Overview for MACiE Entry M0074
EC Number: 18.104.22.168 (A member of the Ligases, Forming carbon-nitrogen bonds, Cyclo-ligases)
Enzyme Name: dethiobiotin synthase
Biological Species: Escherichia coli (Bacteria)
Catalytic Chain UniprotKB Accession Codes:
- P13000 - ATP-dependent dethiobiotin synthetase BioD 1
Representative PDB Code: 1bs1 - DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANICPHOSPHATE AND MAGNESIUM (Resolution = 1.80 Å).
Catalytic CATH Codes:
- 22.214.171.1240 - P-loop containing nucleotide triphosphate hydrolases
Display structure information
Overall Comment: Mg(II) can be replaced by any divalent metal ion.
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Stepwise Description of the Reaction
|Step 1||Water deprotonates the 7,8-diaminononanoate substrate, activating it for a nucleophilic attack upon the carbon dioxide in an addition reaction. Lys37 stabilises the formation of the negatively charged intermediate.|
|Step 2||The carboxylated intermediate acts as a nucleophile and attacks the gamma phosphate of ATP in a substitution reaction. Lys37, Lys15 and two Mg(II) ions stabilise the intermediates.|
|Step 3||The newly attached phosphate group deprotonates the terminal primary amine, which in turn acts as a nucleophile to attack the phosphorylated carbonyl carbon in an internal addition reaction. Lys37, Lys15 and the main chain amide of Ser41 all stabilise the intermediates.|
|Step 4||The oxyanion formed re-forms the carbonyl group, cleaving the P-O bond in a conjugate base elimination reaction. The leaving phosphate group deprotonates the newly formed secondary amine. Lys15, Lys37 and the main chain amide of Ser41 all stabilise the intermediates.|
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Catalytic Residues Involved
||Location of Function
||Main Chain Amide
Metal Cofactors for M0074
- G. Yang et al. (1997), Biochemistry, 36, 4751-4760. Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties.
- H. Kack et al. (1998), Proc. Natl Acad. Sci. USA, 95, 5495-5500. Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
- H. Kack et al. (1998), Protein Sci., 7, 2560-2566. Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate.
Homologue information for M0074 (1bs1)
MACiE Homologues (within the PDB)
MACiE Homologues (within UniprotKB/SwissProt)
Entries with at least one Catalytic CATH code in common (different mechanisms):
|M0212 ||nitrogenase |
|M0290 ||adenylate kinase |
|M0154 ||estrone sulfotransferase |
|M0178 ||H+-transporting two-sector ATPase |
View a comparison of the other reactions in MACiE with the CATH domain 126.96.36.1990
Links to this entry in other databases