8AX0

Crystal structure of Trametes versicolor glutathione transferase Omega 3S in complex with sodium nitroprusside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the interactions of glutathione transferases with a nitric oxide carrier and sodium nitroprusside.

Schwartz, M.Perrot, T.Beurton, J.Zannini, F.Morel-Rouhier, M.Gelhaye, E.Neiers, F.Schaniel, D.Favier, F.Jacquot, J.P.Leroy, P.Clarot, I.Boudier, A.Didierjean, C.

(2023) Biochem Biophys Res Commun 649: 79-86

  • DOI: https://doi.org/10.1016/j.bbrc.2023.01.099
  • Primary Citation of Related Structures:  
    8AWZ, 8AX0, 8AX1, 8AX2

  • PubMed Abstract: 

    Glutathione transferases are detoxification enzymes with multifaceted roles, including a role in the metabolism and scavenging of nitric oxide (NO) compounds in cells. Here, we explored the ability of Trametes versicolor glutathione transferases (GSTs) from the Omega class (TvGSTOs) to bind metal-nitrosyl compounds. TvGSTOs have been studied previously for their ligandin role and are interesting models to study protein‒ligand interactions. First, we determined the X-ray structure of the TvGSTO3S isoform bound to the dinitrosyl glutathionyl iron complex (DNGIC), a physiological compound involved in the storage of nitric oxide. Our results suggested a different binding mode compared to the one previously described in human GST Pi 1 (GSTP1). Then, we investigated the manner in which TvGSTO3S binds three nonphysiological metal-nitrosyl compounds with different metal cores (iron, ruthenium and osmium). We assayed sodium nitroprusside, a well-studied vasodilator used in cases of hypertensive crises or heart failure. Our results showed that the tested GST can bind metal-nitrosyls at two distinct binding sites. Thermal shift analysis with six isoforms of TvGSTOs identified TvGSTO6S as the best interactant. Using the Griess method, TvGSTO6S was found to improve the release of nitric oxide from sodium nitroprusside in vitro, whereas the effects of human GST alpha 1 (GSTA1) and GSTP1 were moderate. Our results open new structural perspectives for understanding the interactions of glutathione transferases with metal-nitrosyl compounds associated with the biochemical mechanisms of NO uptake/release in biological systems.


  • Organizational Affiliation

    Université de Lorraine, CNRS, CRM2, F-54000, Nancy, France; CSGA, INRAE, University of Burgundy, CNRS, Institut Agro, F-21000, Dijon, France. Electronic address: mathieu.schwartz@inrae.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione transferase
A, B
246Trametes versicolorMutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for A0A384E145 (Trametes versicolor)
Explore A0A384E145 
Go to UniProtKB:  A0A384E145
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A384E145
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NT3 (Subject of Investigation/LOI)
Query on NT3

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A],
H [auth B],
J [auth B]
Nitroprusside ion
C5 H Fe N6 O
FXHPAMQNLMZRAK-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth B],
L [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.51α = 90
b = 104.31β = 90
c = 107.38γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-11-LAS-0002-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description