4USS | pdb_00004uss

Populus trichocarpa glutathione transferase X1-1 (GHR1), complexed with glutathione

• PDB DOI: https://doi.org/10.2210/pdb4USS/pdb

• Classification: TRANSFERASE
• Organism(s): Populus trichocarpa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-13 Released: 2014-12-03 
• Deposition Author(s): Lallement, P.A., Meux, E., Gualberto, J.M., Dumaracay, S., Favier, F., Didierjean, C., Saul, F., Haouz, A., Morel-Rouhier, M., Gelhaye, E., Rouhier, N., Hecker, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.233 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Glutathionyl-Hydroquinone Reductases from Poplar are Plastidial Proteins that Deglutathionylate Both Reduced and Oxidized Glutathionylated Quinones.

Lallement, P., Meux, E., Gualberto, J.M., Dumarcay, S., Favier, F., Didierjean, C., Saul, F., Haouz, A., Morel-Rouhier, M., Gelhaye, E., Rouhier, N., Hecker, A.

(2015) FEBS Lett 589: 37

• PubMed: 25455804 
• DOI: https://doi.org/10.1016/j.febslet.2014.11.021
• Primary Citation Related Structures: 
  4USS


• PubMed Abstract: 
  

  Glutathionyl-hydroquinone reductases (GHRs) catalyze the deglutathionylation of quinones via a catalytic cysteine. The two GHR genes in the Populus trichocarpa genome, Pt-GHR1 and Pt-GHR2, are primarily expressed in reproductive organs. Both proteins are localized in plastids. More specifically, Pt-GHR2 localizes in nucleoids. At the structural level, Pt-GHR1 adopts a typical GHR fold, with a dimerization interface comparable to that of the bacterial and fungal GHR counterparts. Pt-GHR1 catalyzes the deglutathionylation of both reduced and oxidized glutathionylated quinones, but the enzyme is more catalytically efficient with the reduced forms.

---

Organizational Affiliation: 
• Université de Lorraine, Interactions Arbres - Microorganismes, UMR1136, F-54500 Vandœuvre-lès-Nancy, France; INRA, Interactions Arbres - Microorganismes, UMR1136, F-54280 Champenoux, France.
Institut de Biologie Moléculaire des Plantes, CNRS-UPR 2357, 67084 Strasbourg, France.
Laboratoire d'Etudes et de Recherches sur le Matériau Bois, EA 1093, Vandœuvre-lès-Nancy F-54506, France.
Université de Lorraine, CRM(2), Equipe BioMod, UMR 7036, Faculté des Sciences et Technologies, BP 70239, 54506 Vandœuvre-lès-Nancy, France; CNRS, CRM(2), Equipe BioMod, UMR 7036, Faculté des Sciences et Technologies, BP 70239, 54506 Vandœuvre-lès-Nancy, France.
Institut Pasteur, Plate-Forme de Cristallographie, CNRS-UMR3528, 75724 Paris, France.
Université de Lorraine, Interactions Arbres - Microorganismes, UMR1136, F-54500 Vandœuvre-lès-Nancy, France; INRA, Interactions Arbres - Microorganismes, UMR1136, F-54280 Champenoux, France. Electronic address: [e-mail].

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)

Macromolecule Content 

• Total Structure Weight: 37.68 kDa 
• Atom Count: 2,579 
• Modeled Residue Count: 306 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTATHIONYL HYDROQUINONE REDUCTASE	A	325	Populus trichocarpa	Mutation(s): 0  EC: 2.5.1.18

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	B [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.233 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.53	α = 90
b = 92.409	β = 90
c = 86.901	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Lallement, P.A., Meux, E., Gualberto, J.M., Dumaracay, S., Favier, F., Didierjean, C., Saul, F., Haouz, A., Morel-Rouhier, M., Gelhaye, E., Rouhier, N., Hecker, A.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references
• Version 1.2: 2014-12-31
  Changes: Database references
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Other
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description