› 2x9p

X-ray diffraction
2.1Å resolution

X-ray structure of the substrate-free cytochrome P450 PimD - a polyene macrolide antibiotic pimaricin epoxidase

Released:
DOI: 10.2210/pdb2x9p/pdb
PDB entry 2x9p coloured by chain, front view.
PDB entry 2x9p coloured by chain, side view.
PDB entry 2x9p coloured by chain, top view.
Source organism: Streptomyces natalensis
Primary publication:
Structure of cytochrome P450 PimD suggests epoxidation of the polyene macrolide pimaricin occurs via a hydroperoxoferric intermediate.
Kells PM, Ouellet H, Santos-Aberturas J, Aparicio JF, Podust LM
Chem Biol 17 841-51 (2010)
PMID: 20797613

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190211 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
PimD protein Chain: A
Molecule details ›
Chain: A
Length: 404 amino acids
Theoretical weight: 44.53 KDa
Source organism: Streptomyces natalensis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9EW92 (Residues: 5-397; Coverage: 99%)
Gene name: pimD
Sequence domains: Cytochrome P450
Structure domains: Cytochrome P450

Ligands and Environments

2 bound ligands:
Ligand HEM 1 x HEM
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2221
Unit cell:
a: 118.603Å b: 139.38Å c: 70.041Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.239
Expression system: Escherichia coli

Quick links

Citations

7 review citations

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

4 mentions without citation

Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function.
Rudolf et al. (2017)
3 more