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.

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 96.23 kDa 
• Atom Count: 6773 
• Modelled Residue Count: 878 
• Deposited Residue Count: 884 
• Unique protein chains: 1

2D3Q

Crystal Structure of a Decolorizing Peroxidase (DyP) That Catalyses the Biological Oxidation of Anthraquinone Derivatives

• PDB DOI: 10.2210/pdb2D3Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bjerkandera adusta
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2005-09-30 Released: 2006-09-30 
• Deposition Author(s): Sato, T., Sugano, Y., Shoda, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.234 
• R-Value Observed: 0.265 

Literature

The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue

Yoshida, T., Tsuge, H., Konno, H., Hisabori, T., Sugano, Y.

(2011) FEBS J 278: 2387-2394

• PubMed: 21569205 
• DOI: 10.1111/j.1742-4658.2011.08161.x
• Primary Citation of Related Structures:  
  2D3Q, 3AFV, 3MM1, 3MM2, 3MM3


• PubMed Abstract: 
  

The dye-decolorizing peroxidase (DyP)-type peroxidase family is a unique heme peroxidase family. The primary and tertiary structures of this family are obviously different from those of other heme peroxidases. However, the details of the structure-function relationships of this family remain poorly understood. We show four high-resolution structures of DyP (EC1.11.1.19), which is representative of this family: the native DyP (1.40 Å), the D171N mutant DyP (1.42 Å), the native DyP complexed with cyanide (1.45 Å), and the D171N mutant DyP associated with cyanide (1.40 Å). These structures contain four amino acids forming the binding pocket for hydrogen peroxide, and they are remarkably conserved in this family. Moreover, these structures show that OD2 of Asp171 accepts a proton from hydrogen peroxide in compound I formation, and that OD2 can swing to the appropriate position in response to the ligand for heme iron. On the basis of these results, we propose a swing mechanism in compound I formation. When DyP reacts with hydrogen peroxide, OD2 swings towards an optimal position to accept the proton from hydrogen peroxide bound to the heme iron.

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Related Citations: 

• A unique dye-decolorizing peroxidase, DyP, from Thanatephorus cucumeris Dec 1: heterologous expression, crystallization and preliminary X-ray analysis
  Sato, T., Hara, S., Matsui, T., Sazaki, G., Saijo, S., Ganbe, T., Tanaka, N., Sugano, Y., Shoda, M.
  (2004) Acta Crystallogr D Biol Crystallogr 60: 149

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Organizational Affiliation: 

R1-7 Chemical Resources Laboratory, Tokyo Institute of Technology, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decolorizing Peroxidase	A, B	442	Bjerkandera adusta	Mutation(s): 0  Gene Names: dyp EC: 1.11.1.19
UniProt
Find proteins for Q8WZK8 (Bjerkandera adusta) Explore Q8WZK8  Go to UniProtKB:  Q8WZK8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.234 
• R-Value Observed: 0.265 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.212	α = 90
b = 136.212	β = 90
c = 363.596	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
TRUNCATE	data reduction
MLPHARE	phasing
CNS	refinement
CrystalClear	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-30 
• Released Date: 2006-09-30 
Deposition Author(s): Sato, T., Sugano, Y., Shoda, M.

Revision History  

• Version 1.0: 2006-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-10-26
  Changes: Database references, Source and taxonomy