6F71

Crystal structure of glutathione transferase Omega 6S from Trametes versicolor in complex with naringenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor.

Schwartz, M.Perrot, T.Aubert, E.Dumarcay, S.Favier, F.Gerardin, P.Morel-Rouhier, M.Mulliert, G.Saiag, F.Didierjean, C.Gelhaye, E.

(2018) Sci Rep 8: 8472-8472

  • DOI: 10.1038/s41598-018-26601-3
  • Primary Citation of Related Structures:  
    6HT6, 6F4B, 6F43, 6F51, 6F4F, 6F4K, 6F6A, 6F67, 6F66, 6F69

  • PubMed Abstract: 
  • Wood decay fungi have complex detoxification systems that enable them to cope with secondary metabolites produced by plants. Although the number of genes encoding for glutathione transferases is especially expanded in lignolytic fungi, little is known about their target molecules ...

    Wood decay fungi have complex detoxification systems that enable them to cope with secondary metabolites produced by plants. Although the number of genes encoding for glutathione transferases is especially expanded in lignolytic fungi, little is known about their target molecules. In this study, by combining biochemical, enzymatic and structural approaches, interactions between polyphenols and six glutathione transferases from the white-rot fungus Trametes versicolor have been demonstrated. Two isoforms, named TvGSTO3S and TvGSTO6S have been deeply studied at the structural level. Each isoform shows two distinct ligand-binding sites, a narrow L-site at the dimer interface and a peculiar deep hydrophobic H-site. In TvGSTO3S, the latter appears optimized for aromatic ligand binding such as hydroxybenzophenones. Affinity crystallography revealed that this H-site retains the flavonoid dihydrowogonin from a partially purified wild-cherry extract. Besides, TvGSTO6S binds two molecules of the flavonoid naringenin in the L-site. These data suggest that TvGSTO isoforms could interact with plant polyphenols released during wood degradation.


    Organizational Affiliation

    Université de Lorraine, INRA, IAM, Nancy, France. eric.gelhaye@univ-lorraine.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glutathione transferaseA, B, C, D252Trametes versicolorMutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for A0A384E158 (Trametes versicolor)
Explore A0A384E158 
Go to UniProtKB:  A0A384E158
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CWE
Query on CWE

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]R-naringenin
C15 H12 O5
FTVWIRXFELQLPI-CYBMUJFWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.81α = 90
b = 78.88β = 101.49
c = 93.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-11-LABX-0002-01
CNRS-University of LorraineFrancePEPS MIRABELLE 2016

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references, Structure summary