5A4V

AtGSTF2 from Arabidopsis thaliana in complex with quercetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands.

Ahmad, L.Rylott, E.L.Bruce, N.C.Edwards, R.Grogan, G.

(2017) FEBS Open Bio 7: 122-132

  • DOI: 10.1002/2211-5463.12168
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutathione transferases (GSTs) are involved in many processes in plant biochemistry, with their best characterised role being the detoxification of xenobiotics through their conjugation with glutathione. GSTs have also been implicated in noncatalyti ...

    Glutathione transferases (GSTs) are involved in many processes in plant biochemistry, with their best characterised role being the detoxification of xenobiotics through their conjugation with glutathione. GSTs have also been implicated in noncatalytic roles, including the binding and transport of small heterocyclic ligands such as indole hormones, phytoalexins and flavonoids. Although evidence for ligand binding and transport has been obtained using gene deletions and ligand binding studies on purified GSTs, there has been no structural evidence for the binding of relevant ligands in noncatalytic sites. Here we provide evidence of noncatalytic ligand-binding sites in the phi class GST from the model plant Arabidopsis thaliana, AtGSTF2, revealed by X-ray crystallography. Complexes of the AtGSTF2 dimer were obtained with indole-3-aldehyde, camalexin, the flavonoid quercetrin and its non-rhamnosylated analogue quercetin, at resolutions of 2.00, 2.77, 2.25 and 2.38 Å respectively. Two symmetry-equivalent-binding sites (L1) were identified at the periphery of the dimer, and one more (L2) at the dimer interface. In the complexes, indole-3-aldehyde and quercetrin were found at both L1 and L2 sites, but camalexin was found only at the L1 sites and quercetin only at the L2 site. Ligand binding at each site appeared to be largely determined through hydrophobic interactions. The crystallographic studies support previous conclusions made on ligand binding in noncatalytic sites by AtGSTF2 based on isothermal calorimetry experiments (Dixon et al. (2011) Biochem J438, 63-70) and suggest a mode of ligand binding in GSTs commensurate with a possible role in ligand transport.


    Organizational Affiliation

    York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkUK; Department of BiologyCentre for Novel Agricultural ProductsUniversity of YorkUK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE S-TRANSFERASE F2
A, B, C, D, E, F
212Arabidopsis thalianaMutation(s): 0 
Gene Names: GSTF2 (PM24.1)
EC: 2.5.1.18
Find proteins for P46422 (Arabidopsis thaliana)
Go to UniProtKB:  P46422
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

Download SDF File 
Download CCD File 
B, D, F
3,5,7,3',4'-PENTAHYDROXYFLAVONE
QUERCETIN
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.030α = 90.00
b = 94.830β = 90.00
c = 153.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references, Structure summary
  • Version 1.2: 2017-03-01
    Type: Database references