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HAMAP rule MF_00027

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General rule information [?]

Accession MF_00027
Dates 1-JUN-2001 (Created)
13-JAN-2023 (Last updated, Version 33)
Name CobB/CbiA
Scope
Bacteria
Archaea
Templates P29946 (CBIA_SALTY); P21632 (COBB_SINSX); Q8TK00 (CBIA_METAC); Q46FL0 (CBIA_METBF): [Recover all]
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

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
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
cbiA, 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
cbiA
end case

Comments [?]

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 RHEA:12544: 2 ATP + 2 H2O + hydrogenobyrinate + 2 L-glutamine = 2 ADP + 2 H(+) + hydrogenobyrinate a,c-diamide + 2 L-glutamate + 2 phosphate
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 RHEA:26289: 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
EC 6.3.5.11
RHEA:52896: 2 ATP + 2 H2O + 2 L-glutamine + Ni-sirohydrochlorin = 2 ADP + 2 H(+) + 2 L-glutamate + Ni-sirohydrochlorin a,c-diamide + 2 phosphate
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 RHEA:26289: 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
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 Mg(2+)
Similarity Belongs to the CobB/CbiA family.

Keywords [?]

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 [?]

GO:0005524; Molecular function: ATP binding.
case <OC:Hyphomicrobiales> or <OC:Rhodobacterales> or <OC:Pseudomonadales> or <OC:Actinomycetota>
GO:0043802; Molecular function: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) activity.
else
GO:0042242; Molecular function: cobyrinic acid a,c-diamide synthase activity.
end case
GO:0009236; Biological process: cobalamin biosynthetic process.

Cross-references [?]

Pfam PF01656; CbiA; 1;
PF07685; GATase_3; 1;
TIGRFAMs TIGR00379; CobB; 1;
PROSITE PS51274; GATASE_COBBQ; 1; trigger=PRU00606;

Features [?]

From: COBB_SINSX (P21632)
Key     From     To       Description   Tag   Condition   FTGroup
ACT_SITE     326     326       Nucleophile     C  
SITE     426     426       Increases nucleophilicity of active site Cys     H  

Additional information [?]

Size range 429-486 amino acids
Related rules MF_00028 (COBQ)
Fusion None


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