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 PISA (software)

Macromolecule Content

• Total Structure Weight: 47.60 kDa 
• Atom Count: 4045 
• Modelled Residue Count: 446 
• Deposited Residue Count: 449 
• Unique protein chains: 1

4W7O

CRYSTAL STRUCTURE OF A DECOLORIZING PEROXIDASE (DYP) FROM AURICULARIA AURICULA-JUDAE. G169L, Y147S AND W377S TRIPLE MUTANT

• PDB DOI: 10.2210/pdb4W7O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Auricularia auricula-judae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-08-22 Released: 2015-03-11 
• Deposition Author(s): Medrano, F.J., Romero, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.153 
• R-Value Work: 0.141 
• R-Value Observed: 0.141 

Literature

Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.

Linde, D., Pogni, R., Canellas, M., Lucas, F., Guallar, V., Baratto, M.C., Sinicropi, A., Saez-Jimenez, V., Coscolin, C., Romero, A., Medrano, F.J., Ruiz-Duenas, F.J., Martinez, A.T.

(2015) Biochem J 466: 253-262

• PubMed: 25495127 
• DOI: 10.1042/BJ20141211
• Primary Citation of Related Structures:  
  4W7J, 4W7K, 4W7L, 4W7M, 4W7N, 4W7O


• PubMed Abstract: 
  

Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H₂O₂-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.

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Organizational Affiliation: 

*Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dye-decolorizing peroxidase	A	449	Auricularia auricula-judae	Mutation(s): 3  Gene Names: dyp1 EC: 1.11.1.19 (PDB Primary Data), 1.11.1.7 (UniProt)
UniProt
Find proteins for I2DBY1 (Auricularia auricula-judae) Explore I2DBY1  Go to UniProtKB:  I2DBY1

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.153 
• R-Value Work: 0.141 
• R-Value Observed: 0.141 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.37	α = 90
b = 56.095	β = 96.9
c = 82.041	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-22 
• Released Date: 2015-03-11 
Deposition Author(s): Medrano, F.J., Romero, A.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release