› 1dag

X-ray diffraction
1.64Å resolution

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID AND 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE

Released:
DOI: 10.2210/pdb1dag/pdb
PDB entry 1dag coloured by chain, front view.
PDB entry 1dag coloured by chain, side view.
PDB entry 1dag coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate.
Huang W, Jia J, Gibson KJ, Taylor WS, Rendina AR, Schneider G, Lindqvist Y
Biochemistry 34 10985-95 (1995)
PMID: 7669756

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

2 bound ligands:
Ligand DSD 1 x DSD
Ligand ACP 1 x ACP
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2
Unit cell:
a: 73.2Å b: 49.2Å c: 61.8Å
α: 90° β: 107.1° γ: 90°
R-values:
R R work R free
0.18 0.18 not available
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

1 mention without citation

Nanosilicon-Based Composites for (Bio)sensing Applications: Current Status, Advantages, and Perspectives.
Myndrul et al. (2019)