1CPG

A CATION BINDING MOTIF STABILIZES THE COMPOUND I RADICAL OF CYTOCHROME C PEROXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase.

Miller, M.A.Han, G.W.Kraut, J.

(1994) Proc Natl Acad Sci U S A 91: 11118-11122

  • DOI: 10.1073/pnas.91.23.11118
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cytochrome c peroxidase reacts with peroxide to form compound I, which contains an oxyferryl heme and an indolyl radical at Trp-191. The indolyl free radical has a half-life of several hours at room temperature, and this remarkable stability is essen ...

    Cytochrome c peroxidase reacts with peroxide to form compound I, which contains an oxyferryl heme and an indolyl radical at Trp-191. The indolyl free radical has a half-life of several hours at room temperature, and this remarkable stability is essential for the catalytic function of cytochrome c peroxidase. To probe the protein environment that stabilizes the compound I radical, we used site-directed mutagenesis to replace Trp-191 with Gly or Gln. Crystal structures of these mutants revealed a monovalent cation binding site in the cavity formerly occupied by the side chain of Trp-191. Comparison of this site with those found in other known cation binding enzymes shows that the Trp-191 side chain resides in a consensus K+ binding site. Electrostatic potential calculations indicate that the cation binding site is created by partial negative charges at the backbone carbonyl oxygen atoms of residues 175 and 177, the carboxyl end of a long alpha-helix (residues 165-175), the heme propionates, and the carboxylate side chain of Asp-235. These features create a negative potential that envelops the side chain of Trp-191; the calculated free energy change for cation binding in this site is -27 kcal/mol (1 cal = 4.184J). This is more than sufficient to account for the stability of the Trp-191 radical, which our estimates suggest is stabilized by 7.8 kcal/mol relative to a Trp radical in solution.


    Related Citations: 
    • X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme Cleft Mutants Prepared by Site-Directed Mutagenesis
      Wang, J., Mauro, J.M., Edwards, S.L., Oatley, S.J., Fishel, L.A., Ashford, V.A., Xuong, N.-H., Kraut, J.
      (1990) Biochemistry 29: 7160
    • Yeast Cytochrome C Peroxidase: Mutagenesis and Expression in Escherichia Coli Show Tryptophan-51 is not the Radical Site in Compound I
      Fishel, L.A., Villafranca, J.E., Mauro, J.M., Kraut, J.
      (1987) Biochemistry 26: 351
    • Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7 Angstroms Resolution
      Finzel, B.C., Poulos, T.L., Kraut, J.
      (1984) J Biol Chem 259: 13027

    Organizational Affiliation

    Department of Chemistry, University of California at San Diego, La Jolla 92093-0317.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C PEROXIDASEA296Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.11.1.5
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.17α = 90
b = 74.18β = 90
c = 45.22γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    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 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description