4IS0

Structural Insights into Omega-Class Glutathione Transferases: A Snapshot of Enzyme Reduction and Identification of the Non-Catalytic Ligandin Site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.201 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDSClick on this verticalbar to view detailsBest fitted 1R4Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Structural insights into omega-class glutathione transferases: a snapshot of enzyme reduction and identification of a non-catalytic ligandin site.

Brock, J.Board, P.G.Oakley, A.J.

(2013) PLoS One 8: e60324-e60324

  • DOI: https://doi.org/10.1371/journal.pone.0060324
  • Primary Citation of Related Structures:  
    4IS0

  • PubMed Abstract: 

    Glutathione transferases (GSTs) are dimeric enzymes containing one active-site per monomer. The omega-class GSTs (hGSTO1-1 and hGSTO2-2 in humans) are homodimeric and carry out a range of reactions including the glutathione-dependant reduction of a range of compounds and the reduction of S-(phenacyl)glutathiones to acetophenones. Both types of reaction result in the formation of a mixed-disulfide of the enzyme with glutathione through the catalytic cysteine (C32). Recycling of the enzyme utilizes a second glutathione molecule and results in oxidized glutathione (GSSG) release. The crystal structure of an active-site mutant (C32A) of the hGSTO1-1 isozyme in complex with GSSG provides a snapshot of the enzyme in the process of regeneration. GSSG occupies both the G (GSH-binding) and H (hydrophobic-binding) sites and causes re-arrangement of some H-site residues. In the same structure we demonstrate the existence of a novel "ligandin" binding site deep within in the dimer interface of this enzyme, containing S-(4-nitrophenacyl)glutathione, an isozyme-specific substrate for hGSTO1-1. The ligandin site, conserved in Omega class GSTs from a range of species, is hydrophobic in nature and may represent the binding location for tocopherol esters that are uncompetitive hGSTO1-1 inhibitors.


  • Organizational Affiliation

    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase omega-1241Homo sapiensMutation(s): 1 
Gene Names: GSTO1GSTTLP28
EC: 2.5.1.18 (PDB Primary Data), 1.8.5.1 (PDB Primary Data), 1.20.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P78417 (Homo sapiens)
Explore P78417 
Go to UniProtKB:  P78417
PHAROS:  P78417
GTEx:  ENSG00000148834 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78417
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDS
Query on GDS

Download Ideal Coordinates CCD File 
D [auth A]OXIDIZED GLUTATHIONE DISULFIDE
C20 H32 N6 O12 S2
YPZRWBKMTBYPTK-BJDJZHNGSA-N
1R4
Query on 1R4

Download Ideal Coordinates CCD File 
F [auth A]L-gamma-glutamyl-S-[2-(4-nitrophenyl)-2-oxoethyl]-L-cysteinylglycine
C18 H22 N4 O9 S
DFOFAMKKGYFIOO-STQMWFEESA-N
DTT
Query on DTT

Download Ideal Coordinates CCD File 
E [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.6α = 90
b = 57.6β = 90
c = 140.176γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDSClick on this verticalbar to view detailsBest fitted 1R4Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-09-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary