6F05

ARABIDOPSIS THALIANA GSTF9, GSO3 BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
A, B, C, D, E, F, G, H, I, J
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
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  • 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]
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
K [auth A],
O [auth B],
S [auth C],
U [auth D],
W [auth E],
Y [auth F]
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]
BA [auth G],
DA [auth H],
FA [auth I],
N [auth A],
R [auth B],
T [auth C],
V [auth D],
X [auth E],
Z [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • 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

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Ligand Structure Quality Assessment 


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