Enzyme - Dethiobiotin synthase

Alternative Name(s)
  • DTB synthetase.

Catalytic Activity

7,8-diaminononanoate + ATP + CO2 = ADP + dethiobiotin + 3 H(+) + phosphate


There are no Cofactors for this Enzyme

Reaction Mechanism

    Dethiobiotin 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.

    Detailed 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.
    Catalytic Residues
    AA Uniprot Uniprot Resid PDB PDB Resid
    Thr P13000 12 1bs1 11
    Lys P13000 38 1bs1 37
    Lys P13000 16 1bs1 15
    Ser P13000 42 1bs1 41
    Asp P13000 55 1bs1 54
    Thr P13000 17 1bs1 16
    Glu P13000 13 1bs1 12
    Ser P13000 42 1bs1 41
    Glu P13000 116 1bs1 115
    Step Components

    dephosphorylation, intermediate formation, intermediate terminated, bimolecular nucleophilic addition, intramolecular nucleophilic addition, proton transfer, cyclisation, overall reactant used, unimolecular elimination by the conjugate base, bimolecular nucleophilic substitution, intermediate collapse, overall product formed

    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.


    The products of the reaction.

Reaction Parameters

  • Kinetic Parameters
    Organism KM Value [mM] Substrate Comment
    Mycobacterium tuberculosis 0.002 7,8-diaminononanoate pH 7.5, temperature not specified in the publication
    Lysinibacillus sphaericus 0.045 7,8-diaminononanoate
  • Temperature

    There are no reaction parameters information for this Enzyme.

  • pH

    There are no reaction parameters information for this Enzyme.

Associated Proteins

Protein name Organism
ATP-dependent dethiobiotin synthetase BioD Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
ATP-dependent dethiobiotin synthetase BioD 1 Escherichia coli (strain K12)
Dethiobiotin synthetase Baker's yeast
ATP-dependent dethiobiotin synthetase BioD 2 Escherichia coli (strain K12)
Biotin biosynthesis bifunctional protein BioCD Bordetella avium (strain 197N)