1LGF

Crystal structure of OxyB, a Cytochrome P450 Implicated in an Oxidative Phenol Coupling Reaction During Vancomycin Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of OxyB, a Cytochrome P450 Implicated in an Oxidative Phenol Coupling Reaction during Vancomycin Biosynthesis.

Zerbe, K.Pylypenko, O.Vitali, F.Zhang, W.Rouset, S.Heck, M.Vrijbloed, J.W.Bischoff, D.Bister, B.Sussmuth, R.D.Pelzer, S.Wohlleben, W.Robinson, J.A.Schlichting, I.

(2002) J.Biol.Chem. 277: 47476-47485

  • DOI: 10.1074/jbc.M206342200
  • Primary Citation of Related Structures:  1LFK, 1LG9

  • PubMed Abstract: 
  • Gene-inactivation studies point to the involvement of OxyB in catalyzing the first oxidative phenol coupling reaction during glycopeptide antibiotic biosynthesis. The oxyB gene has been cloned and sequenced from the vancomycin producer Amycolatopsis ...

    Gene-inactivation studies point to the involvement of OxyB in catalyzing the first oxidative phenol coupling reaction during glycopeptide antibiotic biosynthesis. The oxyB gene has been cloned and sequenced from the vancomycin producer Amycolatopsis orientalis, and the hemoprotein has been produced in Escherichia coli, crystallized, and its structure determined to 1.7-A resolution. OxyB gave UV-visible spectra characteristic of a P450-like hemoprotein in the low spin ferric state. After reduction to the ferrous state by dithionite or by spinach ferredoxin and ferredoxin reductase, the CO-ligated form gave a 450-nm peak in a UV-difference spectrum. Addition of putative heptapeptide substrates to resting OxyB produced type I changes to the UV spectrum, but no turnover was observed in the presence of ferredoxin and ferredoxin reductase, showing that either the peptides or the reduction system, or both, are insufficient to support a full catalytic cycle. OxyB exhibits the typical P450-fold, with helix L containing the signature sequence FGHGXHXCLG and Cys(347) being the proximal axial thiolate ligand of the heme iron. The structural similarity of OxyB is highest to P450nor, P450terp, CYP119, and P450eryF. In OxyB, the F and G helices are rotated out of the active site compared with P450nor, resulting in a much more open active site, consistent with the larger size of the presumed heptapeptide substrate.


    Related Citations: 
    • The Biosynthesis of Vancomycin-Type Glycopeptide Antibiotics - The Order of the Cyclization Steps
      Bischoff, D.,Pelzer, S.,Bister, B.,Nicholson, G.J.,Stockert, S.,Schirle, M.,Wohlleben, W.,Jung, G.,Suessmuth, R.D.
      (2001) Angew.Chem.Int.Ed.Engl. 40: 4688


    Organizational Affiliation

    Institute of Organic Chemistry, University of Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P450 monooxygenase
A
398Amycolatopsis orientalisGene Names: cyp165B3 (oxyB)
EC: 1.14.-.-
Find proteins for Q8RN04 (Amycolatopsis orientalis)
Go to UniProtKB:  Q8RN04
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.700α = 90.00
b = 60.100β = 122.90
c = 90.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing
ProDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description