› 3a4g

X-ray diffraction
1.75Å resolution

Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (trigonal crystal form)

Released:
DOI: 10.2210/pdb3a4g/pdb
PDB entry 3a4g coloured by chain, front view.
PDB entry 3a4g coloured by chain, side view.
PDB entry 3a4g coloured by chain, top view.
Source organism: Pseudonocardia autotrophica
Primary publication:
Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 vitamin D3 hydroxylase.
Yasutake Y, Fujii Y, Nishioka T, Cheon WK, Arisawa A, Tamura T
J Biol Chem 285 31193-201 (2010)
PMID: 20667833

Function and Biology Details

Reaction catalysed: 
(1a) 5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol + 2 reduced adrenodoxin + 2 H(+) + O(2) = (25R)-5-beta-cholestane-3-alpha,7-alpha,12-alpha,26-tetraol + 2 oxidized adrenodoxin + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111277 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vitamin D(3) 25-hydroxylase Chain: A
Molecule details ›
Chain: A
Length: 411 amino acids
Theoretical weight: 45.49 KDa
Source organism: Pseudonocardia autotrophica
Expression system: Rhodococcus erythropolis
UniProt:
  • Canonical: C4B644 (Residues: 1-403; Coverage: 100%)
Gene name: vdh
Sequence domains: Cytochrome P450
Structure domains: Cytochrome P450

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM
1 bound ligand:
Ligand PG0 1 x PG0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P31
Unit cell:
a: 61.675Å b: 61.675Å c: 98.799Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.185 0.236
Expression system: Rhodococcus erythropolis

Quick links

Citations

5 review citations

Diversity of P450 enzymes in the biosynthesis of natural products.
Podust et al. (2012)
4 more

7 mentions without citation

Cytochrome P450-mediated metabolism of vitamin D.
Jones et al. (2014)
6 more