1S6V

Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure and characterization of a cytochrome c peroxidase-cytochrome c site-specific cross-link

Guo, M.Bhaskar, B.Li, H.Barrows, T.P.Poulos, T.L.

(2004) Proc Natl Acad Sci U S A 101: 5940-5945

  • DOI: 10.1073/pnas.0306708101
  • Primary Citation of Related Structures:  
    1S6V

  • PubMed Abstract: 
  • A specific covalently cross-linked complex between redox partners yeast cytochrome c peroxidase (CCP) and cytochrome c (cyt. c) has been made by engineering cysteines into CCP and cyt. c that form an intermolecular disulfide bond in high yield. The crystal structure of the cross-linked complex has been solved to 1 ...

    A specific covalently cross-linked complex between redox partners yeast cytochrome c peroxidase (CCP) and cytochrome c (cyt. c) has been made by engineering cysteines into CCP and cyt. c that form an intermolecular disulfide bond in high yield. The crystal structure of the cross-linked complex has been solved to 1.88-A resolution and closely resembles the structure of the noncovalent complex [Pellitier, H. & Kraut, J. (1992) Science 258, 1748-1755]. The higher resolution of the covalent complex has enabled the location of ordered water molecules at the peroxidase-cytochrome c interface that serve to bridge between the two proteins by hydrogen bonding. As in the noncovalent complex, direct electrostatic interactions between protein groups appear not to be critical in complex formation. UV-visible spectroscopic and stopped-flow studies indicate that CCP in the covalent complex reacts normally with H(2)O(2) to give compound I. Stopped-flow kinetic studies also show that intramolecular electron transfer between the cross-linked ferrocytochrome c and the Trp-191 cation radical site in CCP compound I occurs fast and is nearly complete within the dead time ( approximately 2 ms) of the instrument. These results indicate that the structure of the covalent complex closely mimics the physiological electron transfer complex. In addition, single-turnover and steady-state experiments reveal that CCP compound I in the covalent complex oxidizes exogenously added ferrocytochrome c at a slow rate (t(1/2) approximately 2 min), indicating that CCP does not have a second independent site for physiologically relevant electron transfer.


    Related Citations: 
    • Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c
      Pelletier, H., Kraut, J.
      (1992) Science 258: 1748

    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c peroxidase, mitochondrialA, C294Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: CCP1CCPCPOYKR066C
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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c, iso-1B, D108Saccharomyces cerevisiaeMutation(s): 2 
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.24α = 90
b = 107.92β = 104.42
c = 88.38γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-03-03
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary