› 1dak

X-ray diffraction
1.6Å resolution

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE

Released:
DOI: 10.2210/pdb1dak/pdb
PDB entry 1dak coloured by chain, front view.
PDB entry 1dak coloured by chain, side view.
PDB entry 1dak coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Käck H, Gibson KJ, Lindqvist Y, Schneider G
Proc Natl Acad Sci U S A 95 5495-500 (1998)
PMID: 9576910

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146426 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ATP-dependent dethiobiotin synthetase BioD 1 Chain: A
Molecule details ›
Chain: A
Length: 224 amino acids
Theoretical weight: 24.03 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P13000 (Residues: 2-225; Coverage: 100%)
Gene names: JW0761, b0778, bioD1
Sequence domains: CobQ/CobB/MinD/ParA nucleotide binding domain
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

4 bound ligands:
Ligand PO4 1 x PO4
Ligand MG 2 x MG
Ligand DPU 1 x DPU
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID09
Spacegroup: C2
Unit cell:
a: 72.68Å b: 48.19Å c: 61.07Å
α: 90° β: 106.58° γ: 90°
R-values:
R R work R free
0.184 0.184 0.21
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production.
Streit et al. (2003)
3 more

3 mentions without citation

Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
Käck et al. (1998)
2 more