3EXB

Crystal structure of Cytochrome C Peroxidase with a Proposed Electron Pathway Excised in a Complex with a Peptide Wire


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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This is version 1.3 of the entry. See complete history


Literature

Replacement of an electron transfer pathway in cytochrome c peroxidase with a surrogate peptide

Hays Putnam, A.M.Lee, Y.T.Goodin, D.B.

(2009) Biochemistry 48: 1-3

  • DOI: 10.1021/bi8020263
  • Primary Citation of Related Structures:  
    3EXB

  • PubMed Abstract: 
  • A proposed electron transfer pathway in cytochrome c peroxidase was previously excised from the structure by design. The engineered channel mutant was shown to bind peptide surrogates without restoration of cyt c oxidation. Here, we report the 1.6 A crystal structure of (N-benzimidazole-propionic acid)-Gly-Ala-Ala bound within the engineered channel ...

    A proposed electron transfer pathway in cytochrome c peroxidase was previously excised from the structure by design. The engineered channel mutant was shown to bind peptide surrogates without restoration of cyt c oxidation. Here, we report the 1.6 A crystal structure of (N-benzimidazole-propionic acid)-Gly-Ala-Ala bound within the engineered channel. The peptide retains many features of the native electron transfer pathway: placement of benzimidazole at the position of the Trp-191 radical, hydrogen bonding to Asp235, and positioning of the C-terminus near the point where wild type CcP makes closest contact to cyt c. The inability of this surrogate pathway to restore function supports proposals that electron transfer requires the Trp-191 radical.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c peroxidaseA295Saccharomyces cerevisiaeMutation(s): 4 
Gene Names: CCP1CCPCPO
EC: 1.11.1.5
UniProt
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
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-[3-(1H-BENZIMIDAZOL-1-YL)PROPANOYL]GLYCYL-L-ALANYL-L-ALANINAMIDEB5synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.029α = 90
b = 75.07β = 90
c = 50.79γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2020-11-11
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary