1GM4

OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 at pH 7.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • DOI: 10.1074/jbc.M107136200
  • Primary Citation of Related Structures:  1GMB
  • Also Cited By: 1UP9, 1UPD

  • PubMed Abstract: 
  • Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. There is great interest in determining at the molecular ...

    Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. There is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates. Tetraheme cytochrome c(3) is a small soluble and monomeric protein that performs a central step in the bioenergetic metabolism of sulfate reducing bacteria, termed "proton-thrusting," linking the oxidation of molecular hydrogen with the reduction of sulfate. The mechano-chemical coupling involved in the transfer of multiple electrons and protons in cytochrome c(3) from Desulfovibrio desulfuricans ATCC 27774 is described using results derived from the microscopic thermodynamic characterization of the redox and acid-base centers involved, crystallographic studies in the oxidized and reduced states of the cytochrome, and theoretical studies of the redox and acid-base transitions. This proton-assisted two-electron step involves very small, localized structural changes that are sufficient to generate the complex network of functional cooperativities leading to energy transduction, while using molecular mechanisms distinct from those established for other Desulfovibrio sp. cytochromes from the same structural family.


    Related Citations: 
    • Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstroms Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstrom S Resolution
      Simoes, P.,Matias, P.M.,Morais, J.,Wilson, K.,Dauter, Z.,Carrondo, M.A.
      (1998) Inorg.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 Quimica e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6, Apt. 127, Oeiras 2780-156, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C3
A
107Desulfovibrio desulfuricansGene 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: 2.05 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.189 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.490α = 90.00
b = 61.490β = 90.00
c = 105.660γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-05
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2017-06-28
    Type: Data collection