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: 110.63 kDa 
• Atom Count: 7712 
• Modelled Residue Count: 925 
• Deposited Residue Count: 986 
• Unique protein chains: 1

4G2C

DyP2 from Amycolatopsis sp. ATCC 39116

• PDB DOI: 10.2210/pdb4G2C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amycolatopsis sp. ATCC 39116
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-11 Released: 2012-10-24 
• Deposition Author(s): Brown, M.E., Barros, T., Chang, M.C.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.243 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium.

Brown, M.E., Barros, T., Chang, M.C.

(2012) ACS Chem Biol 7: 2074-2081

• PubMed: 23054399 
• DOI: 10.1021/cb300383y
• Primary Citation of Related Structures:  
  4G2C


• PubMed Abstract: 
  

Plant biomass represents a renewable feedstock that has not yet been fully tapped because of the difficulty in accessing the carbon in its structural biopolymers. Lignin is an especially challenging substrate, but select microbes have evolved complex systems of enzymes for its breakdown through a radical-mediated oxidation process. Fungal systems are well-characterized for their ability to depolymerize lignin, but the ability of bacteria to react with this substrate remains elusive. We have therefore focused on elucidating strategies used by lignin-reactive soil bacteria and describing their oxidative enzyme systems. We now report the identification and characterization of an unusual C-type dye-decolorizing peroxidase from Amycolatopsis sp. 75iv2 (DyP2), which belongs to a family of heme peroxidases reported to be involved in bacterial lignin degradation. Biochemical studies indicate that DyP2 has novel function for this family, with versatile and high activity both as a peroxidase and Mn peroxidase (k(cat)/K(M) ≈ 10(5)-10(6) M(-1) s(-1)). It also has a Mn-dependent oxidase mode of action that expands its substrate scope. Crystallographic studies of DyP2 at 2.25 Å resolution show the existence of a Mn binding pocket and support its key role in catalysis.

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Organizational Affiliation: 

Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DyP2	A, B	493	Amycolatopsis sp. ATCC 39116	Mutation(s): 0  Gene Names: dyp2 EC: 1 (PDB Primary Data), 1.11.1.16 (UniProt), 1.11.1.19 (UniProt), 1.11.1.7 (UniProt)
UniProt
Find proteins for K7N5M8 (Amycolatopsis sp. (strain ATCC 39116 / 75iv2)) Explore K7N5M8  Go to UniProtKB:  K7N5M8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], DA [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ACT	AA [auth A], BA [auth A], CA [auth A], E [auth A], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	D [auth A], EA [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.243 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.131	α = 90
b = 77.952	β = 90
c = 252.353	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-11 
• Released Date: 2012-10-24 
Deposition Author(s): Brown, M.E., Barros, T., Chang, M.C.Y.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references