3ZCF

Structure of recombinant human cytochrome c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Hydrogen Peroxide Induced Radical Behaviour in Human Cytochrome C Phospholipid Complexes: Implications for the Enhanced Pro-Apoptotic Activity of the G41S Mutant

Rajagopal, B.S.Edzuma, A.N.Hough, M.A.Blundell, K.L.I.M.Kagan, V.E.Kapralov, A.A.Fraser, L.A.Butt, J.N.Silkstone, G.G.Wilson, M.T.Svistunenko, D.A.Worrall, J.A.R.

(2013) Biochem.J. 456: 441

  • DOI: 10.1042/BJ20130758
  • Primary Citation of Related Structures:  3ZOO

  • PubMed Abstract: 
  • We have investigated whether the pro-apoptotic properties of the G41S mutant of human cytochrome c can be explained by a higher than wild-type peroxidase activity triggered by phospholipid binding. A key complex in mitochondrial apoptosis involves cy ...

    We have investigated whether the pro-apoptotic properties of the G41S mutant of human cytochrome c can be explained by a higher than wild-type peroxidase activity triggered by phospholipid binding. A key complex in mitochondrial apoptosis involves cytochrome c and the phospholipid cardiolipin. In this complex cytochrome c has its native axial Met(80) ligand dissociated from the haem-iron, considerably augmenting the peroxidase capability of the haem group upon H2O2 binding. By EPR spectroscopy we reveal that the magnitude of changes in the paramagnetic haem states, as well as the yield of protein-bound free radical, is dependent on the phospholipid used and is considerably greater in the G41S mutant. A high-resolution X-ray crystal structure of human cytochrome c was determined and, in combination with the radical EPR signal analysis, two tyrosine residues, Tyr(46) and Tyr(48), have been rationalized to be putative radical sites. Subsequent single and double tyrosine-to-phenylalanine mutations revealed that the EPR signal of the radical, found to be similar in all variants, including G41S and wild-type, originates not from a single tyrosine residue, but is instead a superimposition of multiple EPR signals from different radical sites. We propose a mechanism of multiple radical formations in the cytochrome c-phospholipid complexes under H2O2 treatment, consistent with the stabilization of the radical in the G41S mutant, which elicits a greater peroxidase activity from cytochrome c and thus has implications in mitochondrial apoptosis.


    Organizational Affiliation

    *School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
A, B, C, D
104Homo sapiensGene Names: CYCS (CYC)
Find proteins for P99999 (Homo sapiens)
Go to Gene View: CYCS
Go to UniProtKB:  P99999
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.545α = 76.54
b = 53.915β = 88.57
c = 58.723γ = 72.10
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references