› 6e06

X-ray diffraction
2.5Å resolution

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine triphosphate solved by precipitant-ligand exchange (crystals grown in citrate precipitant)

Released:
DOI: 10.2210/pdb6e06/pdb
PDB entry 6e06 coloured by chain, front view.
PDB entry 6e06 coloured by chain, side view.
PDB entry 6e06 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase.
Thompson AP, Wegener KL, Booker GW, Polyak SW, Bruning JB
Acta Crystallogr D Struct Biol 74 965-972 (2018)
PMID: 30289406

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

Assembly composition:
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: 235 amino acids
Theoretical weight: 23.47 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P9WPQ5 (Residues: 2-226; Coverage: 100%)
Gene names: MTCY336.33c, Rv1570, bioD
Sequence domains: AAA domain
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand CTP 4 x CTP
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE D03B-MX1
Spacegroup: P212121
Unit cell:
a: 56.68Å b: 105.7Å c: 153.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.217 0.288
Expression system: Escherichia coli BL21

Quick links

Citations

1 citations in other articles

Explicit molecular dynamics simulation studies to discover novel natural compound analogues as Mycobacterium tuberculosis inhibitors.
Rampogu et al. (2023)