› 4c3y

X-ray diffraction
2.3Å resolution

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione

Released:
DOI: 10.2210/pdb4c3y/pdb
PDB entry 4c3y coloured by chain, front view.
PDB entry 4c3y coloured by chain, side view.
PDB entry 4c3y coloured by chain, top view.
Source organism: Rhodococcus erythropolis
Primary publication:
Crystal structure and site-directed mutagenesis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism.
Rohman A, van Oosterwijk N, Thunnissen AM, Dijkstra BW
J Biol Chem 288 35559-68 (2013)
PMID: 24165124

Function and Biology Details

Reaction catalysed: 
A 3-oxosteroid + acceptor = a 3-oxo-Delta(1)-steroid + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193120 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
FAD-dependent oxidoreductase 2 FAD binding domain-containing protein Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 530 amino acids
Theoretical weight: 55.26 KDa
Source organism: Rhodococcus erythropolis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9RA02 (Residues: 1-510; Coverage: 100%)
Gene names: BS297_24040, kstD1
Sequence domains: FAD binding domain
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 8 x FAD
3 bound ligands:
Ligand NA 4 x NA
Ligand PG4 6 x PG4
Ligand ANB 8 x ANB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 107.747Å b: 132.142Å c: 363.597Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.21 0.249
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

Steroids as Environmental Compounds Recalcitrant to Degradation: Genetic Mechanisms of Bacterial Biodegradation Pathways.
Olivera et al. (2019)
2 more

4 mentions without citation

Crystal structure and site-directed mutagenesis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism.
Rohman et al. (2013)
3 more