1AQE

CRYSTAL STRUCTURE OF THE Y73E MUTANT OF CYTOCHROME C OF CLASS III (AMBLER) 26 KD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and kinetic studies of the Y73E mutant of octaheme cytochrome c3 (Mr = 26 000) from Desulfovibrio desulfuricans Norway.

Aubert, C.Giudici-Orticoni, M.T.Czjzek, M.Haser, R.Bruschi, M.Dolla, A.

(1998) Biochemistry 37: 2120-2130

  • DOI: 10.1021/bi971656g

  • PubMed Abstract: 
  • A combination of structural, kinetic, and interaction experiments has been used to study the role of a highly conserved aromatic residue, Tyr73, parallel to the sixth heme axial ligand of heme 4 in multiheme cytochrome c3 (Mr = 26 000), also called c ...

    A combination of structural, kinetic, and interaction experiments has been used to study the role of a highly conserved aromatic residue, Tyr73, parallel to the sixth heme axial ligand of heme 4 in multiheme cytochrome c3 (Mr = 26 000), also called cytochrome cc3 or octaheme cytochrome, from Desulfovibrio desulfuricans Norway. This residue is expected to be involved in intermolecular electron transfer and protein-protein interaction, since heme 4 is described to be the interaction site between physiological partners. The kinetic experiments show that the Y73E replacement provokes no significant change in the electron-transfer reaction with the physiological partner, the [NiFeSe] hydrogenase, but that the protein-protein interaction between cytochrome c3 (Mr = 26 000) and hydrogenase is strongly affected by the mutation. The aromatic residue does not play a role in maintaining the axial heme ligand in a particular orientation, since the mutation did not affect the orientation of histidine 77, the sixth axial ligand of heme 4. The structural analysis by X-ray crystallography clearly shows that a rearrangement of the charged residues in the vicinity of the mutation site is responsible for the change in protein-protein interaction, which is of an electrostatic nature. Lys22 and Arg66, residues which are located at the interacting surface, are twisted toward the mutated position Glu73 in order to compensate for the negative charge and therefore are no longer accessible for the docking with a physiological partner. Tyr73 has instead a structural function and probably a role in maintaining the hydrophobic environment of the heme 4 cavity rather than a function in the intermolecular electron transfer with the physiological partners.


    Related Citations: 
    • Crystal Structure of a Dimeric Octaheme Cytochrome C3 (Mr 26,000) from Desulfovibrio Desulfuricans Norway
      Czjzek, M.,Guerlesquin, F.,Bruschi, M.,Haser, R.
      (1996) Structure 4: 395
    • A Single Mutation in the Heme 4 Environment of Desulfovibrio Desulfuricans Norway Cytochrome C3 (Mr 26,000) Greatly Affects the Molecule Reactivity
      Aubert, C.,Leroy, G.,Bruschi, M.,Wall, J.D.,Dolla, A.
      (1997) J.Biol.Chem. 272: 15128


    Organizational Affiliation

    Unite de Bioenergetique et Ingenierie de Proteines, UPR 9036, CNRS, 13402 Marseille Cedex 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C3
A
111Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310)N/A
Find proteins for P38554 (Desulfomicrobium norvegicum (strain DSM 1741 / NCIMB 8310))
Go to UniProtKB:  P38554
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
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.620α = 90.00
b = 72.620β = 90.00
c = 60.322γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-07-29 
  • Released Date: 1998-02-04 
  • Deposition Author(s): Czjzek, M., Haser, R.

Revision History 

  • Version 1.0: 1998-02-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance