hydrogenobyrinic/cobyrinic acid a,c-diamide synthase catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of hydrogenobyrinate or cobyrinate, using either L-glutamine or ammonia as the nitrogen source
Cobyrinic acid a,c-diamide synthase [Coenzyme transport and metabolism]; Cobyrinic acid a, ...
2-424
1.65e-164
Cobyrinic acid a,c-diamide synthase [Coenzyme transport and metabolism]; Cobyrinic acid a,c-diamide synthase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis
Pssm-ID: 441402 [Multi-domain] Cd Length: 459 Bit Score: 470.36 E-value: 1.65e-164
cobyrinic acid a,c-diamide synthase; This model describes cobyrinic acid a,c-diamide synthase, ...
4-424
1.61e-100
cobyrinic acid a,c-diamide synthase; This model describes cobyrinic acid a,c-diamide synthase, the cobB (cbiA in Salmonella) protein of cobalamin biosynthesis. It is responsible for the amidation of carboxylic groups at positions A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine and one molecule of ATP hydrogenolyzed for each amidation. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 273044 [Multi-domain] Cd Length: 449 Bit Score: 307.11 E-value: 1.61e-100
Ni-sirohydrochlorin a,c-diamide synthase; Members of this family are Ni-sirohydrochlorin a, ...
4-424
2.87e-91
Ni-sirohydrochlorin a,c-diamide synthase; Members of this family are Ni-sirohydrochlorin a,c-diamide synthase, involving in synthesizing coenzyme F430, used in methanogens by coenzyme M reductase. Members of this family are restricted to archaeal methanogens, and resemble (and may be misannotated as) the enzyme cobyrinic acid a,c-diamide synthase, involved in cobalamin biosynthesis.
Pssm-ID: 467990 [Multi-domain] Cd Length: 451 Bit Score: 283.31 E-value: 2.87e-91
N-terminal domain of cobyrinic acid a,c-diamide synthase; Cobyrinic acid a,c-diamide synthase (CobB, CbiA). Biosynthesis of cobalamin (vitamin B12) requires more than two dozen different enzymes. CobB catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of cobyrinic acid, via the formation of a phosphorylated intermediate, using glutamine or ammonia as the nitrogen source. CobB is comprised of two protein domains: the C-terminal glutaminase domain and the N-terminal ATP-binding domain. The glutaminase domain catalyzes the hydrolysis of glutamine to glutamate and ammonia. It belongs to the triad class of glutamine amidotransferases. This classification is based on the N-terminal domain which catalyzes the ultimate synthesis of the diamide product by using energy from the hydrolysis of ATP and ammonia transferred from the C-terminal domain.
Pssm-ID: 349773 [Multi-domain] Cd Length: 193 Bit Score: 228.25 E-value: 1.84e-73
Cobyrinic acid a,c-diamide synthase [Coenzyme transport and metabolism]; Cobyrinic acid a, ...
2-424
1.65e-164
Cobyrinic acid a,c-diamide synthase [Coenzyme transport and metabolism]; Cobyrinic acid a,c-diamide synthase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis
Pssm-ID: 441402 [Multi-domain] Cd Length: 459 Bit Score: 470.36 E-value: 1.65e-164
cobyrinic acid a,c-diamide synthase; This model describes cobyrinic acid a,c-diamide synthase, ...
4-424
1.61e-100
cobyrinic acid a,c-diamide synthase; This model describes cobyrinic acid a,c-diamide synthase, the cobB (cbiA in Salmonella) protein of cobalamin biosynthesis. It is responsible for the amidation of carboxylic groups at positions A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine and one molecule of ATP hydrogenolyzed for each amidation. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]
Pssm-ID: 273044 [Multi-domain] Cd Length: 449 Bit Score: 307.11 E-value: 1.61e-100
Ni-sirohydrochlorin a,c-diamide synthase; Members of this family are Ni-sirohydrochlorin a, ...
4-424
2.87e-91
Ni-sirohydrochlorin a,c-diamide synthase; Members of this family are Ni-sirohydrochlorin a,c-diamide synthase, involving in synthesizing coenzyme F430, used in methanogens by coenzyme M reductase. Members of this family are restricted to archaeal methanogens, and resemble (and may be misannotated as) the enzyme cobyrinic acid a,c-diamide synthase, involved in cobalamin biosynthesis.
Pssm-ID: 467990 [Multi-domain] Cd Length: 451 Bit Score: 283.31 E-value: 2.87e-91
N-terminal domain of cobyrinic acid a,c-diamide synthase; Cobyrinic acid a,c-diamide synthase (CobB, CbiA). Biosynthesis of cobalamin (vitamin B12) requires more than two dozen different enzymes. CobB catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of cobyrinic acid, via the formation of a phosphorylated intermediate, using glutamine or ammonia as the nitrogen source. CobB is comprised of two protein domains: the C-terminal glutaminase domain and the N-terminal ATP-binding domain. The glutaminase domain catalyzes the hydrolysis of glutamine to glutamate and ammonia. It belongs to the triad class of glutamine amidotransferases. This classification is based on the N-terminal domain which catalyzes the ultimate synthesis of the diamide product by using energy from the hydrolysis of ATP and ammonia transferred from the C-terminal domain.
Pssm-ID: 349773 [Multi-domain] Cd Length: 193 Bit Score: 228.25 E-value: 1.84e-73
Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide ...
242-424
4.30e-53
Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. CobB plays a role in cobalamin biosythesis catalyzing the conversion of cobyrinic acid to cobyrinic acid a,c-diamide. CobB belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobB.
Pssm-ID: 153224 [Multi-domain] Cd Length: 198 Bit Score: 175.86 E-value: 4.30e-53
CobQ/CobB/MinD/ParA nucleotide binding domain; This family consists of various cobyrinic acid ...
4-189
1.23e-31
CobQ/CobB/MinD/ParA nucleotide binding domain; This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyze amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.
Pssm-ID: 426369 [Multi-domain] Cd Length: 228 Bit Score: 120.53 E-value: 1.23e-31
AAA domain; This domain is found in a number of proteins involved in cofactor biosynthesis ...
2-180
2.68e-11
AAA domain; This domain is found in a number of proteins involved in cofactor biosynthesis such as dethiobiotin synthase and cobyric acid synthase. This domain contains a P-loop motif.
Pssm-ID: 433259 [Multi-domain] Cd Length: 198 Bit Score: 62.66 E-value: 2.68e-11
dethiobiotin synthetase; Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the ...
2-153
9.17e-11
dethiobiotin synthetase; Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Pssm-ID: 349763 [Multi-domain] Cd Length: 189 Bit Score: 60.66 E-value: 9.17e-11
Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Type ...
257-423
1.06e-10
Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ). CobQ plays a role in cobalamin biosythesis. CobQ catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. CobQ belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobQ.
Pssm-ID: 153221 [Multi-domain] Cd Length: 194 Bit Score: 60.72 E-value: 1.06e-10
N-terminal domain of cobyric acid synthase; Cobyric acid synthase (CobQ, CbiP) N-terminal domain. CobQ plays a role in the cobalamin (vitamin B12) biosynthesis pathway. CobQ catalyzes the ATP-dependent amidation of adenosyl-cobyrinic acid a,c-diamide at carboxylates positions b, d, e, and g to produce cobyric acid using glutamine or ammonia as the nitrogen source. The C-terminal glutaminase domain catalyzes the hydrolysis of glutamine to glutamate and ammonia. Ammonia is translocated via an intramolecular tunnel to the N-terminal domain for the synthesis of cobyric acid.
Pssm-ID: 349774 Cd Length: 223 Bit Score: 49.51 E-value: 8.75e-07
Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase ...
243-329
7.55e-05
Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA. and, the A4 beta-galactosidase middle domain. The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site. Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase.
Pssm-ID: 153210 [Multi-domain] Cd Length: 115 Bit Score: 41.82 E-value: 7.55e-05
Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase ...
243-329
2.28e-04
Type 1 glutamine amidotransferase (GATase1)-like domain; Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E. The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site. Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain.
Pssm-ID: 153222 [Multi-domain] Cd Length: 92 Bit Score: 39.88 E-value: 2.28e-04
SIMIBI (signal recognition particle, MinD and BioD)-class NTPases; SIMIBI (after signal ...
4-149
1.27e-03
SIMIBI (signal recognition particle, MinD and BioD)-class NTPases; SIMIBI (after signal recognition particle, MinD, and BioD), consists of signal recognition particle (SRP) GTPases, the assemblage of MinD-like ATPases, which are involved in protein localization, chromosome partitioning, and membrane transport, and a group of metabolic enzymes with kinase or related phosphate transferase activity. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Pssm-ID: 349751 [Multi-domain] Cd Length: 107 Bit Score: 38.18 E-value: 1.27e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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