6EZY | pdb_00006ezy

ARABIDOPSIS THALIANA GSTF9, GSH AND GSOH BOUND

PDB DOI: https://doi.org/10.2210/pdb6EZY/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-16 Released: 2018-08-15
Deposition Author(s): Tossounian, M.A., Wahni, K., VanMolle, I., Rosado, L., Vertommen, D., Messens, J.
Funding Organization(s): FWO, VIB-Marie Curie Cofund, VUB, Hercules

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.197 (Depositor), 0.178 (DCC)
R-Value Work:
0.156 (Depositor)
R-Value Observed:
0.158 (Depositor)

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

PubMed: 29732642 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.3440
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 49.24 kDa
Atom Count: 3,580
Modeled Residue Count: 423
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase F9	A, B	215	Arabidopsis thaliana	Mutation(s): 0 Gene Names: GSTF9, GLUTTR, GSTF7, At2g30860, F7F1.7 EC: 2.5.1.18
UniProt
Find proteins for O80852 (Arabidopsis thaliana) Explore O80852 Go to UniProtKB: O80852
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O80852
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GS8 Query on GS8 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	S-Hydroxy-Glutathione C₁₀ H₁₇ N₃ O₇ S PFXSQLOWBQWLCX-WDSKDSINSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	E [auth B]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.197 (Depositor), 0.178 (DCC)
R-Value Work: 0.156 (Depositor)
R-Value Observed: 0.158 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.125	α = 90
b = 114.125	β = 90
c = 89.81	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-15

Deposition Author(s):

Funding Organization	Location	Grant Number
FWO	Belgium	--
VIB-Marie Curie Cofund	Belgium	--
VUB	Belgium	SRP34
FWO	Belgium	G0D7914N
Hercules	Belgium	HERC16

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