1CIH

STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional effects of multiple mutations at distal sites in cytochrome c.

Lo, T.P.Komar-Panicucci, S.Sherman, F.McLendon, G.Brayer, G.D.

(1995) Biochemistry 34: 5259-5268

  • Primary Citation of Related Structures:  1CIE, 1CIF, 1CIG

  • PubMed Abstract: 
  • Multiple mutations at distally located sites have been introduced into yeast iso-1 cytochrome c to determine the contributions of three amino acids to the structural and functional properties of this protein. The mutant proteins, for which high-resol ...

    Multiple mutations at distally located sites have been introduced into yeast iso-1 cytochrome c to determine the contributions of three amino acids to the structural and functional properties of this protein. The mutant proteins, for which high-resolution structures were determined, included all possible combinations of the substitutions Arg38Ala, Asn52Ile, and Phe82Ser. Arg38, Asn52, and Phe82 are all conserved in the primary sequences of eukaryotic cytochromes c and have been shown to significantly affect several properties of these proteins including protein stability, heme reduction potential, and oxidation state dependent conformational changes. The present studies show that the structural consequences of each amino acid substitution in combinatorial mutant proteins were similar to those observed in the related single-mutant proteins, and therefore no synergistic effect between mutation sites was observed for this feature. With respect to protein stability, the effect of individual mutations can be understood from the structural changes observed for each. It is found that stability effects of the three mutation sites are independent and cumulative in multiple-mutant proteins. This reflects the independent nature of the structural changes induced at the three distally located mutation sites. In terms of heme reduction potential two effects are observed. For substitution of Phe82 by serine, the mechanism by which reduction potential is lowered is different from that occurring at either the Arg38 or the Asn52 site and is independent of residue replacements at these latter two positions. For Arg38 and Asn52, overlapping interactions lead to a higher reduction potential than expected from a strict additive effect of substitutions at these residues. This appears to arise from interaction of these two amino acids with a common heme element, namely, the heme propionate A group. The present results underscore the difficulty of predicting synergistic effects of multiple mutations within a protein.


    Related Citations: 
    • Yeast Iso-1-Cytochrome C. A 2.8 Angstrom Resolution Three-Dimensional Structure Determination
      Louie, G.V.,Hutcheon, W.L.B.,Brayer, G.D.
      (1988) J.Mol.Biol. 199: 295
    • A Polypeptide Chain-Refolding Event Occurs in the Gly82 Variant of Yeast Iso-1-Cytochrome C
      Louie, G.V.,Brayer, G.D.
      (1989) J.Mol.Biol. 210: 313
    • 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.,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
    • Role of Phenylalanine-82 in Yeast Iso-1-Cytochrome C and Remote Conformational Changes Induced by a Serine Residue at This Position
      Louie, G.V.,Pielak, G.J.,Smith, M.,Brayer, G.D.
      (1988) Biochemistry 27: 7870
    • 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, 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: 1.8 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.480α = 90.00
b = 36.480β = 90.00
c = 137.280γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-09-26 
  • Released Date: 1995-01-26 
  • Deposition Author(s): Lo, T.P., Brayer, G.D.

Revision History 

  • Version 1.0: 1995-01-26
    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