8A0I

Crystal structure of poplar glutathione transferase U20 in complex with glutathionylphenylacetophenone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biochemical and Structural Insights on the Poplar Tau Glutathione Transferase GSTU19 and 20 Paralogs Binding Flavonoids.

Sylvestre-Gonon, E.Morette, L.Viloria, M.Mathiot, S.Boutilliat, A.Favier, F.Rouhier, N.Didierjean, C.Hecker, A.

(2022) Front Mol Biosci 9: 958586-958586

  • DOI: https://doi.org/10.3389/fmolb.2022.958586
  • Primary Citation of Related Structures:  
    7ZS3, 7ZVP, 7ZZN, 8A08, 8A0I, 8A0O, 8A0P, 8A0Q, 8A0R

  • PubMed Abstract: 

    Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in xenobiotic detoxification and/or in specialized metabolism. Populus trichocarpa genome (V4.1 assembly, Phytozome 13) consists of 74 genes coding for full-length GSTs and ten likely pseudogenes. These GSTs are divided into 11 classes, in which the tau class (GSTU) is the most abundant with 54 isoforms. PtGSTU19 and 20, two paralogs sharing more than 91% sequence identity (95% of sequence similarity), would have diverged from a common ancestor of P. trichocarpa and P. yatungensis species. These enzymes display the distinctive glutathione (GSH)-conjugation and peroxidase activities against model substrates. The resolution of the crystal structures of these proteins revealed significant structural differences despite their high sequence identity. PtGSTU20 has a well-defined deep pocket in the active site whereas the bottom of this pocket is disordered in PtGSTU19. In a screen of potential ligands, we were able to identify an interaction with flavonoids. Some of them, previously identified in poplar (chrysin, galangin, and pinocembrin), inhibited GSH-conjugation activity of both enzymes with a more pronounced effect on PtGSTU20. The crystal structures of PtGSTU20 complexed with these molecules provide evidence for their potential involvement in flavonoid transport in P. trichocarpa .


  • Organizational Affiliation

    Université de Lorraine, INRAE, IAM, Nancy, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione transferase219Populus trichocarpaMutation(s): 0 
Gene Names: POPTR_008G175000POPTR_1996s00210g
EC: 2.5.1.18
UniProt
Find proteins for D2X9R3 (Populus trichocarpa)
Explore D2X9R3 
Go to UniProtKB:  D2X9R3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2X9R3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CNZ (Subject of Investigation/LOI)
Query on CNZ

Download Ideal Coordinates CCD File 
B [auth A]L-gamma-glutamyl-S-(2-biphenyl-4-yl-2-oxoethyl)-L-cysteinylglycine
C24 H28 N3 O7 S
JIZFTRGOFNRYSA-OALUTQOASA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.62α = 90
b = 56.62β = 90
c = 181.79γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-09-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description