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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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: 
    • 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
    • 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) Inorg.Chim.Acta. 273: 213


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C3
A
107Desulfovibrio desulfuricansMutation(s): 0 
Gene Names: cytc3
Find proteins for Q9L915 (Desulfovibrio desulfuricans)
Go to UniProtKB:  Q9L915
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.203 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.360α = 90.00
b = 61.360β = 90.00
c = 106.920γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXL-97refinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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