6HTA | pdb_00006hta

Crystal structure of glutathione transferase Xi 3 mutant C56S from Trametes versicolor

• PDB DOI: https://doi.org/10.2210/pdb6HTA/pdb

• Classification: TRANSFERASE
• Organism(s): Trametes versicolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-03 Released: 2018-10-10 
• Deposition Author(s): Schwartz, M., Favier, F., Didierjean, C.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Trametes versicolor glutathione transferase Xi 3, a dual Cys-GST with catalytic specificities of both Xi and Omega classes.

Schwartz, M., Perrot, T., Deroy, A., Roret, T., Morel-Rouhier, M., Mulliert, G., Gelhaye, E., Favier, F., Didierjean, C.

(2018) FEBS Lett 592: 3163-3172

• PubMed: 30112765 
• DOI: https://doi.org/10.1002/1873-3468.13224
• Primary Citation Related Structures: 
  6GC9, 6GCA, 6GCB, 6GCC, 6HTA


• PubMed Abstract: 
  

  Glutathione transferases (GSTs) from the Xi and Omega classes have a catalytic cysteine residue, which gives them reductase activities. Until now, they have been assigned distinct substrates. While Xi GSTs specifically reduce glutathionyl-(hydro)quinones, Omega GSTs are specialized in the reduction of glutathionyl-acetophenones. Here, we present the biochemical and structural analysis of TvGSTX1 and TvGSTX3 isoforms from the wood-degrading fungus Trametes versicolor. TvGSTX1 reduces GS-menadione as expected, while TvGSTX3 reduces both Xi and Omega substrates. An in-depth structural analysis indicates a broader active site for TvGSTX3 due to specific differences in the nature of the residues situated in the C-terminal helix α9. This feature could explain the catalytic duality of TvGSTX3. Based on phylogenetic analysis, we propose that this duality might exist in saprophytic fungi and ascomycetes.

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Organizational Affiliation: 
• CNRS, CRM2, Université de Lorraine, Nancy, France.
INRA, IAM, Université de Lorraine, Nancy, France.
CNRS, LBI2M, Sorbonne Université, Roscoff, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 74.51 kDa 
• Atom Count: 5,321 
• Modeled Residue Count: 593 
• Deposited Residue Count: 650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione transferase Xi 3 C56S	A, B	325	Trametes versicolor	Mutation(s): 0
UniProt
Find proteins for A0A3F2YM29 (Trametes versicolor) Explore A0A3F2YM29  Go to UniProtKB:  A0A3F2YM29

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	C [auth A], E [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.903	α = 90
b = 56.653	β = 107.17
c = 93.793	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Schwartz, M., Favier, F., Didierjean, C.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-11-LAS-0002-01

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary