PDBsum entry 3fmi

Ligase

PDB id: 3fmi

Contents

Protein chains

231 a.a. *

Ligands

SO4 ×4

KAP ×3

Waters ×210

* Residue conservation analysis

PDB id:

3fmi

Name:

Ligase

Title:

Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase complexed with 7-keto 8-aminopelargonic acid

Structure:

Dethiobiotin synthetase. Chain: a, b, c, d. Synonym: dtb synthetase, dtbs. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: h37rv. Gene: biod, mt1621, mtcy336.33c, rv1570. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.18Å R-factor: 0.216 R-free: 0.264

Authors:

S.Dey,J.C.Sacchettini

Key ref:

S.Dey et al. (2010). Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Biochemistry, 49, 6746-6760. PubMed id: 20565114

Date:

22-Dec-08 Release date: 30-Jun-09

Protein chains

P9WPQ5  (BIOD_MYCTU) -  Dethiobiotin synthetase BioD from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 226 a.a.

Struc: 231 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.6.3.3.3 - dethiobiotin synthase.
• Reaction: (7R,8S)-7,8-diammoniononanoate + CO2 + ATP = (4R,5S)-dethiobiotin + ADP + phosphate + 3 H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Biochemistry 49:6746-6760 (2010)

PubMed id: 20565114

Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .

S.Dey, J.M.Lane, R.E.Lee, E.J.Rubin, J.C.Sacchettini.

ABSTRACT

Mycobacterium tuberculosis (Mtb) depends on biotin synthesis for survival during infection. In the absence of biotin, disruption of the biotin biosynthesis pathway results in cell death rather than growth arrest, an unusual phenotype for an Mtb auxotroph. Humans lack the enzymes for biotin production, making the proteins of this essential Mtb pathway promising drug targets. To this end, we have determined the crystal structures of the second and third enzymes of the Mtb biotin biosynthetic pathway, 7,8-diaminopelargonic acid synthase (DAPAS) and dethiobiotin synthetase (DTBS), at respective resolutions of 2.2 A and 1.85 A. Superimposition of the DAPAS structures bound either to the SAM analog sinefungin or to 7-keto-8-aminopelargonic acid (KAPA) allowed us to map the putative binding site for the substrates and to propose a mechanism by which the enzyme accommodates their disparate structures. Comparison of the DTBS structures bound to the substrate 7,8-diaminopelargonic acid (DAPA) or to ADP and the product dethiobiotin (DTB) permitted derivation of an enzyme mechanism. There are significant differences between the Mtb enzymes and those of other organisms; the Bacillus subtilis DAPAS, presented here at a high resolution of 2.2 A, has active site variations and the Escherichia coli and Helicobacter pylori DTBS have alterations in their overall folds. We have begun to exploit the unique characteristics of the Mtb structures to design specific inhibitors against the biotin biosynthesis pathway in Mtb.