Cofactors

There are no Cofactors for this Enzyme

Reaction Mechanism

dethiobiotin synthase By Reference

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.




• Summary
• Step 1
• Step 2
• Step 3
• Step 4
• Products

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.



Products.

The products of the reaction.

View Reaction Mechanisms in M-CSA

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

Citations

• Inhibition of Mycobacterium tuberculosis Dethiobiotin Synthase (MtDTBS): Toward Next-Generation Antituberculosis Agents.
• Dethiobiotin uptake and utilization by bacteria possessing bioYB operon.
• Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ.
• Explicit molecular dynamics simulation studies to discover novel natural compound analogues as Mycobacterium tuberculosis inhibitors.
• Meta-learning approach for bacteria classification and identification of informative genes of the Bacillus megaterium: tomato roots tissue interaction.
• Mechanisms of low susceptibility to the disinfectant benzalkonium chloride in a multidrug-resistant environmental isolate of Aeromonas hydrophila.
• Metabolomics reveals the response of hydroprimed maize to mitigate the impact of soil salinization.
• A conserved and seemingly redundant Escherichia coli biotin biosynthesis gene expressed only during anaerobic growth.
• Cryo-EM structure of the plant nitrate transporter AtCLCa reveals characteristics of the anion-binding site and the ATP-binding pocket.
• Combining transcriptomics and metabolomics to identify key response genes for aluminum toxicity in the root system of Brassica napus L. seedlings.
• Structure of ATP-dependent carboxylase, dethiobiotin synthase.