-like
Glycerol-3-phosphate dehydrogenase [NAD(P)+]
NAD(P)H-dependent glycerol-3-phosphate dehydrogenase
Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.
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.
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
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 reduction of hydroxylamine to form NH(3) and H(2)O.
Glutamyl-tRNA reductase, N-terminal domain
GLUTAMYL-TRNA REDUCTASE 1, CHLOROPLASTIC
Glutamyl tRNA-reductase catalytic, N-terminal domain
Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA).
Possesses an unusual extended V-shaped dimeric structure with each monomer consisting of three distinct domains arranged along a curved 'spinal' alpha-helix. The N-terminal catalytic domain specifically recognizes the glutamate moiety of the substrate. The second domain is the NADPH-binding domain, and the third C-terminal domain is responsible for dimerization.
During catalysis, the active site Cys acts as a nucleophile attacking the alpha-carbonyl group of tRNA-bound glutamate with the formation of a thioester intermediate between enzyme and glutamate, and the concomitant release of tRNA(Glu). The thioester intermediate is finally reduced by direct hydride transfer from NADPH, to form the product GSA.
Belongs to the glutamyl-tRNA reductase family.
Lacks the conserved histidine residue in position 89 which is potentially part of the active site; it is replaced by a tyrosine residue.
Porphobilinogen deaminase, C-terminal domain
Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.
Binds 1 dipyrromethane group covalently.
The porphobilinogen subunits are added to the dipyrromethane group.
Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose.
Contains a large N-terminal NADP-binding domain, and a smaller C-terminal substrate-binding domain.
Belongs to the NAD(P)-dependent epimerase/dehydratase family. HldD subfamily.
K(+)-INSENSITIVE PYROPHOSPHATE-ENERGIZED PROTON PUMP
Putative K(+)-stimulated pyrophosphate-energized sodium pump
Membrane-bound sodium-translocating pyrophosphatase
Pyrophosphate-energized inorganic pyrophosphatase
Sodium pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for Na(+) movement across the membrane.
Belongs to the H(+)-translocating pyrophosphatase (TC 3.A.10) family. K(+)-stimulated subfamily.
Catalyzes the ATP- as well as the pyrophosphate-dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK/P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P-Ser-HPr) (By similarity).
This protein is composed of two complete HPrK/P domains fused in tandem. This unusual organization may lead to a separation of the two antagonistic activities in F.nucleatum, with the C-terminal copy carrying the kinase and the N-terminal copy carrying the phosphorylase.
Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
HEAT-INDUCIBLE TRANSCRIPTION REPRESSOR HRCA
Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons.
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.
Metalloproteases ('zincins'), catalytic domain
Catalyzes the conversion of N-formimidoyl-L-glutamate to L-glutamate and formamide.
Contains an active site 4-methylidene-imidazol-5-one (MIO), which is formed autocatalytically by cyclization and dehydration of residues Ser-Ser-Gly.
Composite domain of metallo-dependent hydrolases
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.
TRANSLATION INITIATION FACTOR IF-1, CHLOROPLASTIC
One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex.
Component of the 30S ribosomal translation pre-initiation complex which assembles on the 30S ribosome in the order IF-2 and IF-3, IF-1 and N-formylmethionyl-tRNA(fMet); mRNA recruitment can occur at any time during PIC assembly.
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.
Translation initiation factor 3 (IF-3), C-terminal domain
Translation initiation factor 3 (IF-3), N-terminal domain
TRANSLATION INITIATION FACTOR IF-3, MITOCHONDRIAL
Translation initiation factor IF3, C-terminal domain
Translation initiation factor IF3, N-terminal domain
IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins.
the drug/metabolite transporter (dmt) superfamily
Multidrug resistance efflux transporter EmrE
Expression is probably regulated by riboflavin, via an FMN riboswitch.
2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
4-diphosphocytidyl-2C-methyl-D-erythritol synthase
Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).
Belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily.
Positions MEP for the nucleophilic attack
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE, CHLOROPLASTIC
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase
Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol.
Belongs to the GHMP kinase family. IspE subfamily.
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, CHLOROPLASTIC
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP).
Binds 1 divalent metal cation per subunit.
4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE
4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE (FERREDOXIN), CHLOROPLASTIC
Nitrite and sulphite reductase 4Fe-4S domain-like
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase
Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate.
4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain
4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE
Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP/MEP pathway for isoprenoid precursor biosynthesis.
In the N-terminal section; belongs to the IspH family.
DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE FAMILY MEMBER
Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids.
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.
Involved in the anaerobic fermentation of lysine. Catalyzes the deamination of L-3-aminobutyryl-CoA to produce crotonoyl-CoA.
150.9 nmol/min/ug enzyme with crotonyl-CoA as substrate
Catalyzes the interconversion of L-alpha-lysine and L-beta-lysine.
Belongs to the radical SAM superfamily. KamA family.
L-beta-lysine 5,6-aminomutase alpha subunit
Catalyzes the migration of the L-beta-lysine and D-lysine epsilon amino group to the delta carbon to produce 3,5-diaminohexanoate and 2,5-diaminohexanoate, respectively.
