Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 37192.40 
• Atom Count: 2632 
• Residue Count: 299 
• Unique protein chains: 1

2CIY

Chloroperoxidase complexed with cyanide and DMSO

• DOI: 10.2210/pdb2CIY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leptoxyphium fumago


• Deposited: 2006-03-26 Released: 2006-06-12 
• Deposition Author(s): Kuhnel, K., Blankenfeldt, W., Terner, J., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 

Literature

Crystal Structures of Chloroperoxidase with its Bound Substrates and Complexed with Formate, Acetate, and Nitrate.

Kuhnel, K., Blankenfeldt, W., Terner, J., Schlichting, I.

(2006) J.Biol.Chem. 281: 23990

• PubMed: 16790441 
• DOI: 10.1074/jbc.M603166200
• Primary Citation of Related Structures:  
  2CJ2, 2CJ1, 2CJ0, 2CIZ, 2CIX, 2CIW, 2CIV


• PubMed Abstract: 
  

Chloroperoxidase (CPO) is a heme-thiolate enzyme that catalyzes hydrogen peroxide-dependent halogenation reactions. Structural data on substrate binding have not been available so far. CPO was therefore crystallized in the presence of iodide or bromide. One halide binding site was identified at the surface near a narrow channel that connects the surface with the heme. Two other halide binding sites were identified within and at the other end of this channel. Together, these sites suggest a pathway for access of halide anions to the active site. The structure of CPO complexed with its natural substrate cyclopentanedione was determined at a resolution of 1.8 A. This is the first example of a CPO structure with a bound organic substrate. In addition, structures of CPO bound with nitrate, acetate, and formate and of a ternary complex with dimethylsulfoxide (Me2SO) and cyanide were determined. These structures have implications for the mechanism of compound I formation. Before binding to the heme, the incoming hydrogen peroxide first interacts with Glu-183. The deprotonated Glu-183 abstracts a proton from hydrogen peroxide. The hydroperoxo-anion then binds at the heme, yielding compound 0. Glu-183 protonates the distal oxygen of compound 0, water is released, and compound I is formed.

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Organizational Affiliation: 

Abteilung Biomolekulare Mechanismen, Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CHLOROPEROXIDASE	A	299	Leptoxyphium fumago	Mutation(s): 0  Gene Names: CPO EC: 1.11.1.10
Find proteins for P04963 (Leptoxyphium fumago) Go to Gene View: CPO Go to UniProtKB:  P04963

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CYN	A	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BR	A	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 58.210	α = 90.00
b = 151.030	β = 90.00
c = 101.110	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-03-26 
• Released Date: 2006-06-12 
• Deposition Author(s): Kuhnel, K., Blankenfeldt, W., Terner, J., Schlichting, I.

Revision History 

• Version 1.0: 2006-06-12
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance