8OHY

Native Structure of Dictyostelium discoideum dye-decolorizing peroxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme.

Kalkan, O.Kantamneni, S.Brings, L.Han, H.Bean, R.Mancuso, A.P.Koua, F.H.M.

(2023) Front Chem 11: 1220543-1220543

  • DOI: https://doi.org/10.3389/fchem.2023.1220543
  • Primary Citation of Related Structures:  
    8OHY

  • PubMed Abstract: 

    The Dictyostelium discoideum dye-decolorizing peroxidase ( Dd DyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. Dd DyP catalyzes the H 2 O 2 -dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of Dd DyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the Dd DyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of Dd DyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native Dd DyP active site and its implication on DyP catalysis.


  • Organizational Affiliation

    European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxidase306Dictyostelium discoideum AX4Mutation(s): 0 
Gene Names: DDB0168077DDB0217308
UniProt
Find proteins for Q556V8 (Dictyostelium discoideum)
Explore Q556V8 
Go to UniProtKB:  Q556V8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ556V8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.88α = 90
b = 99.88β = 90
c = 73.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-03-29 
  • Deposition Author(s): Koua, F.H.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection, Database references