1UP9

REDUCED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT PH 7.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.203 
  • R-Value Observed: 0.159 

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This is version 1.2 of the entry. See complete history


Literature

Molecular Basis for Redox-Bohr and Cooperative Effects in Cytochrome C3 from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies of Oxidized and Reduced High-Resolution Structures at Ph 7.6

Bento, I.Matias, P.M.Baptista, A.M.Da Costa, P.N.Van Dongen, W.M.A.M.Saraiva, L.M.Schneider, T.R.Soares, C.M.Carrondo, M.A.

(2004) Proteins 54: 135

  • DOI: 10.1002/prot.10431
  • Primary Citation of Related Structures:  
    1UPD, 1UP9

  • PubMed Abstract: 
  • The tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. The three-dimensional structure of the oxidized and reduced forms of cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7 ...

    The tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. The three-dimensional structure of the oxidized and reduced forms of cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were determined using high-resolution X-ray crystallography and were compared with the previously determined oxidized form at pH 4.0. Theoretical calculations were performed with both structures, using continuum electrostatic calculations and Monte Carlo sampling of protonation and redox states, in order to understand the molecular basis of the redox-Bohr and cooperativity effects related to the coupled transfer of electrons and protons. We were able to identify groups that showed redox-linked conformational changes. In particular, Glu61, His76, and propionate D of heme II showed important contributions to the redox-cooperativity, whereas His76, propionate A of heme I, and propionate D of heme IV were the key residues for the redox-Bohr effect. Upon reduction, an important movement of the backbone region surrounding hemes I and II was also identified, that, together with a few redox-linked conformational changes in side-chain residues, results in a significant decrease in the solvent accessibility of hemes I and II.


    Related Citations: 
    • Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome
      Louro, R.O., Bento, I., Matias, P.M., Catarino, T., Baptista, A.M., Soares, C.M., Carrondo, M.A., Turner, D.L., Xavier, A.V.
      (2001) J Biol Chem 276: 44044
    • Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 A Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 A Resolution
      Simoes, P., Matias, P.M., Morais, J., Wilson, K., Dauter, Z., Carrondo, M.A.
      (1998) Inorganica Chim Acta 273: 213
    • Structure of the Tetraheme Cytochrome from Desulfovibrio Desulfuricans Atcc 27774: X-Ray Diffraction and Electron Paramagnetic Resonance Studies
      Morais, J., Palma, P.N., Frazao, C., Caldeira, J., Legall, J., Moura, I., Moura, J.J., Carrondo, M.A.
      (1995) Biochemistry 34: 12830

    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C3A107Desulfovibrio desulfuricansMutation(s): 0 
Gene Names: cytc3SAMN02910291_00073
UniProt
Find proteins for Q9L915 (Desulfovibrio desulfuricans)
Explore Q9L915 
Go to UniProtKB:  Q9L915
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.203 
  • R-Value Observed: 0.159 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.36α = 90
b = 61.36β = 90
c = 106.92γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-30
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-05-22
    Changes: Advisory, Data collection, Derived calculations, Other, Refinement description