HAMAP rule MF_00027
General rule information
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| Accession | MF_00027 |
| Dates | 1-JUN-2001 (Created)
1-JUN-2023 (Last updated, Version 34) |
| Name | CobB/CbiA |
| Scope(s) |
Bacteria Archaea |
| Template(s) | P29946 (CBIA_SALTY); P21632 (COBB_SINSX); Q8TK00 (CBIA_METAC); Q46FL0 (CBIA_METBF); [ Recover all ] |
| Triggered by |
HAMAP; MF_00027 (Get profile general information and statistics) |
Propagated annotation
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Identifier, protein and gene names
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| case <OC:Hyphomicrobiales> or <OC:Rhodobacterales> or <OC:Pseudomonadales> or <OC:Actinomycetota> | |
| Identifier | COBB |
| Protein name | RecName: Full=Hydrogenobyrinate a,c-diamide synthase; EC=6.3.5.9; AltName: Full=Hydrogenobyrinic acid a,c-diamide synthase; |
| Gene name | Name=cobB; |
| else case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanomicrobia> or <OC:Methanopyri> | |
| Identifier | CBIA |
| Protein name | RecName: Full=Cobyrinate a,c-diamide synthase; EC=6.3.5.11; AltName: Full=Cobyrinic acid a,c-diamide synthetase; AltName: Full=Ni-sirohydrochlorin a,c-diamide synthase; EC=6.3.5.12; AltName: Full=Ni-sirohydrochlorin a,c-diamide synthetase; |
| Gene name | Name=cbiA; Synonyms=cfbB; |
| else | |
| Identifier | CBIA |
| Protein name | RecName: Full=Cobyrinate a,c-diamide synthase; EC=6.3.5.11; AltName: Full=Cobyrinic acid a,c-diamide synthetase; |
| Gene name | Name=cbiA; |
| end case | |
Comments
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| case <OC:Hyphomicrobiales> or <OC:Rhodobacterales> or <OC:Pseudomonadales> or <OC:Actinomycetota> | |
| FUNCTION | Catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of hydrogenobyrinate, using either L- glutamine or ammonia as the nitrogen source. |
| CATALYTIC ACTIVITY | Reaction=2 ATP + 2 H2O + hydrogenobyrinate + 2 L-glutamine = 2 ADP + 2 H(+) + hydrogenobyrinate a,c-diamide + 2 L-glutamate + 2 phosphate; Xref=Rhea:RHEA:12544, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58359, ChEBI:CHEBI:77873, ChEBI:CHEBI:77874, ChEBI:CHEBI:456216; EC=6.3.5.9; |
| PATHWAY | Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from precorrin-2 (aerobic route): step 9/10. |
| DOMAIN | 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 hydrogenobyrinate 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. |
| MISCELLANEOUS | The a and c carboxylates of hydrogenobyrinate are activated for nucleophilic attack via formation of a phosphorylated intermediate by ATP. CobB catalyzes first the amidation of the c- carboxylate, and then that of the a-carboxylate. |
| else case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanomicrobia> or <OC:Methanopyri> | |
| FUNCTION | 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. Involved in the biosynthesis of the unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which plays a key role in methanogenesis and anaerobic methane oxidation. Catalyzes the ATP- dependent amidation of the two carboxylate groups at positions a and c of Ni-sirohydrochlorin, using L-glutamine or ammonia as the nitrogen source. |
| CATALYTIC ACTIVITY | Reaction=2 ATP + cob(II)yrinate + 2 H2O + 2 L-glutamine = 2 ADP + cob(II)yrinate a,c diamide + 2 H(+) + 2 L-glutamate + 2 phosphate; Xref=Rhea:RHEA:26289, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58359, ChEBI:CHEBI:58537, ChEBI:CHEBI:58894, ChEBI:CHEBI:456216; EC=6.3.5.11; |
| CATALYTIC ACTIVITY | Reaction=2 ATP + 2 H2O + 2 L-glutamine + Ni-sirohydrochlorin = 2 ADP + 2 H(+) + 2 L-glutamate + Ni-sirohydrochlorin a,c-diamide + 2 phosphate; Xref=Rhea:RHEA:52896, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58359, ChEBI:CHEBI:136841, ChEBI:CHEBI:136887, ChEBI:CHEBI:456216; EC=6.3.5.12; |
| PATHWAY | Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 10/10. |
| DOMAIN | 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 or Ni-sirohydrochlorin, 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. |
| MISCELLANEOUS | The a and c carboxylates of cobyrinate and Ni- sirohydrochlorin 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. |
| else | |
| FUNCTION | 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. |
| CATALYTIC ACTIVITY | Reaction=2 ATP + cob(II)yrinate + 2 H2O + 2 L-glutamine = 2 ADP + cob(II)yrinate a,c diamide + 2 H(+) + 2 L-glutamate + 2 phosphate; Xref=Rhea:RHEA:26289, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58359, ChEBI:CHEBI:58537, ChEBI:CHEBI:58894, ChEBI:CHEBI:456216; EC=6.3.5.11; |
| PATHWAY | Cofactor biosynthesis; adenosylcobalamin biosynthesis; cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route): step 10/10. |
| DOMAIN | 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. |
| MISCELLANEOUS | 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. |
| end case | |
| COFACTOR | Name=Mg(2+); Xref=ChEBI:CHEBI:18420; |
| SIMILARITY | Belongs to the CobB/CbiA family. |
Keywords
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| Cobalamin biosynthesis | |
| Glutamine amidotransferase | |
| ATP-binding | |
| Nucleotide-binding | |
| Ligase | |
| Magnesium | |
| case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanomicrobia> or <OC:Methanopyri> | |
| Methanogenesis | |
| end case | |
Gene Ontology
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| GO:0005524; Molecular function:ATP binding | |
| case <OCellular component:Hyphomicrobiales> or <OC:Rhodobacterales> or <OC:Pseudomonadales> or <OC:Actinomycetota> | |
| GO:0043802; Molecular function:hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) activity | |
| else; https://www.ebi.ac.uk/QuickGO/term/else | |
| GO:0042242; Molecular function:cobyrinic acid a,c-diamide synthase activity | |
| end case | |
| GO:0009236; Biological process:cobalamin biosynthetic process | |
Cross-references
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| Pfam | PF01656; CbiA; 1; |
| Pfam | PF07685; GATase_3; 1; |
| NCBIfam | TIGR00379; CobB; 1; |
| PROSITE | PS51274; GATASE_COBBQ; 1; |
Features
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| From: COBB_SINSX (P21632) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| ACT_SITE | 326 | 326 | /note="Nucleophile" | C | ||||||||
| SITE | 426 | 426 | /note="Increases nucleophilicity of active site Cys" | H | ||||||||
Additional information
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| Size range | 429-486 amino acids |
| Related rules |
MF_00028 |
| Fusion | Nter: None Cter: None |