5FW4

Structure of Thermobifida fusca DyP-type Peroxidase and Activity towards Kraft Lignin and Lignin Model Compounds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Literature

Structure of Thermobifida Fusca Dyp-Type Peroxidase and Activity Towards Kraft Lignin and Lignin Model Compounds.

Rahmanpour, R.Rea, D.Jamshidi, S.Fulop, V.Bugg, T.D.H.

(2016) Arch Biochem Biophys 594: 54

  • DOI: https://doi.org/10.1016/j.abb.2016.02.019
  • Primary Citation of Related Structures:  
    5FW4

  • PubMed Abstract: 

    A Dyp-type peroxidase enzyme from thermophilic cellulose degrader Thermobifida fusca (TfuDyP) was investigated for catalytic ability towards lignin oxidation. TfuDyP was characterised kinetically against a range of phenolic substrates, and a compound I reaction intermediate was observed via pre-steady state kinetic analysis at λmax 404 nm. TfuDyP showed reactivity towards Kraft lignin, and was found to oxidise a β-aryl ether lignin model compound, forming an oxidised dimer. A crystal structure of TfuDyP was determined, to 1.8 Å resolution, which was found to contain a diatomic oxygen ligand bound to the heme centre, positioned close to active site residues Asp-203 and Arg-315. The structure contains two channels providing access to the heme cofactor for organic substrates and hydrogen peroxide. Site-directed mutant D203A showed no activity towards phenolic substrates, but reduced activity towards ABTS, while mutant R315Q showed no activity towards phenolic substrates, nor ABTS.


  • Organizational Affiliation

    Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DYE-DECOLORIZING PEROXIDASE TFU_3078
A, B
430Thermobifida fusca YXMutation(s): 0 
EC: 1.11.1.19
UniProt
Find proteins for Q47KB1 (Thermobifida fusca (strain YX))
Explore Q47KB1 
Go to UniProtKB:  Q47KB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47KB1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.36α = 90
b = 110.21β = 90
c = 46.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description