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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1dak

E.C. namedethiobiotin synthase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 6.3.3.3
CSA Homologues of 1dakThere are 15 Homologs
CSA Entries With UniProtID P13000
CSA Entries With EC Number 6.3.3.3
PDBe Entry 1dak
PDBSum Entry 1dak
MACiE Entry M0074

Literature Report

IntroductionDethiobiotin synthase is the penultimate enzyme in the biotin synthesis pathway in E. coli and other microorganisms. The enzyme catalyses the formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanic acid (DAPA) and carbon dioxide. The enzyme requires ATP and divalent cations as cofactors. The enzyme represents a third enzymatic mechanism for carboxylation reactions, after the biotin-dependent carboxylases and ribulose-bisphosphate carboxylase.
MechansimDetailed mechanistic information is sparse. However, speculations can be made on the basis of site-directed mutagenesis and crystal structures. The first step in the reaction is the formation of a carbamate of the substrate DAPA. Evidence is conflicting over whether this is on the N7 or N8 position of the substrate. The second step is the formation of a carbamic-phosphoric mixed anhydride as a second intermediate, followed by ring closure. This is most likely to occur via nucleophilic attack of the activated carbamate with a substrate nitrogen, with release of inorganic phosphate.
Reaction

Catalytic Sites for 1dak

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA1516macie:sideChain
LysA3738macie:sideChain
ThrA1112macie:sideChain
SerA4142macie:sideChain

Literature References

Notes:
Käck H
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Proc Natl Acad Sci U S A 1998 95 5495-5500
PubMed: 9576910
Yang G
Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties.
Biochemistry 1997 36 4751-4760
PubMed: 9125495
Käck H
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
Protein Sci 1998 7 2560-2566
PubMed: 9865950
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