Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,609 
• Modelled Residue Count: 293 
• Deposited Residue Count: 294 
• Unique protein chains: 1

 2CYP

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

• PDB DOI:  https://doi.org/10.2210/pdb2CYP/pdb
• Entry: 2CYP supersedes: 1CYP

• Classification: OXIDOREDUCTASE (H2O2(A))
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1985-08-27 Released: 1986-01-21 
• Deposition Author(s): Finzel, B.C., Poulos, T.L., Kraut, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.202 

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

• PubMed: 6092361 
• Primary Citation of Related Structures:  
  2CYP


• 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 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.

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Related Citations: 

• 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

• 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

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Organizational Affiliation: 

Unité Propre de Recherche 9002 du Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C PEROXIDASE	A	294	Saccharomyces cerevisiae	Mutation(s): 0  EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431  Go to UniProtKB:  P00431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
O	C [auth A]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.4	α = 90
b = 76.8	β = 90
c = 51.4	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1986-01-21 
Deposition Author(s): Finzel, B.C., Poulos, T.L., Kraut, J.
• This entry supersedes: 1CYP

Revision History  

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