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PROSITE documentation PDOC51274 [for PROSITE entry PS51274]

CobBQ-type GATase domain profile





Description

Vitamin B12 (cobalamin) is an essential nutrient that serves as a co-factor for enzymatic reactions. The biosynthesis of this coenzyme is a complex process that is confined to certain prokaryotes and requires circa 25 different enzymes. During the assembly, six amide groups are introduced at the a, b, c, d, e and g carboxylates. In the aerobic and anaerobic biosynthetic pathways, the six amidation steps are carried out by two seperate enzymes. Cobyrinic acid a,c-diamide synthethase (cbiA and cobB) is responsible for the introduction of the two amide groups at the a and c positions in either cobyrinic acid or hydrogenobrynic acid. The amidation of the b, d, e, and g carboxylate groups in adenosyl-Cob(I)yrinic acid a,c-diamide is catalyzed by cobyric acid synthetase (cbiP and cobQ). Many of the enzymatic reactions for the aerobic biosynthesis of cobalamin are known for Pseudomonas denitrificans. The anaerobic pathway is found in other bacteria and archaea, such as Salmonella typhimurium, Bacillus megaterium, Methanococcus jannaschii and Propionibacterium freudenreichii [1].

The cobB and cobQ family proteins contain two separate domains involved in cobalamin biosynthesis, i.e. a synthetase domain including ATP-binding motifs in the N-terminal part and a glutamine amidotransferase (GATase) domain in the C-terminal part. The GATase domain is involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to an acceptor. This domain resembles the GATases of class I, which are characterized by a conserved Cys-His-Glu active site (see <PDOC00405>), but the cobBQ-type GATases lack the Glu residue in this typical triad [2,3]. The cobBQ-type GATase domain shows also similarity to other GATase type 1 related domains/families, like PdxT/SNO (see <PDOC00950>), γ-glutamyl hydrolase (see <PDOC51275>) and PfpI endopeptidase (see <PDOC51276>).

Some proteins known to contain a cobBQ-type GATase domain:

  • Salmonella typhimurium cobyrinic acid a,c-diamide synthase (cbiA), which is responsible for the amidation of carboxylic groups at positions a and c of either cobyrinic acid or hydrogenobrynic acid.
  • Pseudomonas denitrificans cobyrinic acid a,c-diamide synthase (cobB), which is responsible for the amidation of carboxylic groups at positions a and c of either cobyrinic acid or hydrogenobrynic acid.
  • Salmonella typhimurium cobyric acid synthase (cbiP), which catalyzes amidations at positions b, d, e, and g on adenosylcobyrinic a,c-diamide.
  • Pseudomonas denitrificans cobyric acid synthase (cobQ), which catalyzes amidations at positions b, d, e, and g on adenosylcobyrinic a,c-diamide.

The profile we developed covers the entire cobBQ-type GATase domain.

Note:

The cobBQ-type GATase domain profile is in competition with profiles of related domains, which include GATase type 1 (see <PDOC00405>) and pdxT/SNO (see <PDOC00950>).

Last update:

December 2006 / First entry.

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Technical section

PROSITE method (with tools and information) covered by this documentation:

GATASE_COBBQ, PS51274; CobBQ-type GATase domain profile  (MATRIX)


References

1AuthorsFresquet V. Williams L. Raushel F.M.
TitleMechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2.
SourceBiochemistry 43:10619-10627(2004).
PubMed ID15311923
DOI10.1021/bi048972x

2AuthorsMassiere F. Badet-Denisot M.A.
TitleThe mechanism of glutamine-dependent amidotransferases.
SourceCell. Mol. Life Sci. 54:205-222(1998).
PubMed ID9575335

3AuthorsGalperin M.Y. Grishin N.V.
TitleThe synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase.
SourceProteins 41:238-247(2000).
PubMed ID10966576
DOI10.1002/1097-0134(20001101)41:2<238::AID-PROT80>3.0.CO;2-L



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