Heterotetramer of 2 alpha and 2 beta subunits.
D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain
L-beta-lysine 5,6-aminomutase beta subunit
3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME-RELATED
Involved in the anaerobic fermentation of lysine. Catalyzes the reversible reaction between 3-keto-5-aminohexanoate (KAH) and acetyl-CoA to form 3-aminobutyryl-CoA and acetoacetate. The reaction involves the deprotonation of KAH, the nucleophilic addition onto acetyl-CoA and the intramolecular transfer of the CoA moiety. It can also use beta-alanyl-CoA as substrate.
3-fold increase in activity by addition of 10 mM 2-mercaptoethanol. Addition of CoCl(2) and to a lesser extent MnCl(2) increase the activity but not MgCl(2). Inhibited by phosphate buffers but not by 5,5'-dithio-2-nitrobenzoic acid.
Optimum pH is 6.5-7.0. The half-maximal rate is observed at 5.2 and 8.1.
CYTIDYLATE KINASE/PANTOATE-BETA-ALANINE LIGASE
Belongs to the cytidylate kinase family. Type 1 subfamily.
Medium-chain alcohol dehydrogenases, catalytic domain
L-erythro-3,5-diaminohexanoate dehydrogenase
Involved in the anaerobic fermentation of lysine. Catalyzes the oxidative deamination of L-erythro-3,5-diaminohexanoate (3,5-DAH) to 3-keto-5-aminohexanoate (KAH). It can use NAD or NADP.
3.2 uM for 3,5-DAH (with NAD as cofactor)
197.8 uM for 3,5-DAH (with NADP as cofactor)
4.1 nmol/min/ug enzyme with 3,5-DAH as substrate (with NAD as cofactor)
4.5 nmol/min/ug enzyme with 3,5-DAH as substrate (with NADP as cofactor)
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.
RIBOSE-PHOSPHATE DIPHOSPHOKINASE FAMILY MEMBER
RIBOSE-PHOSPHATE PYROPHOSPHOKINASE 5, CHLOROPLASTIC
5-phospho-D-ribosyl alpha-1-diphosphate synthase
Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P).
Belongs to the ribose-phosphate pyrophosphokinase family. Class I subfamily.
RNA 2'-phosphotransferase, Tpt1/KptA family, N-terminal domain
Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP-ribose 1''-2''-cyclic phosphate (APPR>P). May function as an ADP-ribosylase.
Beta-D-phosphogalactoside galactohydrolase
Inhibited by both galactose-6-phosphate and ATP.
50.94 umol/min/mg enzyme with oNPbetagal6P as substrate
Induced during growth on lactose or lactulose.
Belongs to the glycosyl hydrolase 1 family.
Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+))
Catalyzes the conversion of lactate to pyruvate.
Belongs to the LDH/MDH superfamily. LDH 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.
ALPHA-D-RIBOSE 1-METHYLPHOSPHONATE 5-TRIPHOSPHATE SYNTHASE SUBUNIT PHNL
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.
Udp N-acetylglucosamine O-acyltransferase, C-terminal domain
ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE, MITOCHONDRIAL-RELATED
Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.
Belongs to the transferase hexapeptide repeat family. LpxA subfamily.
UDP-3-O-ACYLGLUCOSAMINE N-ACYLTRANSFERASE
UDP-3-O-ACYLGLUCOSAMINE N-ACYLTRANSFERASE 1, MITOCHONDRIAL-RELATED
Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.
Belongs to the transferase hexapeptide repeat family. LpxD subfamily.
This protein specifically catalyzes the removal of signal peptides from prolipoproteins.
Hydrolyzes a wide variety of 6-phospho-alpha-D-glucosides including maltose-6'P, trehalose-6P and the 6'-phosphorylated derivatives of the five linkage-isomeric alpha-D-glucosyl-D-fructoses: trehalulose-6'P, turanose-6'P, maltulose-6'P, leucrose-6'P, and palatinose-6'P. However, sucrose-6P is not a substrate for MalH, and this enzyme also fails to hydrolyze beta-O-linked phosphorylated disaccharides such as cellobiose-6'P and gentobiose-6'P.
Divalent metal ion. Manganese, iron, cobalt and nickel ions enhance activity whereas magnesium, zinc, calcium and strontium do not.
Optimum temperature is 40 degrees Celsius.
By the five sucrose isomers and other alpha-glucosides (but not by sucrose or glucose).
Belongs to the glycosyl hydrolase 4 family.
Catalyzes the alpha,gamma-elimination of L-methionine to produce methanethiol, 2-oxobutanoate and ammonia, and that of L-homocysteine (By similarity). Can also use L-cysteine as substrate, catalyzing its alpha,beta-elimination; this activity seems to only minimally contribute to the production of hydrogen sulfide (H2S) by F.nucleatum in the oral cavity, which is toxic for a large variety of cells in periodontal regions (PubMed:21798982).
kcat is 0.69 sec(-1) for the production of H(2)S from L-cysteine.
