› 3mgx

X-ray diffraction
2.1Å resolution

Crystal Structure of P450 OxyD that is involved in the Biosynthesis of Vancomycin-type Antibiotics

Released:
DOI: 10.2210/pdb3mgx/pdb
PDB entry 3mgx coloured by chain, front view.
PDB entry 3mgx coloured by chain, side view.
PDB entry 3mgx coloured by chain, top view.
Source organism: Amycolatopsis balhimycina
Primary publication:
Structural characterization of OxyD, a cytochrome P450 involved in beta-hydroxytyrosine formation in vancomycin biosynthesis.
Cryle MJ, Meinhart A, Schlichting I
J Biol Chem 285 24562-74 (2010)
PMID: 20519494

Function and Biology Details

Reaction catalysed: 
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188033 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative P450 monooxygenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 415 amino acids
Theoretical weight: 45.38 KDa
Source organism: Amycolatopsis balhimycina
Expression system: Escherichia coli
UniProt:
  • Canonical: Q939Y1 (Residues: 1-396; Coverage: 100%)
Gene name: oxyD
Sequence domains: Cytochrome P450
Structure domains: Cytochrome P450

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
1 bound ligand:
Ligand GOL 10 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 65.85Å b: 61.05Å c: 100.64Å
α: 90° β: 102.48° γ: 90°
R-values:
R R work R free
0.209 0.208 0.233
Expression system: Escherichia coli

Quick links

Citations

12 review citations

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

5 mentions without citation

Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions.
Jaremko et al. (2020)
4 more