› 3fpa

X-ray diffraction
2.3Å resolution

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with dethiobiotin and phosphate

Released:
DOI: 10.2210/pdb3fpa/pdb
PDB entry 3fpa coloured by chain, front view.
PDB entry 3fpa coloured by chain, side view.
PDB entry 3fpa coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .
Dey S, Lane JM, Lee RE, Rubin EJ, Sacchettini JC
Biochemistry 49 6746-60 (2010)
PMID: 20565114

Function and Biology Details

Reaction catalysed: 
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-162006 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dethiobiotin synthetase BioD Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 251 amino acids
Theoretical weight: 25.33 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WPQ5 (Residues: 1-226; Coverage: 100%)
Gene names: MTCY336.33c, Rv1570, bioD
Sequence domains: AAA domain
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

3 bound ligands:
Ligand PO4 8 x PO4
Ligand DTB 3 x DTB
Ligand MG 4 x MG
1 modified residue:
Ligand CSX 4 x CSX

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 55.128Å b: 104.453Å c: 151.133Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.205 0.26
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Closing in on complete pathways of biotin biosynthesis.
Lin et al. (2011)
6 more

2 mentions without citation

Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .
Dey et al. (2010)
1 more