6GZW

Ferric DtpA from Streptomyces lividans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

An Aromatic Dyad Motif in Dye Decolourising Peroxidases Has Implications for Free Radical Formation and Catalysis.

Chaplin, A.K.Chicano, T.M.Hampshire, B.V.Wilson, M.T.Hough, M.A.Svistunenko, D.A.Worrall, J.A.R.

(2019) Chemistry 25: 6141-6153

  • DOI: 10.1002/chem.201806290
  • Primary Citation of Related Structures:  
    6GZW

  • PubMed Abstract: 
  • Dye decolouring peroxidases (DyPs) are the most recent class of heme peroxidase to be discovered. On reacting with H 2 O 2 , DyPs form a high-valent iron(IV)-oxo species and a porphyrin radical (Compound I) followed by stepwise oxidation of an organic substrate ...

    Dye decolouring peroxidases (DyPs) are the most recent class of heme peroxidase to be discovered. On reacting with H 2 O 2 , DyPs form a high-valent iron(IV)-oxo species and a porphyrin radical (Compound I) followed by stepwise oxidation of an organic substrate. In the absence of substrate, the ferryl species decays to form transient protein-bound radicals on redox active amino acids. Identification of radical sites in DyPs has implications for their oxidative mechanism with substrate. Using a DyP from Streptomyces lividans, referred to as DtpA, which displays low reactivity towards synthetic dyes, activation with H 2 O 2 was explored. A Compound I EPR spectrum was detected, which in the absence of substrate decays to a protein-bound radical EPR signal. Using a newly developed version of the Tyrosyl Radical Spectra Simulation Algorithm, the radical EPR signal was shown to arise from a pristine tyrosyl radical and not a mixed Trp/Tyr radical that has been widely reported in DyP members exhibiting high activity with synthetic dyes. The radical site was identified as Tyr374, with kinetic studies inferring that although Tyr374 is not on the electron-transfer pathway from the dye RB19, its replacement with a Phe does severely compromise activity with other organic substrates. These findings hint at the possibility that alternative electron-transfer pathways for substrate oxidation are operative within the DyP family. In this context, a role for a highly conserved aromatic dyad motif is discussed.


    Organizational Affiliation

    School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dye type peroxidase AA, B377Streptomyces lividans 1326Mutation(s): 0 
EC: 1.11.1
UniProt
Find proteins for A0A076MAJ9 (Streptomyces lividans TK24)
Explore A0A076MAJ9 
Go to UniProtKB:  A0A076MAJ9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.118α = 90
b = 71.032β = 92.83
c = 78.089γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
EDNAdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2014-355

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release