› 1dam

X-ray diffraction
1.8Å resolution

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM

Released:
DOI: 10.2210/pdb1dam/pdb
PDB entry 1dam coloured by chain, front view.
PDB entry 1dam coloured by chain, side view.
PDB entry 1dam coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
Käck H, Sandmark J, Gibson KJ, Schneider G, Lindqvist Y
Protein Sci 7 2560-6 (1998)
PMID: 9865950

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 MG 2 x MG
Ligand PO4 1 x PO4
Ligand ADP 1 x ADP
Ligand DTB 1 x DTB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 72.7Å b: 48.9Å c: 61.1Å
α: 90° β: 106.7° γ: 90°
R-values:
R R work R free
0.18 0.18 0.233
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structural enzymology of biotin biosynthesis.
Schneider et al. (2001)
8 other articles

4 mentions without citation

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development.
Sharon et al. (2019)
3 more