2CYP

Crystal structure of yeast cytochrome C peroxidase refined at 1.7-angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution

Finzel, B.C.Poulos, T.L.Kraut, J.

(1984) J.Biol.Chem. 259: 13027-13036

  • Also Cited By: 1EBE

  • PubMed Abstract: 
  • The crystal structure of cytochrome c peroxidase (EC 1.11.1.5) has been refined to an R factor of 0.20 computed for all reflections to 1.7 A. The refined molecular model includes 263 bound water molecules and allows for x-ray scattering by amorphous ...

    The crystal structure of cytochrome c peroxidase (EC 1.11.1.5) has been refined to an R factor of 0.20 computed for all reflections to 1.7 A. The refined molecular model includes 263 bound water molecules and allows for x-ray scattering by amorphous solvent. The mean positional error in atomic coordinates is estimated to lie between 0.12 and 0.21 A. Two factors are identified which may account for the ability of the enzyme to stabilize high-oxidation states of the heme iron during catalysis: 1) the proximal histidine forms a hydrogen bond with a buried aspartic acid side chain, Asp-235; and 2) the heme environment is more polar than in the cytochromes c or globins, owing to the presence of the partially buried side-chain of Arg-48 and five water molecules bound in close proximity to the heme. Two of these occupy the presumed peroxide-binding site. Two candidates are likely for the side chain that is oxidized to a free radical during formation of Compound I: 1) Trp-51, which rests 3.3 A above the heme plane in close proximity (2.7 A) to the sixth coordination position; and 2) Met-172, which is 3.7 A from the heme. Nucleophilic stabilization of the methionyl cation radical may be possible via Asp-235. His-181 is found to lie coplanar with the heme in a niche between the two propionates near the suspected cytochrome c-binding site. A network of hydrogen bonds involving this histidine may provide a preferred pathway for electron transfer between hemes.


    Related Citations: 
    • Crystallographic Determination of the Heme Orientation and Location of the Cyanide Binding Site in Yeast Cytochrome C Peroxidase
      Poulos, T.L.,Freer, S.T.,Alden, R.A.,Xuong, N.H.,Edwards, S.L.,Hamlin, R.C.,Kraut, J.
      (1978) J.Biol.Chem. 253: 3730
    • Heme Enzyme Structure and Function
      Poulos, T.L.,Finzel, B.C.
      (1984) Pept.Protein Rev. 4: 115
    • A Hypothetical Model of the Cytochrome C Peroxidase-Cytochrome C Electron Transfer Complex
      Poulos, T.L.,Kraut, J.
      (1980) J.Biol.Chem. 255: 10322
    • The Stereochemistry of Peroxidase Catalysis
      Poulos, T.L.,Kraut, J.
      (1980) J.Biol.Chem. 255: 8199
    • The Crystal Structure of Cytochrome C Peroxidase
      Poulos, T.L.,Freer, S.T.,Alden, R.A.,Edwards, S.L.,Skogland, U.,Takio, K.,Eriksson, B.,Xuong, N.-H.,Yonetani, T.,Kraut, J.
      (1980) J.Biol.Chem. 255: 575



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C PEROXIDASE
A
294Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O
Query on O

Download SDF File 
Download CCD File 
A
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 Ligand Interaction
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: 1.7 Å
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.400α = 90.00
b = 76.800β = 90.00
c = 51.400γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1986-01-21
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other