6ZB6

Crystal structure of Lolium rigidum GSTF in complex with S-(p-nitrobenzyl) glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Phi class glutathione transferases as molecular targets towards multiple-herbicide resistance: Inhibition analysis and pharmacophore design.

Georgakis, N.Poudel, N.Vlachakis, D.Papageorgiou, A.C.Labrou, N.E.

(2021) Plant Physiol Biochem 158: 342-352

  • DOI: https://doi.org/10.1016/j.plaphy.2020.11.018
  • Primary Citation of Related Structures:  
    6ZB6

  • PubMed Abstract: 
  • Multiple-herbicide resistance (MHR) is a global threat to weed control in cereal crops. MHR weeds express a specific phi class glutathione transferase (MHR-GSTF) that confers resistance against multiple herbicides and therefore represents a promising target against MHR weeds ...

    Multiple-herbicide resistance (MHR) is a global threat to weed control in cereal crops. MHR weeds express a specific phi class glutathione transferase (MHR-GSTF) that confers resistance against multiple herbicides and therefore represents a promising target against MHR weeds. Kinetics inhibition analysis of MHR-GSTFs from grass weeds Lolium rigidum (LrGSTF) Alopecurus myosuroides (AmGSTF) and crops Hordeum vulgare (HvGSTF) and Triticum aestivum (TaGSTF) allowed the identification of the acetanilide herbicide butachlor as a potent and selective inhibitor towards MHR-GSTFs. Also, butachlor is a stronger inhibitor for LrGSTF and AmGSTF compared to HvGSTF and TaGSTF from crops. The crystal structure of LrGSTF was determined at 1.90 Å resolution in complex with the inhibitor S-(4-nitrobenzyl)glutathione. A specific 3D pharmacophore targeting the MHR-GSTFs was designed and used to identify structural elements important for potent and selective inhibition. Structural analysis of GSTFs revealed a decisive role of conserved Tyr118 in ligand binding and pharmacophore design. Its positioning is dependent on an outer patch of adjacent residues that span from position 132 to 134 which are similar for both LrGSTF and AmGSTF but different in HvGSTF and TaGSTF. The results presented here provide new knowledge that may be adopted to cope with MHR weeds.


    Organizational Affiliation

    Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR, 11855, Athens, Greece. Electronic address: lambrou@aua.gr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutathione transferase227Lolium rigidumMutation(s): 0 
Gene Names: GST
EC: 2.5.1.18
UniProt
Find proteins for M5BPX4 (Lolium rigidum)
Explore M5BPX4 
Go to UniProtKB:  M5BPX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM5BPX4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTB (Subject of Investigation/LOI)
Query on GTB

Download Ideal Coordinates CCD File 
G [auth A],
M [auth C],
P [auth E],
R [auth B],
Y [auth F]
S-(P-NITROBENZYL)GLUTATHIONE
C17 H22 N4 O8 S
OAWORKDPTSAMBZ-STQMWFEESA-N
 Ligand Interaction
GSH (Subject of Investigation/LOI)
Query on GSH

Download Ideal Coordinates CCD File 
CA [auth D]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth D]
H [auth A]
I [auth A]
N [auth C]
Q [auth E]
DA [auth D],
H [auth A],
I [auth A],
N [auth C],
Q [auth E],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
Z [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
EA [auth D]
J [auth A]
K [auth A]
AA [auth F],
BA [auth F],
EA [auth D],
J [auth A],
K [auth A],
L [auth A],
O [auth C],
W [auth B],
X [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.562α = 90
b = 98.5β = 109.126
c = 95.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hellenic Foundation for Research and Innovation (HFRI)Greece8904/22-09-2017

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references