6TK8 | pdb_00006tk8

GSTF1 F122T variant from Alopecurus myosuroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance.

Schwarz, M.Eno, R.F.M.Freitag-Pohl, S.Coxon, C.R.Straker, H.E.Wortley, D.J.Hughes, D.J.Mitchell, G.Moore, J.Cummins, I.Onkokesung, N.Brazier-Hicks, M.Edwards, R.Pohl, E.Steel, P.G.

(2021) Org Biomol Chem 19: 9211-9222

  • DOI: https://doi.org/10.1039/d1ob01802g
  • Primary Citation Related Structures: 
    6TJS, 6TK8, 6TNL, 6TO3, 7OBO, 7ODM

  • PubMed Abstract: 

    The evolution and growth of multiple-herbicide resistance (MHR) in grass weeds continues to threaten global cereal production. While various processes can contribute to resistance, earlier work has identified the phi class glutathione- S -transferase ( Am GSTF1) as a functional biomarker of MHR in black-grass ( Alopecurus myosuroides ). This study provides further insights into the role of Am GSTF1 in MHR using a combination of chemical and structural biology. Crystal structures of wild-type Am GSTF1, together with two specifically designed variants that allowed the co-crystal structure determination with glutathione and a glutathione adduct of the Am GSTF1 inhibitor 4-chloro-7-nitro-benzofurazan (NBD-Cl) were obtained. These studies demonstrated that the inhibitory activity of NBD-Cl was associated with the occlusion of the active site and the impediment of substrate binding. A search for other selective inhibitors of Am GSTF1, using ligand-fishing experiments, identified a number of flavonoids as potential ligands. Subsequent experiments using black-grass extracts discovered a specific flavonoid as a natural ligand of the recombinant enzyme. A series of related synthetic flavonoids was prepared and their binding to Am GSTF1 was investigated showing a high affinity for derivatives bearing a O -5-decyl-α-carboxylate. Molecular modelling based on high-resolution crystal structures allowed a binding pose to be defined which explained flavonoid binding specificity. Crucially, high binding affinity was linked to a reversal of the herbicide resistance phenotype in MHR black-grass. Collectively, these results present a nature-inspired new lead for the development of herbicide synergists to counteract MHR in weeds.


  • Organizational Affiliation
    • Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK. p.g.steel@durham.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 25.22 kDa 
  • Atom Count: 1,674 
  • Modeled Residue Count: 213 
  • Deposited Residue Count: 219 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione transferaseA [auth AAA]219Alopecurus myosuroidesMutation(s): 1 
Gene Names: GST2c
EC: 2.5.1.18
UniProt
Find proteins for Q9ZS17 (Alopecurus myosuroides)
Explore Q9ZS17 
Go to UniProtKB:  Q9ZS17
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZS17
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH
(Subject of Investigation/LOI)

Query on GSH



Download:Ideal Coordinates CCD File
B [auth AAA]Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.251 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.59α = 90
b = 112.59β = 90
c = 104.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/G006474/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2025-09-17
    Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary