6HPE

Crystal structure of glutathione transferase Omega 3S from Trametes versicolor in complex with the glutathione adduct of phenethyl-isothiocyanate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The structure of Trametes versicolor glutathione transferase Omega 3S bound to its conjugation product glutathionyl-phenethylthiocarbamate reveals plasticity of its active site.

Schwartz, M.Perrot, T.Morel-Rouhier, M.Mulliert, G.Gelhaye, E.Didierjean, C.Favier, F.

(2019) Protein Sci 28: 1143-1150

  • DOI: https://doi.org/10.1002/pro.3620
  • Primary Citation of Related Structures:  
    6HPE

  • PubMed Abstract: 

    Trametes versicolor glutathione transferase Omega 3S (TvGSTO3S) catalyzes the conjugation of isothiocyanates (ITC) with glutathione (GSH). Previously, this isoform was investigated in depth both biochemically and structurally. Structural analysis of complexes revealed the presence of a GSH binding site (G site) and a deep hydrophobic binding site (H site) able to bind plant polyphenols. In the present study, crystals of apo TvGSTO3S were soaked with glutathionyl-phenethylthiocarbamate, the product of the reaction between GSH and phenethyl isothiocyanate (PEITC). On the basis of this crystal structure, we show that the phenethyl moiety binds in a new site at loop β 2 2 while the glutathionyl part exhibits a particular conformation that occupies both the G site and the entrance to the H site. This binding mode is allowed by a conformational change of the loop β 2 2 at the enzyme active site. It forms a hydrophobic slit that stabilizes the phenethyl group at a distinct site from the previously described H site. Structural comparison of TvGSTO3S with drosophila DmGSTD2 suggests that this flexible loop could be the region that binds PEITC for both isoforms. These structural features are discussed in a catalytic context.


  • Organizational Affiliation

    Université de Lorraine, CNRS, CRM2, Nancy, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione transferase Omega 3S
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GVX
Query on GVX

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
L-gamma-glutamyl-S-[(2-phenylethyl)carbamothioyl]-L-cysteinylglycine
C19 H26 N4 O6 S2
WSGBVCNCZSZCGE-KBPBESRZSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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D [auth A],
H [auth B],
I [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

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G [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.26α = 90
b = 104.03β = 90
c = 106.47γ = 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-LAS-0002-01

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description