Belongs to the trans-sulfuration enzymes family. L-methionine gamma-lyase subfamily.
Catalyzes the alpha,gamma-elimination of L-methionine to produce methanethiol, 2-oxobutanoate and ammonia; methanethiol (methyl mercaptan) is considered to be one of the main causes of the oral malodor associated with periodontitis. Also displays homocysteine desulfhydrase activity, degrading homocysteine to produce hydrogen sulfide, 2-oxobutanoate and ammonia. L-cysteine and S-methyl-L-cysteine are poor substrates for the enzyme.
Plays an important role in the resistance of F.nucleatum to the antibacterial agent 3-chloro-DL-alanine (3CA), thanks to its 3CA chloride-lyase (deaminating) activity.
F.nucleatum strain ATCC 10953 is able to grow in medium containing 1 mM 3CA.
Transfers an acetyl group from acetyl-CoA to L-homoserine, forming acetyl-L-homoserine.
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
METHIONINE IMPORT ATP-BINDING PROTEIN METN 2
Methionine import ATP-binding protein MetN
Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system.
The complex is composed of two ATP-binding proteins (MetN), two transmembrane proteins (MetI) and a solute-binding protein (MetQ).
Belongs to the ABC transporter superfamily. Methionine importer (TC 3.A.1.24) family.
CARBOHYDRATE TRANSPORT ATP-BINDING PROTEIN MG119-RELATED
GALACTOSE/METHYL GALACTOSIDE IMPORT ATP-BINDING PROTEIN MGLA
Part of the ABC transporter complex MglABC involved in galactose/methyl galactoside import. Responsible for energy coupling to the transport system.
The complex is composed of one ATP-binding protein (MglA), two transmembrane proteins (MglC) and a solute-binding protein (MglB).
Belongs to the ABC transporter superfamily. Galactose/methyl galactoside importer (TC 3.A.1.2.3) family.
Dimethylallyl diphosphate:tRNA dimethylallyltransferase
Isopentenyl-diphosphate:tRNA isopentenyltransferase
Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A).
Methylthiotransferase, N-terminal domain
CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 1
MITOCHONDRIAL TRNA METHYLTHIOTRANSFERASE CDK5RAP1
radical SAM methylthiotransferase, MiaB/RimO family
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB
Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine.
Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Belongs to the methylthiotransferase family. MiaB subfamily.
Cell-division inhibitor MinC, C-terminal domain
Probable septum site-determining protein MinC
Cell division inhibitor that blocks the formation of polar Z ring septums. Rapidly oscillates between the poles of the cell to destabilize FtsZ filaments that have formed before they mature into polar Z rings. Prevents FtsZ polymerization (By similarity).
Cell division topological specificity factor MinE
Cell division protein MinE topological specificity domain
Cell division topological specificity factor
Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell.
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 5-516
PROPIONYL-COA CARBOXYLASE BETA CHAIN-RELATED
Methylmalonyl-CoA decarboxylase subunit alpha
Carboxyltransferase subunit of the sodium ion pump methylmalonyl-CoA decarboxylase, which converts the chemical energy of a decarboxylation reaction into an electrochemical gradient of Na(+) ions across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis (PubMed:9428714). The alpha subunit catalyzes the Na(+)-independent carboxyltransfer from methylmalonyl-CoA to the prosthetic biotin group located on the gamma subunit (By similarity).
The methylmalonyl-CoA decarboxylase is composed of four subunits: the carboxyltransferase alpha subunit (MmdA), the tunnel beta subunit (MmdB), the biotin-containing gamma subunit (MmdC) and the delta subunit (MmdD).
Methylmalonyl-CoA decarboxylase subunit beta
Tunnel subunit of the sodium ion pump methylmalonyl-CoA decarboxylase, which converts the chemical energy of a decarboxylation reaction into an electrochemical gradient of Na(+) ions across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis (PubMed:9428714). The beta subunit catalyzes the decarboxylation of the carboxybiotin carrier protein and the coupled export of Na(+) ions (By similarity).
Methylmalonyl-CoA decarboxylase subunit gamma
Biotin-containing subunit of the sodium ion pump methylmalonyl-CoA decarboxylase, which converts the chemical energy of a decarboxylation reaction into an electrochemical gradient of Na(+) ions across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis.
Methylmalonyl-CoA decarboxylase subunit delta
Subunit of the sodium ion pump methylmalonyl-CoA decarboxylase, which converts the chemical energy of a decarboxylation reaction into an electrochemical gradient of Na(+) ions across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis (PubMed:9428714). The delta subunit is required for catalytic activity as well as for the proper assembly of the individual subunits to an enzyme complex (By similarity).
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 1
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.
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG 2
Probably functions as a manganese efflux pump.
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.
Crystal structure of the hypothetical protein (FN1578) from Fusobacterium nucleatum, NESG target NR1.
Might be a ribonuclease involved in RNA processing.
Strongly resembles the MrnC Mini-3 enzyme, but is missing a highly conserved, possibly catalytically important site at position 72.
