4G2C

DyP2 from Amycolatopsis sp. ATCC 39116


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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DyP2AB493Amycolatopsis sp. ATCC 39116Mutation(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)
Find proteins for K7N5M8 (Amycolatopsis sp. (strain ATCC 39116 / 75iv2))
Explore K7N5M8 
Go to UniProtKB:  K7N5M8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
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 = 48.131α = 90
b = 77.952β = 90
c = 252.353γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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