1CYF

IDENTIFYING THE PHYSIOLOGICAL ELECTRON TRANSFER SITE OF CYTOCHROME C PEROXIDASE BY STRUCTURE-BASED ENGINEERING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Identifying the physiological electron transfer site of cytochrome c peroxidase by structure-based engineering.

Miller, M.A.Geren, L.Han, G.W.Saunders, A.Beasley, J.Pielak, G.J.Durham, B.Millett, F.Kraut, J.

(1996) Biochemistry 35: 667-673

  • DOI: 10.1021/bi952557a

  • PubMed Abstract: 
  • A technique was developed to evaluate whether electron transfer (ET) complexes formed in solution by the cloned cytochrome c peroxidase [CcP(MI)] and cytochromes c from yeast (yCc) and horse (hCc) are structurally similar to those seen in the respect ...

    A technique was developed to evaluate whether electron transfer (ET) complexes formed in solution by the cloned cytochrome c peroxidase [CcP(MI)] and cytochromes c from yeast (yCc) and horse (hCc) are structurally similar to those seen in the respective crystal structures. Site-directed mutagenesis was used to convert the sole Cys of the parent enzyme (Cys 128) to Ala, and a Cys residue was introduced at position 193 of CcP(MI), the point of closest contact between CcP(MI) and yCc in the crystal structure. Cys 193 was then modified with a bulky sulfhydryl reagent, 3-(N-maleimidylpropionyl)-biocytin (MPB), to prevent yCc from binding at the site seen in the crystal. The MPB modification has no effect on overall enzyme structure but causes 20-100-fold decreases in transient and steady-state ET reaction rates with yCc. The MPB modification causes only 2-3-fold decreases in ET reaction rates with hCc, however. This differential effect is predicted by modeling studies based on the crystal structures and indicates that solution phase ET complexes closely resemble the crystalline complexes. The low rate of catalysis of the MPB-enzyme was constant for yCc in buffers of 20-160 mM ionic strength. This indicates that the low affinity complex formed between CcP(MI) and yCc at low ionic strength is not reactive in ET.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C PEROXIDASE
A
296Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CCP1 (CCP, CPO)
EC: 1.11.1.5
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 101.330α = 90.00
b = 73.880β = 90.00
c = 45.000γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other