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.
Method for producing the FnuDI restriction endonuclease and methylase.
Cytosine-specific methyltransferase FnuDI
A methylase, recognizes the double-stranded sequence 5'-GGCC-3', methylates C-? on both strands, and protects the DNA from cleavage by the FnuDI endonuclease.
Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase 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-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE MURE HOMOLOG, CHLOROPLASTIC
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase
UDP-N-acetylmuramyl-tripeptide synthetase
Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.
Carboxylation is probably crucial for Mg(2+) binding and, consequently, for the gamma-phosphate positioning of ATP.
Belongs to the MurCDEF family. MurE subfamily.
UDP-N-ACETYLGLUCOSAMINE--N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE 1
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)GlcNAc (lipid intermediate II).
Belongs to the glycosyltransferase 28 family. MurG subfamily.
Provides the (R)-glutamate required for cell wall biosynthesis.
Belongs to the aspartate/glutamate racemases family.
DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER
DNA MISMATCH REPAIR PROTEIN MUTS, TYPE 2
Endonuclease that is involved in the suppression of homologous recombination and may therefore have a key role in the control of bacterial genetic diversity.
Belongs to the DNA mismatch repair MutS family. MutS2 subfamily.
DNA MISMATCH REPAIR PROTEIN MSH1, MITOCHONDRIAL
This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.
Belongs to the DNA mismatch repair MutS family.
Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate.
Belongs to the quinolinate synthase family. Type 2 subfamily.
NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE-RELATED
nicotinate (nicotinamide) nucleotide adenylyltransferase
Probable nicotinate-nucleotide adenylyltransferase
Nicotinate mononucleotide adenylyltransferase
Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD).
NH 3 /GLUTAMINE-DEPENDENT NAD + SYNTHETASE
Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source.
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.
Catalyzes the reversible isomerization-deamination of glucosamine 6-phosphate (GlcN6P) to form fructose 6-phosphate (Fru6P) and ammonium ion.
Belongs to the glucosamine/galactosamine-6-phosphate isomerase family. NagB subfamily.
Catalyzes the reversible aldol cleavage of N-acetylneuraminic acid (sialic acid; Neu5Ac) to form pyruvate and N-acetylmannosamine (ManNAc) via a Schiff base intermediate.
Belongs to the DapA family. NanA subfamily.
Involved in proton transfer during cleavage
N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE-RELATED
Putative N-acetylmannosamine-6-phosphate 2-epimerase
Converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P).
NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form.
Belongs to the sirtuin family. Class U subfamily.
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.
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.
GTP-binding protein OBG, C-terminal domain
DEVELOPMENTALLY REGULATED GTP-BINDING PROTEIN-RELATED
MITOCHONDRIAL RIBOSOME-ASSOCIATED GTPASE 2
Obg GTP-binding protein C-terminal domain
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.
Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
DNA-(apurinic or apyrimidinic site) lyase
Catalyzes the excision of an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine = 8-oxoG) from DNA. Also cleaves the DNA backbone at apurinic/apyrimidinic sites (AP sites).
Important for guanine/8-oxoguanine distinction
In vitro, readily hydrolyzes p-nitrophenyl-alpha-D-glucopyranoside 6-phosphate (pNPalphaG6P), a chromogenic analog of the phosphorylated isomers of sucrose. In vivo, is probably involved in the degradation of the 6-phosphate derivatives of the sucrose isomers trehalulose, turanose, maltulose and palatinose, catalyzing their hydrolysis into glucose 6-phosphate (G6P) and fructose, which allows the bacterium to use these sugars as energy sources for growth. Is not able to hydrolyze the C2 or C4 chromogenic stereomers (i.e. pNPalpha-mannopyranoside-6P and pNPalpha-galactopyranoside-6P, respectively).
Induced by growth on the sucrose isomers trehalulose, turanose, maltulose and palatinose.
Phosphoenolpyruvate Carboxykinase, domain 1
Phosphoenolpyruvate Carboxykinase, domain 2
Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA.
Belongs to the phosphoenolpyruvate carboxykinase (ATP) family.
Peptidase C15, pyroglutamyl peptidase I-like
PROTEASE FAMILY C15 PYROGLUTAMYL-PEPTIDASE I-RELATED
Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
Removes 5-oxoproline from various penultimate amino acid residues except L-proline.
Involved in 1,2-propanediol (1,2-PD) utilization within the bacterial microcompartment (BMC) dedicated to 1,2-PD degradation by catalyzing the conversion of propanoyl-CoA to propanoyl-phosphate.
There are 2 Zn(2+) ions per monomer; Zn(2+) and CoA bind inbetween the 2 domains in each monomer.
Formed by 2 beta-barrels, each is capped on both ends by short alpha-helices.
4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE
Isocitrate/Isopropylmalate dehydrogenase-like
Putative D-threonate 4-phosphate dehydrogenase
Catalyzes the NAD-dependent oxidation and subsequent decarboxylation of D-threonate 4-phosphate to produce dihydroxyacetone phosphate (DHAP).
