1OXA | pdb_00001oxa

CYTOCHROME P450 (DONOR:O2 OXIDOREDUCTASE)

• PDB DOI: https://doi.org/10.2210/pdb1OXA/pdb

• Classification: OXIDOREDUCTASE (OXYGENASE)
• Organism(s): Saccharopolyspora erythraea
• Mutation(s): No 


• Deposited: 1995-07-14 Released: 1995-12-07 
• Deposition Author(s): Cupp-Vickery, J.R., Poulos, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Structure of cytochrome P450eryF involved in erythromycin biosynthesis.

Cupp-Vickery, J.R., Poulos, T.L.

(1995) Nat Struct Biol 2: 144-153

• PubMed: 7749919 
• DOI: https://doi.org/10.1038/nsb0295-144
• Primary Citation Related Structures: 
  1OXA


• PubMed Abstract: 
  

  Cytochrome P450eryF catalyzes the 6S-hydroxylation of 6-deoxyerythronolide B, the initial reaction in a multistep pathway to convert 6-deoxyerythronolide B into the antibiotic, erythromycin. The overall structure of P450eryF is similar to that of P450cam but differs in the exact positioning of several alpha-helices. The largest difference occurs in the B' helix and results in the enlargement of the substrate-binding pocket of P450eryF. The substrate is positioned with the macrolide ring perpendicular to the haem plane and contacts seven hydrophobic residues and three solvent molecules. The substrate participates in a network of hydrogen bonds that may provide a proton shuttle pathway in the oxygen cleavage reaction.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, University of California, Irvine 92717, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.52 kDa 
• Atom Count: 3,450 
• Modeled Residue Count: 403 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 ERYF	A	403	Saccharopolyspora erythraea	Mutation(s): 0  EC: 1.14.15.35
UniProt
Find proteins for Q00441 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)) Explore Q00441  Go to UniProtKB:  Q00441

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DEB	C [auth A]	6-DEOXYERYTHRONOLIDE B C21 H38 O6 HQZOLNNEQAKEHT-IBBGRPSASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.16	α = 90
b = 79.67	β = 90
c = 99.48	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
SDMS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-12-07 
Deposition Author(s): Cupp-Vickery, J.R., Poulos, T.L.

Revision History  

• Version 1.0: 1995-12-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other