6F6A | pdb_00006f6a

Crystal structure of glutathione transferase Omega 3S from Trametes versicolor in complex with dihydrowogonin from wild-cherry extract


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.193 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41598-018-26601-3
  • Primary Citation Related Structures: 
    6F43, 6F4B, 6F4F, 6F4K, 6F51, 6F66, 6F67, 6F68, 6F69, 6F6A, 6F70, 6F71, 6HT6

  • 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. 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, CNRS, CRM2, Nancy, France.

Macromolecule Content 

  • Total Structure Weight: 56.76 kDa 
  • Atom Count: 4,232 
  • Modeled Residue Count: 482 
  • Deposited Residue Count: 492 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
glutathione transferase
A, B
246Trametes versicolorMutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for A0A384E145 (Trametes versicolor)
Explore A0A384E145 
Go to UniProtKB:  A0A384E145
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A384E145
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH

Query on GSH



Download:Ideal Coordinates CCD File
D [auth A],
I [auth B]
Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
CU5
(Subject of Investigation/LOI)

Query on CU5



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
S-Dihydrowogonin
C16 H14 O5
FKAOWOSRYSMEBS-ZDUSSCGKSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.193 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.52α = 90
b = 104.49β = 90
c = 107.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description