Belongs to the PdxA family. PdxA2 subfamily.
PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNZ1-RELATED
pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
Pyridoxal 5'-phosphate synthase subunit PdxS
Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively.
In the presence of PdxT, forms a dodecamer of heterodimers.
Schiff-base intermediate with D-ribose 5-phosphate
Bacterial exopeptidase dimerisation domain
Cleaves the N-terminal amino acid of tripeptides.
Cleaves a wide range of dipeptides and tripeptides, but does not display activity against larger peptides. May have a role in the survival of F.nucleatum in the subgingival environment of the mouth.
Binds 2 Zn(2+) or Co(2+) ions per subunit.
Inhibited by the chelating agents EDTA and 1,10-phenanthroline, by bestatin and amastatin, p-hydroxymercuribenzoate and some divalent cations at high concentration.
0.12 umol/min/mg enzyme with Leu-Ala as substrate
0.09 umol/min/mg enzyme with Leu-Gly-Gly as substrate
ATP-DEPENDENT 6-PHOSPHOFRUCTOKINASE, MUSCLE TYPE
Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis.
Allosterically activated by ADP and other diphosphonucleosides, and allosterically inhibited by phosphoenolpyruvate.
Belongs to the phosphofructokinase type A (PFKA) family. ATP-dependent PFK group I subfamily. Prokaryotic clade 'B1' sub-subfamily.
allosteric activator; ligand shared between dimeric partners
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.
FATTY ACID/PHOSPHOLIPID SYNTHESIS PROTEIN PLSX
Acyl-[acyl-carrier-protein]--phosphate acyltransferase
Catalyzes the reversible formation of acyl-phosphate (acyl-PO(4)) from acyl-[acyl-carrier-protein] (acyl-ACP). This enzyme utilizes acyl-ACP as fatty acyl donor, but not acyl-CoA.
Homodimer. Probably interacts with PlsY.
Associated with the membrane possibly through PlsY.
GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE-RELATED
acyl-phosphate glycerol 3-phosphate acyltransferase
Acyl-phosphate--glycerol-3-phosphate acyltransferase
Catalyzes the transfer of an acyl group from acyl-phosphate (acyl-PO(4)) to glycerol-3-phosphate (G3P) to form lysophosphatidic acid (LPA). This enzyme utilizes acyl-phosphate as fatty acyl donor, but not acyl-CoA or acyl-ACP.
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.
Part of the ABC transporter complex PotABCD involved in spermidine/putrescine import. Responsible for energy coupling to the transport system.
The complex is composed of two ATP-binding proteins (PotA), two transmembrane proteins (PotB and PotC) and a solute-binding protein (PotD).
Belongs to the ABC transporter superfamily. Spermidine/putrescine importer (TC 3.A.1.11.1) family.
ELECTRON TRANSFER FLAVOPROTEIN BETA SUBUNIT LYSINE METHYLTRANSFERASE
Belongs to the methyltransferase superfamily. PrmA family.
MTRF1L RELEASE FACTOR GLUTAMINE METHYLTRANSFERASE
Release factor glutamine methyltransferase
Protein-glutamine N-methyltransferase PrmC
Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif.
Belongs to the protein N5-glutamine methyltransferase family. PrmC subfamily.
PHOSPHATIDYLSERINE DECARBOXYLASE PROENZYME 2
Phosphatidylserine decarboxylase proenzyme
Phosphatidylserine decarboxylase alpha chain
Phosphatidylserine decarboxylase beta chain
Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer).
Binds 1 pyruvoyl group covalently per subunit.
Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit.
Is synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase.
Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type II sub-subfamily.
Charge relay system; for autoendoproteolytic cleavage activity
Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activity
Cleavage (non-hydrolytic); by autocatalysis
The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 443-526
CYTOCHROME C-TYPE SYNTHESIS PROTEIN AND PTS TRANSMEMBRANE COMPONENT
PTS system alpha-glucoside-specific EIICB component
PTS system alpha-glucoside-specific EIIC component
Alpha-glucoside-specific phosphotransferase enzyme IIB component
PTS system alpha-glucoside-specific EIIB component
The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active -transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. This system is involved in alpha-glucoside transport.
The EIIC domain forms the PTS system translocation channel and contains the specific substrate-binding site.
The EIIB domain is phosphorylated by phospho-EIIA on a cysteinyl or histidyl residue, depending on the transported sugar. Then, it transfers the phosphoryl group to the sugar substrate concomitantly with the sugar uptake processed by the EIIC domain.
Phosphocysteine intermediate; for EIIB activity
The phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), a major carbohydrate active -transport system, catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. This system is probably involved in transport of the alpha-glucosides trehalulose, turanose, maltulose and palatinose.
Phosphoribosylglycinamide synthetase, C-terminal domain
PHOSPHORIBOSYLAMINE--GLYCINE LIGASE, CHLOROPLASTIC
Binds 1 Mg(2+) or Mn(2+) ion per subunit.
TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3
TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED
Phosphoribosylformylglycinamidine cyclo-ligase
Phosphoribosyl-aminoimidazole synthetase
Phosphoribosylaminoimidazole-succinocarboxamide synthase
Belongs to the SAICAR synthetase family.
BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN ATIC
BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH
Phosphoribosylaminoimidazolecarboxamide formyltransferase
The IMP cyclohydrolase activity resides in the N-terminal region.
Adenylosuccinate Synthetase, subunit A, domain 1
Adenylosuccinate Synthetase, subunit A, domain 2
Adenylosuccinate Synthetase, subunit A, domain 3
Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP.
Belongs to the adenylosuccinate synthetase family.
5-oxoprolinase (ATP-hydrolyzing) subunit A
Catalyzes the cleavage of 5-oxoproline to form L-glutamate coupled to the hydrolysis of ATP to ADP and inorganic phosphate.
Forms a complex composed of PxpA, PxpB and PxpC.
Aspartate/ornithine carbamoyltransferase
ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL
Belongs to the aspartate/ornithine carbamoyltransferase superfamily. ATCase family.
Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate.
Belongs to the metallo-dependent hydrolases superfamily. DHOase family. Class I DHOase subfamily.
DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL-RELATED
Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit
Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor.
Heterotetramer of 2 PyrK and 2 PyrD type B subunits.
Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily.
Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP).
Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrE subfamily.
Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).
Belongs to the OMP decarboxylase family. Type 1 subfamily.
Catalyzes the reversible phosphorylation of UMP to UDP.
Dihydroorotate dehydrogenase, electron transfer subunit
Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
DIHYDROOROTATE DEHYDROGENASE B (NAD(+)), ELECTRON TRANSFER SUBUNIT
DIHYDROOROTATE DEHYDROGENASE B (NAD(+)), ELECTRON TRANSFER SUBUNIT-RELATED
Ferredoxin reductase-like, C-terminal NADP-linked domain
Dihydroorotate oxidase B, electron transfer subunit
Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the PyrD type B subunit to the ultimate electron acceptor NAD(+).
Regulates the transcription of the pyrimidine nucleotide (pyr) operon in response to exogenous pyrimidines.
Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.
Belongs to the purine/pyrimidine phosphoribosyltransferase family. PyrR subfamily.
S-ADENOSYLMETHIONINE:TRNA RIBOSYLTRANSFERASE-ISOMERASE
Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA).
RIBOSOME-BINDING FACTOR A, CHLOROPLASTIC-RELATED
One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.
Monomer. Binds 30S ribosomal subunits, but not 50S ribosomal subunits or 70S ribosomes.
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.
Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template.
Homohexamer. The homohexamer assembles into an open ring structure.
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.
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.
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.
39S RIBOSOMAL PROTEIN L27, MITOCHONDRIAL
Belongs to the bacterial ribosomal protein bL27 family.
Belongs to the bacterial ribosomal protein bL28 family.
50S RIBOSOMAL PROTEIN L29, CHLOROPLASTIC
60S RIBOSOMAL PROTEIN L35/50S RIBOSOMAL PROTEIN L29
Belongs to the universal ribosomal protein uL29 family.
One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.
Part of the 50S ribosomal subunit. Forms a bridge to the 30S subunit in the 70S ribosome.
Belongs to the universal ribosomal protein uL2 family.
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 A subfamily.
Belongs to the bacterial ribosomal protein bL32 family.
50S RIBOSOMAL PROTEIN L33, CHLOROPLASTIC
Belongs to the bacterial ribosomal protein bL33 family.
39S RIBOSOMAL PROTEIN L34, MITOCHONDRIAL
MITOCHONDRIAL RIBOSOMAL PROTEIN 34 FAMILY MEMBER
Belongs to the bacterial ribosomal protein bL34 family.
Belongs to the bacterial ribosomal protein bL35 family.
50S RIBOSOMAL PROTEIN L36, CHLOROPLASTIC
Belongs to the bacterial ribosomal protein bL36 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.
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.
Probable 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.
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.
Required for correct processing of both the 5' and 3' ends of 5S rRNA precursor. Cleaves both sides of a double-stranded region yielding mature 5S rRNA in one step.
RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme.
Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit.
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.
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.
28S RIBOSOMAL PROTEIN S11, MITOCHONDRIAL
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.
Because the enzyme that would modify Asp-89 to 3-methylthioaspartic acid has not been found in the proteome of this organism, that modification is not predicted.
30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18
37S RIBOSOMAL PROTEIN SWS2, MITOCHONDRIAL
Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.
Part of the 30S ribosomal subunit. Forms a loose heterodimer with protein S19. Forms two bridges to the 50S subunit in the 70S ribosome.
Belongs to the universal ribosomal protein uS13 family.
28S RIBOSOMAL PROTEIN S14, MITOCHONDRIAL
Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.
Part of the 30S ribosomal subunit. Contacts proteins S3 and S10.
Belongs to the universal ribosomal protein uS14 family.
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.
30S RIBOSOMAL PROTEIN S2 PROKARYOTIC AND ORGANELLAR
Belongs to the universal ribosomal protein uS2 family.
Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.
Part of the 30S ribosomal subunit. Forms a tight complex with proteins S10 and S14.
Belongs to the 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.
Belongs to the universal ribosomal protein uS9 family.
SMALL RIBOSOMAL SUBUNIT BIOGENESIS GTPASE RSGA
SMALL RIBOSOMAL SUBUNIT BIOGENESIS GTPASE RSGA 1, MITOCHONDRIAL-RELATED
ribosome small subunit-dependent GTPase A
One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit.
Monomer. Associates with 30S ribosomal subunit, binds 16S rRNA.
Belongs to the TRAFAC class YlqF/YawG GTPase family. RsgA subfamily.
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
16S rRNA 7-methylguanosine methyltransferase
Specifically methylates the N7 position of a guanine in 16S rRNA.
Belongs to the methyltransferase superfamily. RNA methyltransferase RsmG family.
Putative methyltransferase TM0872, insert domain
12S RRNA N4-METHYLCYTIDINE METHYLTRANSFERASE
16S rRNA (cytosine(1402)-N(4))-methyltransferase
Ribosomal RNA small subunit methyltransferase H
rRNA (cytosine-N(4)-)-methyltransferase RsmH
Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA.
Belongs to the methyltransferase superfamily. RsmH family.
Holliday junction branch migration complex subunit RuvA
The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair, while the RuvA-RuvB complex plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR). RuvA specifically binds to HJ cruciform DNA, conferring on it an open structure. The RuvB hexamer acts as an ATP-dependent pump, pulling dsDNA into and through the RuvAB complex. HJ branch migration allows RuvC to scan DNA until it finds its consensus sequence, where it cleaves and resolves the cruciform DNA.
Homotetramer. Forms an RuvA(8)-RuvB(12)-Holliday junction (HJ) complex. HJ DNA is sandwiched between 2 RuvA tetramers; dsDNA enters through RuvA and exits via RuvB. An RuvB hexamer assembles on each DNA strand where it exits the tetramer. Each RuvB hexamer is contacted by two RuvA subunits (via domain III) on 2 adjacent RuvB subunits; this complex drives branch migration. In the full resolvosome a probable DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms which resolves the HJ.
Has three domains with a flexible linker between the domains II and III and assumes an 'L' shape. Domain III is highly mobile and contacts RuvB.
HOLLIDAY JUNCTION ATP-DEPENDENT DNA HELICASE RUVB
Holliday junction branch migration complex subunit RuvB
The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair, while the RuvA-RuvB complex plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR). RuvA specifically binds to HJ cruciform DNA, conferring on it an open structure. The RuvB hexamer acts as an ATP-dependent pump, pulling dsDNA into and through the RuvAB complex. RuvB forms 2 homohexamers on either side of HJ DNA bound by 1 or 2 RuvA tetramers; 4 subunits per hexamer contact DNA at a time. Coordinated motions by a converter formed by DNA-disengaged RuvB subunits stimulates ATP hydrolysis and nucleotide exchange. Immobilization of the converter enables RuvB to convert the ATP-contained energy into a lever motion, pulling 2 nucleotides of DNA out of the RuvA tetramer per ATP hydrolyzed, thus driving DNA branch migration. The RuvB motors rotate together with the DNA substrate, which together with the progressing nucleotide cycle form the mechanistic basis for DNA recombination by continuous HJ branch migration. Branch migration allows RuvC to scan DNA until it finds its consensus sequence, where it cleaves and resolves cruciform DNA.
Homohexamer. Forms an RuvA(8)-RuvB(12)-Holliday junction (HJ) complex. HJ DNA is sandwiched between 2 RuvA tetramers; dsDNA enters through RuvA and exits via RuvB. An RuvB hexamer assembles on each DNA strand where it exits the tetramer. Each RuvB hexamer is contacted by two RuvA subunits (via domain III) on 2 adjacent RuvB subunits; this complex drives branch migration. In the full resolvosome a probable DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms which resolves the HJ.
Has 3 domains, the large (RuvB-L) and small ATPase (RuvB-S) domains and the C-terminal head (RuvB-H) domain. The head domain binds DNA, while the ATPase domains jointly bind ATP, ADP or are empty depending on the state of the subunit in the translocation cycle. During a single DNA translocation step the structure of each domain remains the same, but their relative positions change.
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.
270 umol/min/mg enzyme for sucrose 6-phosphate
Belongs to the glycosyl hydrolase 32 family.
Divalent metal cations. Maximum activity was observed with Mg(2+).
74 umol/min/mg enzyme for fructose 6-phosphate
THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED
Tryptophan synthase beta subunit-like PLP-dependent enzymes
Belongs to the serine/threonine dehydratase family. DsdA subfamily.
Helical scaffold and wing domains of SecA
SECA INNER MEMBRANE COMPONENT OF SEC PROTEIN SECRETION SYSTEM
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane.
Monomer and homodimer. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved.
Multidrug efflux transporter AcrB transmembrane domain
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA.
Forms a complex with SecF. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved.
