6CCP

EFFECT OF ARGININE-48 REPLACEMENT ON THE REACTION BETWEEN CYTOCHROME C PEROXIDASE AND HYDROGEN PEROXIDE


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Effect of arginine-48 replacement on the reaction between cytochrome c peroxidase and hydrogen peroxide.

Vitello, L.B.Erman, J.E.Miller, M.A.Wang, J.Kraut, J.

(1993) Biochemistry 32: 9807-9818

  • DOI: 10.1021/bi00088a036
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystallographic structures of two cytochrome c peroxidase (CcP) mutants, CcP(R48L) and CcP(R48K), have been determined. In addition, the electronic absorption spectrum and the hydrogen peroxide reactivity of these two mutants have been determine ...

    The crystallographic structures of two cytochrome c peroxidase (CcP) mutants, CcP(R48L) and CcP(R48K), have been determined. In addition, the electronic absorption spectrum and the hydrogen peroxide reactivity of these two mutants have been determined between pH 4 and 8. Both the crystallographic structure and the electronic absorption spectrum of CcP(R48L) are consistent with exclusive pentacoordination of the heme iron between pH 4 and 6.5. At higher pH, CcP(R48L) forms an alkaline bis-imidazole form of CcP with the distal histidine coordinated to the heme iron. The apparent pKA for this transition is 7.5 in CcP(R48L). The observed pseudo-first-order rate constant for the reaction between CcP(R48L) and hydrogen peroxide saturates at high peroxide concentrations. The data are consistent with a rate-limiting oxygen-oxygen bond scission at high peroxide concentrations. The observed rate of the bond scission step ranges between 1000 and 1950 s-1, an estimated 2 orders of magnitude slower than for wild-type enzyme. The data suggest that the protonated form of His-52 increases the bond scission step by a factor of 2. The properties of the CcP(R48K) mutant are significantly different from those of CcP(R48L). The crystal structure of CcP(R48K) shows Lys-48 occupying the putative peroxide binding site. The electronic absorption spectrum indicates that CcP(R48K) is predominantly pentacoordinate at neutral pH but with detectable amounts of hexacoordinate forms. Two ionizable groups affect the electronic absorption spectrum of CcP(R48K). An apparent ionization near pH 4 produces an enzyme with increased hexacoordination, while an apparent pKA of 6.9 generates the alkaline bis-imidazole form. The peroxide reaction saturates at high peroxide concentrations for CcP(R48K) and is attributed to a conformational-gating mechanism. The maximum rate for the reaction between CcP(R48K) and hydrogen peroxide is probably limited by the movement of either Lys-48 or His-52. This rate is 200 and 290 s-1 in nitrate-containing buffers and phosphate buffers, respectively. Evidence is provided that Arg-48 in wild-type enzyme is responsible for nitrate binding in the heme pocket and for stabilizing CcP Compound I.


    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
    • 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, Northern Illinois University, DeKalb 60115.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C PEROXIDASEA296Saccharomyces cerevisiaeMutation(s): 3 
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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.04α = 90
b = 74.21β = 90
c = 45.5γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-10-05
    Changes: Database references
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other