1CRG

THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 786-799

  • Primary Citation of Related Structures:  1CRH, 1CRI, 1CRJ

  • PubMed Abstract: 
  • High resolution three-dimensional structures for the N52I and N52I-Y67F yeast iso-1-cytochrome c variants have been completed in both oxidation states. The most prominent structural difference observed in both mutant proteins is the displacement of a ...

    High resolution three-dimensional structures for the N52I and N52I-Y67F yeast iso-1-cytochrome c variants have been completed in both oxidation states. The most prominent structural difference observed in both mutant proteins is the displacement of a conserved, internally bound water molecule (Wat166) from the protein matrix. In wild-type yeast iso-1-cytochrome c the position and orientation of this water molecule is found to be dependent on the oxidation state of the heme iron atom. Overall our results suggest the function of Wat166 and its associated hydrogen bond network is threefold. First, the presence of Wat166 provides a convenient mechanism to modify the hydrogen bond network involving several residues near the Met80 ligand in an oxidation state dependent manner. Second, Wat166 is necessary for the maintenance of the spatial relationships between nearby side-chains and the hydrogen bond interactions formed between these groups in this region of the protein. An essential part of this role is ensuring the proper conformation of the side-chain of Tyr67 so that it forms a hydrogen bond interaction with the heme ligand Met80. This hydrogen bond influences the electron withdrawing power of the Met80 ligand and is therefore a factor in controlling the midpoint reduction potential of cytochrome c. Elimination of this interaction in the N52I-Y67F mutant protein or elimination of Wat166 in the N52I protein with the subsequent disruption in the position and interactions of the Tyr67 side-chain, leads to a drop of approximately 56 mV in the observed midpoint reduction potential of the heme group. Third, Wat166 also appears to mediate increases in the mobility of three nearby segments of polypeptide chain when cytochrome c is in the oxidized state. Previous studies have proposed these changes may be related to oxidation state dependent interactions between cytochrome c and its redox partners. Coincident with the absence of Wat166, such mobility changes are not observed in the N52I and N52I-Y67F mutant proteins. It is possible that much of the increased protein stability observed for both mutant proteins may be due to this factor. Finally, our results show that neither heme iron charge nor heme plane distortion are responsible for oxidation state dependent conformational changes in the pyrrole A propionate region. Instead, the changes observed appear to be driven by the change in conformation that the side-chain of Asn52 experiences as the result of oxidation state dependent movement of Wat166.


    Related Citations: 
    • Effect of the Asn 52-> Ile Mutation on the Redox Potential of Yeast Cytochrome C: Theory and Experiment
      Langen, R.,Brayer, G.D.,Berghuis, A.M.,Mclendon, G.,Sherman, F.,Warshel, A.
      (1992) J.Mol.Biol. 224: 589
    • Effects of Reaction Free Energy in Biological Electron Transfer in Vitro and in Vivo (in: Electron Transfer in Inorganic, Organic, and Biological Systems)
      Mclendon, G.,Hickey, D.R.,Berghuis, A.M.,Sherman, F.,Brayer, G.D.
      (1991) Adv.Chem.Ser. 228: 179
    • Enhanced Thermodynamic Stabilities of Yeast Iso-1-Cytochrome C with Amino Acid Replacements at Position 52 and 102
      Hickey, D.R.,Berghuis, A.M.,Lafond, G.,Jaeger, J.A.,Cardillo, T.S.,Mclendon, D.,Das, G.,Sherman, F.,Brayer, G.D.,Mclendon, G.
      (1991) J.Biol.Chem. 266: 11686
    • Oxidation State-Dependent Conformational Changes in Cytochrome C
      Berghuis, A.M.,Brayer, G.D.
      (1992) J.Mol.Biol. 223: 959
    • Mutation of Tyrosine-67 in Cytochrome C Significantly Alters the Local Heme Environment
      Berghuis, A.M.,Guillemette, G.J.,Smith, M.,Brayer, G.D.
      () TO BE PUBLISHED --: --
    • 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


    Organizational Affiliation

    Department of Biochemistry, 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: 2 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.470α = 90.00
b = 36.470β = 90.00
c = 137.020γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other