Belongs to the SecD/SecF family. SecD subfamily.
Forms a complex with SecD. Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved.
Belongs to the SecD/SecF family. SecF subfamily.
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.
SINGLE-STRANDED DNA-BINDING PROTEIN, MITOCHONDRIAL
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.
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.
Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp).
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.
GLYCINE--TRNA LIGASE, CHLOROPLASTIC/MITOCHONDRIAL 2
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 1 subfamily.
LYSINE--TRNA LIGASE, CHLOROPLASTIC/MITOCHONDRIAL
LEUCINE--TRNA LIGASE, MITOCHONDRIAL-RELATED
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 2A subfamily.
ASPARAGINE--TRNA LIGASE, MITOCHONDRIAL-RELATED
MITOCHONDRIAL RIBOSOME PROTEIN L39/PROLYL-TRNA LIGASE FAMILY MEMBER
Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys-tRNA(Pro) is not edited by ProRS.
Consists of three domains: the N-terminal catalytic domain, the editing domain and the C-terminal anticodon-binding domain.
Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 1 subfamily.
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
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 tryptophan to tRNA(Trp).
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 1 subfamily.
Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).
Homodimer. Within each dimer, one monomer is responsible for RNA recognition and catalysis, while the other monomer binds to the replacement base PreQ1.
Belongs to the queuine tRNA-ribosyltransferase family.
RNA binding; important for wobble base 34 recognition
PHOSPHOMETHYLPYRIMIDINE SYNTHASE, CHLOROPLASTIC
Hydroxymethylpyrimidine phosphate synthase
Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.
Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
THIAMINE BIOSYNTHETIC BIFUNCTIONAL ENZYME
Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP).
Belongs to the thiamine-phosphate synthase family.
Catalyzes the rearrangement of 1-deoxy-D-xylulose 5-phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S.
Homotetramer. Forms heterodimers with either ThiH or ThiS.
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.
Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at the wobble position of elongator tRNA(Met), using acetate and ATP as substrates. First activates an acetate ion to form acetyladenylate (Ac-AMP) and then transfers the acetyl group to tRNA to form ac(4)C34.
Involved in the gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P).
Belongs to the triosephosphate isomerase family.
BETA-ELIMINATING LYASE-LIKE PROTEIN-RELATED
Belongs to the beta-eliminating lyase family.
3-Deoxy-D-manno-octulosonic-acid transferase, N-terminal domain
3-DEOXY-D-MANNO-OCTULOSONIC ACID TRANSFERASE, MITOCHONDRIAL-RELATED
Bifunctional glycosyltransferase/methyltransferase
tRNA (guanine(46)-N(7))-methyltransferase
Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA.
In the C-terminal section; belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family.
In the N-terminal section; belongs to the glycosyltransferase 1 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.
The beta subunit is responsible for the synthesis of L-tryptophan from indole and L-serine.
Tetramer of two alpha and two beta chains.
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.
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.
Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.
Belongs to the uracil-DNA glycosylase (UDG) superfamily. UNG 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.
URACIL PHOSPHORIBOSYLTRANSFERASE, CHLOROPLASTIC
Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate.
Binds 1 Mg(2+) ion per subunit. The magnesium is bound as Mg-PRPP.
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage.
Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex.
The beta-hairpin motif is involved in DNA binding.
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.
ATP-SYNT_AB DOMAIN-CONTAINING PROTEIN-RELATED
Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit.
Belongs to the V-ATPase D subunit family.
Belongs to the V-ATPase E subunit family.
Belongs to the V-ATPase F subunit family.
Domain of unknown function (DUF1846), C-terminal subdomain
MEMBRANE METALLOPROTEASE ARASP2, CHLOROPLASTIC-RELATED
Sigma3 and sigma4 domains of RNA polymerase sigma factors
Might take part in the signal recognition particle (SRP) pathway. This is inferred from the conservation of its genetic proximity to ftsY/ffh. May be a regulatory protein (By similarity).
UPF0735 ACT domain-containing protein FN1487
TRANSCRIPTIONAL REGULATORY PROTEIN YEBC-RELATED
DNA-binding regulatory protein, YebC/PmpR family
Probable transcriptional regulatory protein FN1661
23S RRNA (URACIL(747)-C(5))-METHYLTRANSFERASE RLMC
Uncharacterized RNA methyltransferase FN1713
Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.
GANGLIOSIDE INDUCED DIFFERENTIATION ASSOCIATED PROTEIN 2-RELATED
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.
CYTOCHROME C OXIDASE ASSEMBLY PROTEIN COX18, MITOCHONDRIAL
Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins (By similarity).
Interacts with the Sec translocase complex via SecD. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration (By similarity).
Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily.
MEMBRANE PROTEIN INSERTION EFFICIENCY FACTOR-RELATED
putative membrane protein insertion efficiency factor
Could be involved in insertion of integral membrane proteins into the membrane.
POLYNUCLEOTIDYL TRANSFERASE, RIBONUCLEASE H-LIKE SUPERFAMILY PROTEIN
Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA.