1EBE

Laue diffraction study on the structure of cytochrome c peroxidase compound I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

Starting Model: experimental
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Literature

Laue Diffraction Study on the Structure of Cytochrome C Peroxidase Compound I

Fulop, V.Phizackerley, R.P.Soltis, S.M.Clifton, I.J.Wakatsuki, S.Erman, J.E.Hajdu, J.Edwards, S.L.

(1994) Structure 2: 201

  • DOI: https://doi.org/10.1016/s0969-2126(00)00021-6
  • Primary Citation of Related Structures:  
    1EBE

  • PubMed Abstract: 

    Cytochrome c peroxidase from yeast is a soluble haem-containing protein found in the mitochondrial electron transport chain where it probably protects against toxic peroxides. The aim of this study was to obtain a reliable structure for the doubly oxidized transient intermediate (termed compound I) in the reaction of cytochrome c peroxidase with hydrogen peroxide. This intermediate contains a semistable free radical on Trp191, and an oxyferryl haem group. Compound I was produced in crystals of yeast cytochrome c peroxidase by reacting the crystalline enzyme with hydrogen peroxide in a flow cell. The reaction was monitored by microspectrophotometry and Laue crystallography in separate experiments. A nearly complete conversion to compound I was achieved within two minutes of the addition of hydrogen peroxide, and the concentration of the intermediate remained at similar levels for an additional half an hour. The structure of the intermediate was determined by Laue diffraction. The refined Laue structure for compound I shows clear structural changes at the peroxide-binding site but no significant changes at the radical site. The photographs were processed with a new software package (LEAP), overcoming many of the former problems encountered in extracting structural information from Laue exposures. The geometry of the haem environment in this protein allows structural changes to be extremely small, similar in magnitude to those observed for the Fe2+/Fe3+ transition in cytochrome c. The results suggest that these molecules have evolved to transfer electrons with a minimal need for structural adjustment.


  • Organizational Affiliation

    Oxford Centre for Molecular Sciences, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C PEROXIDASE294Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00431
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
O
Query on O

Download Ideal Coordinates CCD File 
C [auth A]OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.4α = 90
b = 76.8β = 90
c = 51.4γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
LEAPdata reduction
LEAPdata scaling
CCP4phasing
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-26
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Data collection
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Refinement description