1DCC

2.2 ANGSTROM STRUCTURE OF OXYPEROXIDASE: A MODEL FOR THE ENZYME:PEROXIDE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

2.2 A structure of oxy-peroxidase as a model for the transient enzyme: peroxide complex.

Miller, M.A.Shaw, A.Kraut, J.

(1994) Nat Struct Biol 1: 524-531

  • DOI: 10.1038/nsb0894-524
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Fe+3-OOH complex of peroxidases has a very short half life, and its structure cannot be determined by conventional methods. The Fe+2-O2 complex provides a useful structural model for this intermediate, as it differs by only one electron and one p ...

    The Fe+3-OOH complex of peroxidases has a very short half life, and its structure cannot be determined by conventional methods. The Fe+2-O2 complex provides a useful structural model for this intermediate, as it differs by only one electron and one proton from the transient Fe+3-OOH complex. We therefore determined the crystal structure of the Fe+2-O2 complex formed by a yeast cytochrome c peroxidase mutant with Trp 191 replaced by Phe. The refined structure shows that dioxygen can form a hydrogen bond with the conserved distal His residue, but not with the conserved distal Arg residue. When the transient Fe+3-OOH complex is modelled in a similar orientation, the active site of peroxidase appears to be optimized for catalysing proton transfer between the vicinal oxygen atoms of the peroxy-anion.


    Related Citations: 
    • Reaction of Ferrous Cytochrome C Peroxidase with Dioxygen: Site-Directed Mutagenesis Provides Evidence for Rapid Reduction of Dioxygen by Intramolecular Electron Transfer from the Compound I Radical Site
      Miller, M.A., Bandyopadhyay, D., Mauro, J.M., Taylor, T.G., Kraut, J.
      (1992) Biochemistry 31: 2789
    • X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme Cleft Mutants Prepared by Site-Directed Mutagenesis
      Wang, J., Mauro, J.M., Edwards, S.L., Oatley, S.J., Fishel, L.A., Ashford, V.A., Xuong, N.-H., Kraut, J.
      (1990) Biochemistry 29: 7160
    • Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7 Angstroms Resolution
      Finzel, B.C., Poulos, T.L., Kraut, J.
      (1984) J Biol Chem 259: 13027

    Organizational Affiliation

    Department of Chemistry, University of California, San Diego La Jolla 92093-0317.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C PEROXIDASEA296Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.11.1.5
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
OXY
Query on OXY

Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.722α = 90
b = 74.446β = 90
c = 45.17γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    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: 2017-11-29
    Changes: Derived calculations, Other