Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 37.14 kDa 
• Atom Count: 3030 
• Modelled Residue Count: 299 
• Deposited Residue Count: 299 
• Unique protein chains: 1

2CIY

Chloroperoxidase complexed with cyanide and DMSO

• PDB DOI: 10.2210/pdb2CIY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leptoxyphium fumago
• Mutation(s): No 


• 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: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

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:  
  2CIV, 2CIW, 2CIX, 2CIY, 2CIZ, 2CJ0, 2CJ1, 2CJ2


• 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

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	D	2		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G53402KW GlyCosmos:  G53402KW GlyGen:  G53402KW

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BR	S [auth A], T [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
DMS	W [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	U [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CYN	V [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	D	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.21	α = 90
b = 151.03	β = 90
c = 101.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-03-11
  Changes: Data collection, Derived calculations, Other, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary