1YEA

STRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.190 

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This is version 2.0 of the entry. See complete history


Literature

Structure determination and analysis of yeast iso-2-cytochrome c and a composite mutant protein.

Murphy, M.E.Nall, B.T.Brayer, G.D.

(1992) J Mol Biol 227: 160-176

  • DOI: https://doi.org/10.1016/0022-2836(92)90689-h
  • Primary Citation of Related Structures:  
    1YEA, 1YEB

  • PubMed Abstract: 

    As part of a study of protein folding and stability, the three-dimensional structures of yeast iso-2-cytochrome c and a composite protein (B-2036) composed of primary sequences of both iso-1 and iso-2-cytochromes c have been solved to 1.9 A and 1.95 A resolutions, respectively, using X-ray diffraction techniques. The sequences of iso-1 and iso-2-cytochrome c share approximately 84% identity and the B-2036 composite protein has residues 15 to 63 from iso-2-cytochrome c with the rest being derived form the iso-1 protein. Comparison of these structures reveals that amino acid substitutions result in alterations in the details of intramolecular interactions. Specifically, the substitution Leu98Met results in the filling of an internal cavity present in iso-1-cytochrome c. Further substitutions of Val20Ile and Cys102Ala alter the packing of secondary structure elements in the iso-2 protein. Blending the isozymic amino acid sequences in this latter area results in the expansion of the volume of an internal cavity in the B-2036 structure to relieve a steric clash between Ile20 and Cys102. Modification of hydrogen bonding and protein packing without disrupting the protein fold is illustrated by the His26Asn and Asn63Ser substitutions between iso-1 and iso-2-cytochromes c. Alternatively, a change in main-chain fold is observed at Gly37 apparently due to a remote amino acid substitution. Further structural changes occur at Phe82 and the amino terminus where a four residue extension is present in yeast iso-2-cytochrome c. An additional comparison with all other eukaryotic cytochrome c structures determined to date is presented, along with an analysis of conserved water molecules. Also determined are the midpoint reduction potentials of iso-2 and B-2036 cytochromes c using direct electrochemistry. The values obtained are 286 and 288 mV, respectively, indicating that the amino acid substitutions present have had only a small impact on the heme reduction potential in comparison to iso-1-cytochrome c, which has a reduction potential of 290 mV.


  • Organizational Affiliation

    Department of Biochemistry, University of British Columbia, Vancouver, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C112Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P00045 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00045 
Go to UniProtKB:  P00045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00045
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
A
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.190 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.44α = 90
b = 36.44β = 90
c = 137.86γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2021-03-03
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary