5CCP

HISTIDINE 52 IS A CRITICAL RESIDUE FOR RAPID FORMATION OF CYTOCHROME C PEROXIDASE COMPOUND I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Histidine 52 is a critical residue for rapid formation of cytochrome c peroxidase compound I.

Erman, J.E.Vitello, L.B.Miller, M.A.Shaw, A.Brown, K.A.Kraut, J.

(1993) Biochemistry 32: 9798-9806

  • DOI: 10.1021/bi00088a035
  • Primary Citation of Related Structures:  
    5CCP

  • PubMed Abstract: 
  • The crystal structure and reactivity with hydrogen peroxide are reported for a mutant of a cloned cytochrome c peroxidase [CcP(MI)], in which the conserved distal His (His-52) is replaced with Leu. The reaction of the H52L enzyme with peroxide was examined as a function of pH in 0 ...

    The crystal structure and reactivity with hydrogen peroxide are reported for a mutant of a cloned cytochrome c peroxidase [CcP(MI)], in which the conserved distal His (His-52) is replaced with Leu. The reaction of the H52L enzyme with peroxide was examined as a function of pH in 0.1 M phosphate buffers and buffers in which nitrate was used to adjust the ionic strength. The pH-independent bimolecular rate constant for the reaction of H52L with peroxide was 731 +/- 44 and 236 +/- 14 M-1 s-1 in phosphate and nitrate-containing buffers, respectively. This represents a 10(5)-fold decrease in rate relative to the CcP(MI) parent under comparable conditions. Single-crystal diffraction studies showed that no dramatic changes in the structure or in the accessibility of the heme binding site were caused by the mutation. Rather, the mutation caused significant structural changes only at residue 52 and the nearby active-site water molecules. The residual reactivity of the H52L enzyme with peroxide was pH- and buffer-dependent. In nitrate-containing buffer, the apparent bimolecular rate constant for the reaction with peroxide decreased with decreasing pH; the loss of reactivity correlated with protonation of a group with an apparent pKA = 4.5. Protonation of the group caused a loss of reactivity with peroxide. This is in contrast to the CcP(MI) parent enzyme, as well as all other mutants that have been examined, where the loss of reactivity correlates with protonation of an enzyme group with an apparent pKA = 5.4.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Active-Site Mutations in Cytochrome C Peroxidase: A Critical Role for Histidine-52 in the Rate of Formation of Compound I
      Erman, J.E., Vitello, L.B., Miller, M.A., Kraut, J.
      (1992) J Am Chem Soc 114: 6592
    • Conformational Change and Histidine Control of Heme Chemistry in Cytochrome C Peroxidase: Resonance Raman Evidence from Leu-52 and Gly-181 Mutants of C Peroxidase
      Smulevich, G., Miller, M.A., Kraut, J., Spiro, T.G.
      (1991) Biochemistry 30: 9546
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C PEROXIDASEA296Saccharomyces cerevisiaeMutation(s): 3 
EC: 1.11.1.5
UniProt
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 (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth 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: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.9α = 90
b = 74.18β = 90
c = 45.17γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    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