1GTI

MODIFIED GLUTATHIONE S-TRANSFERASE (PI) COMPLEXED WITH S (P-NITROBENZYL)GLUTATHIONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The three-dimensional structure of Cys-47-modified mouse liver glutathione S-transferase P1-1. Carboxymethylation dramatically decreases the affinity for glutathione and is associated with a loss of electron density in the alphaB-310B region.

Vega, M.C.Walsh, S.B.Mantle, T.J.Coll, M.

(1998) J.Biol.Chem. 273: 2844-2850

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional structure of mouse liver glutathione S-transferase P1-1 carboxymethylated at Cys-47 and its complex with S-(p-nitrobenzyl)glutathione have been determined by x-ray diffraction analysis. The structure of the modified enzyme descr ...

    The three-dimensional structure of mouse liver glutathione S-transferase P1-1 carboxymethylated at Cys-47 and its complex with S-(p-nitrobenzyl)glutathione have been determined by x-ray diffraction analysis. The structure of the modified enzyme described here is the first structural report for a Pi class glutathione S-transferase with no glutathione, glutathione S-conjugate, or inhibitor bound. It shows that part of the active site area, which includes helix alphaB and helix 310B, is disordered. However, the environment of Tyr-7, an essential residue for the catalytic reaction, remains unchanged. The position of the sulfur atom of glutathione is occupied in the ligand-free enzyme by a water molecule that is at H-bond distance from Tyr-7. We do not find any structural evidence for a tyrosinate form, and therefore our results suggest that Tyr-7 is not acting as a general base abstracting the proton from the thiol group of glutathione. The binding of the inhibitor S-(p-nitrobenzyl)-glutathione to the carboxymethylated enzyme results in a partial restructuring of the disordered area. The modification of Cys-47 sterically hinders structural organization of this region, and although it does not prevent glutathione binding, it significantly reduces the affinity. A detailed kinetic study of the modified enzyme indicates that the carboxymethylation increases the Km for glutathione by 3 orders of magnitude, although the enzyme can function efficiently under saturating conditions.


    Related Citations: 
    • Molecular Structure at 1.8 A of Mouse Liver Class Pi Glutathione S-Transferase Complexed with S-(P-Nitrobenzyl)Glutathione and Other Inhibitors
      Garcia-Saez, I.,Parraga, A.,Phillips, M.F.,Mantle, T.J.,Coll, M.
      (1994) J.Mol.Biol. 237: 298


    Organizational Affiliation

    Departament de Biologia Molecular i Cel.lular, Centre d'Investigació i Desenvolupament-Consell Superior d'Investigacions Científiques, Jordi Girona 18-26, 08034 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE S-TRANSFERASE
A, B, C, D, E, F
209Mus musculusMutation(s): 0 
Gene Names: Gstp1 (Gstpib)
EC: 2.5.1.18
Find proteins for P19157 (Mus musculus)
Go to UniProtKB:  P19157
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTB
Query on GTB

Download SDF File 
Download CCD File 
A, B, C, D, E, F
S-(P-NITROBENZYL)GLUTATHIONE
C17 H22 N4 O8 S
OAWORKDPTSAMBZ-STQMWFEESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.450α = 90.00
b = 132.690β = 90.00
c = 214.470γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-01-09 
  • Released Date: 1999-03-02 
  • Deposition Author(s): Vega, M.C., Coll, M.

Revision History 

  • Version 1.0: 1999-03-02
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance