3LFL | pdb_00003lfl

Crystal Structure of human Glutathione Transferase Omega 1, delta 155


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.255 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Novel folding and stability defects cause a deficiency of human glutathione transferase omega 1.

Zhou, H.Brock, J.Casarotto, M.G.Oakley, A.J.Board, P.G.

(2011) J Biological Chem 286: 4271-4279

  • DOI: https://doi.org/10.1074/jbc.M110.197822
  • Primary Citation Related Structures: 
    3LFL

  • PubMed Abstract: 

    The polymorphic deletion of Glu-155 from human glutathione transferase omega1 (GSTO1-1) occurs in most populations. Although the recombinant ΔGlu-155 enzyme expressed in Escherichia coli is active, the deletion causes a deficiency of the active enzyme in vivo. The crystal structure and the folding/unfolding kinetics of the ΔGlu-155 variant were determined in order to investigate the cause of the rapid loss of the enzyme in human cells. The crystal structure revealed altered packing around the Glu-155 deletion, an increase in the predicted solvent-accessible area and a corresponding reduction in the buried surface area. This increase in solvent accessibility was consistent with an elevated Stern-Volmer constant. The unfolding of both the wild type and ΔGlu-155 enzyme in urea is best described by a three-state model, and there is evidence for the more pronounced population of an intermediate state by the ΔGlu-155 enzymes. Studies using intrinsic fluorescence revealed a free energy change around 14.4 kcal/mol for the wild type compared with around 8.6 kcal/mol for the ΔGlu-155 variant, which indicates a decrease in stability associated with the Glu-155 deletion. Urea induced unfolding of the wild type GSTO1-1 was reversible through an initial fast phase followed by a second slow phase. In contrast, the ΔGlu-155 variant lacks the slow phase, indicating a refolding defect. It is possible that in some conditions in vivo, the increased solvent-accessible area and the low stability of the ΔGlu-155 variant may promote its unfolding, whereas the refolding defect limits its refolding, resulting in GSTO1-1 deficiency.


  • Organizational Affiliation
    • John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia.

Macromolecule Content 

  • Total Structure Weight: 83.8 kDa 
  • Atom Count: 5,959 
  • Modeled Residue Count: 686 
  • Deposited Residue Count: 720 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione S-transferase omega-1
A, B, C
240Homo sapiensMutation(s): 0 
Gene Names: GSTO1GSTTLP28
EC: 2.5.1.18 (PDB Primary Data), 1.20.4.2 (UniProt), 1.8.5.1 (UniProt)
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
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Reference Sequence

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.255 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.009α = 90
b = 201.942β = 90
c = 53.387γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2010-11-24 
  • Deposition Author(s): Brock, J.

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-14
    Changes: Non-polymer description
  • Version 1.3: 2012-05-09
    Changes: Data collection
  • Version 1.4: 2017-11-01
    Changes: Advisory, Refinement description, Structure summary
  • Version 1.5: 2024-02-21
    Changes: Advisory, Data collection, Database references, Derived calculations