1IRV

CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY MET AND CYS 102 REPLACED BY THR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanistic and structural contributions of critical surface and internal residues to cytochrome c electron transfer reactivity.

Rafferty, S.P.Guillemette, J.G.Berghuis, A.M.Smith, M.Brayer, G.D.Mauk, A.G.

(1996) Biochemistry 35: 10784-10792

  • DOI: 10.1021/bi960430v
  • Primary Citation of Related Structures:  1IRW

  • PubMed Abstract: 
  • The influence of mutations in two conserved regions of yeast iso-1-cytochrome c believed to be critical to the mechanism of cytochrome c electron transfer reactions has been investigated. The variants Asn52Ala, Tyr67Phe, Ile75Met, and Thr78Gly involv ...

    The influence of mutations in two conserved regions of yeast iso-1-cytochrome c believed to be critical to the mechanism of cytochrome c electron transfer reactions has been investigated. The variants Asn52Ala, Tyr67Phe, Ile75Met, and Thr78Gly involve perturbation of critical hydrogen-bonding interactions with an internal water molecule (Wat166) and have been studied in terms of their electrochemical properties and the kinetics with which they are reduced by Fe(EDTA)2- and oxidized by Co(phen)3(3+). In parallel studies, the Co(phen)3(3+) oxidation kinetics of Tyr, Leu, Ile, Ala, Ser, and Gly variants of the phylogenetically conserved residue Phe82 have been studied and correlated with previous electrochemical and kinetic results. To assist mechanistic interpretation of these results, the three-dimensional structures of the Asn52Ala and Ile75Met ferrocytochrome c variants have been determined. The reduction potentials of the variants modified in the region of Wat166 were at least 33 mV (pH 6, 25 degrees C, and mu = 0.1 M) lower than that of the wild-type protein. Electron transfer reactivity of this family of variants in both the oxidation and reduction reactions was increased as much as 10-fold over that of the wild-type cytochrome. On the other hand, the reactivity of the position-82 variants in both oxidation and reduction depended on the structural characteristics of the oxidation-reduction reagent with which they reacted, and this reactivity was related to the nature of the residue at this position. These findings have been interpreted as demonstrating that the principal influence of modification at position-82 arises from changes in the nature of reactant-protein interaction at the surface of the protein and in maintaining the high reduction potential of the cytochrome while the principal influence of internal modifications near Wat166 results from alteration of the reorganization energy for the oxidation state-linked conformational change defined by crystallographic analysis of the wild-type protein.


    Related Citations: 
    • The Role of a Conserved Internal Water Molecule and its Associated Hydrogen Bond Network in Cytochrome C
      Berghuis, A.M.,Guillemette, J.G.,Mclendon, G.,Sherman, F.,Smith, M.,Brayer, G.D.
      (1994) J.Mol.Biol. 236: 786
    • Oxidation State-Dependent Conformational Changes in Cytochrome C
      Berghuis, A.M.,Brayer, G.D.
      (1992) J.Mol.Biol. 223: 959
    • High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C
      Louie, G.V.,Brayer, G.D.
      (1990) J.Mol.Biol. 214: 527
    • Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique
      Leung, C.J.,Nall, B.T.,Brayer, G.D.
      (1989) J.Mol.Biol. 206: 783
    • Mutation of Tyrosine-67 to Phenylalanine in Cytochrome C Significantly Alters the Local Heme Environment
      Berghuis, A.M.,Guillemette, J.G.,Smith, M.,Brayer, G.D.
      (1994) J.Mol.Biol. 235: 1326


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
A
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CYC1
Go to UniProtKB:  P00044
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.550α = 90.00
b = 36.550β = 90.00
c = 138.590γ = 90.00
Software Package:
Software NamePurpose
IN-HOUSEdata reduction
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other