6F05 | pdb_00006f05

ARABIDOPSIS THALIANA GSTF9, GSO3 BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GTSClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Redox-regulated methionine oxidation of Arabidopsis thaliana glutathione transferase Phi9 induces H-site flexibility.

Tossounian, M.A.Wahni, K.Van Molle, I.Vertommen, D.Astolfi Rosado, L.Messens, J.

(2019) Protein Sci 28: 56-67

  • DOI: https://doi.org/10.1002/pro.3440
  • Primary Citation of Related Structures:  
    6EZY, 6F01, 6F05

  • PubMed Abstract: 

    Glutathione transferase enzymes help plants to cope with biotic and abiotic stress. They mainly catalyze the conjugation of glutathione (GSH) onto xenobiotics, and some act as glutathione peroxidase. With X-ray crystallography, kinetics, and thermodynamics, we studied the impact of oxidation on Arabidopsis thaliana glutathione transferase Phi 9 (GSTF9). GSTF9 has no cysteine in its sequence, and it adopts a universal GST structural fold characterized by a typical conserved GSH-binding site (G-site) and a hydrophobic co-substrate-binding site (H-site). At elevated H 2 O 2 concentrations, methionine sulfur oxidation decreases its transferase activity. This oxidation increases the flexibility of the H-site loop, which is reflected in lower activities for hydrophobic substrates. Determination of the transition state thermodynamic parameters shows that upon oxidation an increased enthalpic penalty is counterbalanced by a more favorable entropic contribution. All in all, to guarantee functionality under oxidative stress conditions, GSTF9 employs a thermodynamic and structural compensatory mechanism and becomes substrate of methionine sulfoxide reductases, making it a redox-regulated enzyme.


  • Organizational Affiliation

    VIB-VUB Center for Structural Biology, Brussels, B-1050, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase F9
A, B, C, D, E
215Arabidopsis thalianaMutation(s): 0 
Gene Names: GSTF9GLUTTRGSTF7At2g30860F7F1.7
EC: 2.5.1.18
UniProt
Find proteins for O80852 (Arabidopsis thaliana)
Explore O80852 
Go to UniProtKB:  O80852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO80852
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTS
Query on GTS

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
EA [auth I]
GA [auth J]
K [auth A]
GLUTATHIONE SULFONIC ACID
C10 H17 N3 O9 S
QGWRMTHFAZVWAM-WDSKDSINSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
FA [auth I]
N [auth A]
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.43α = 93.19
b = 93.97β = 101.57
c = 107.71γ = 101.97
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GTSClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FWOBelgium--
VIB-Marie Curie CofundBelgium--
VUBBelgiumSRP34
FWOBelgiumG0D7914N
HerculesBelgiumHERC16

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description