1PGT

CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] COMPLEXED WITH S-HEXYLGLUTATHIONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase.

Ji, X.Tordova, M.O'Donnell, R.Parsons, J.F.Hayden, J.B.Gilliland, G.L.Zimniak, P.

(1997) Biochemistry 36: 9690-9702

  • DOI: 10.1021/bi970805s
  • Primary Citation of Related Structures:  2PGT

  • PubMed Abstract: 
  • Complex structures of a naturally occurring variant of human class pi glutathione S-transferase 1-1 (hGSTP1-1) with either S-hexylglutathione or (9R,10R)-9-(S-glutathionyl)-10-hydroxy-9, 10-dihydrophenanthrene [(9R,10R)-GSPhen] have been determined a ...

    Complex structures of a naturally occurring variant of human class pi glutathione S-transferase 1-1 (hGSTP1-1) with either S-hexylglutathione or (9R,10R)-9-(S-glutathionyl)-10-hydroxy-9, 10-dihydrophenanthrene [(9R,10R)-GSPhen] have been determined at resolutions of 1.8 and 1.9 A, respectively. The crystal structures reveal that the xenobiotic substrate-binding site (H-site) is located at a position similar to that observed in class mu GST 1-1 from rat liver (rGSTM1-1). In rGSTM1-1, the H-site is a hydrophobic cavity defined by the side chains of Y6, W7, V9, L12, I111, Y115, F208, and S209. In hGSTP1-1, the cavity is approximately half hydrophobic and half hydrophilic and is defined by the side chains of Y7, F8, V10, R13, V104, Y108, N204, and G205 and five water molecules. A hydrogen bond network connects the five water molecules and the side chains of R13 and N204. V104 is positioned such that the introduction of a methyl group (the result of the V104I mutation) disturbs the H-site water structure and alters the substrate-binding properties of the isozyme. The hydroxyl group of Y7 forms a hydrogen bond (3.2 A) with the sulfur atom of the product. There is a short hydrogen bond (2.5 A) between Y108 (OH) and (9R, 10R)-GSPhen (O5), indicating the hydroxyl group of Y108 as an electrophilic participant in the addition of glutathione to epoxides. An N-(2-hydroxethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) molecule is found in the cavity between beta2 and alphaI. The location and properties of this HEPES-binding site fit a possible non-substrate-binding site that is involved in noncompetitive inhibition of the enzyme.


    Related Citations: 
    • Three-Dimensional Structure of Class Pi Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 A Resolution
      Reinemer, P.,Dirr, H.W.,Ladenstein, R.,Huber, R.,Lo Bello, M.,Federici, G.,Parker, M.W.
      (1992) J.Mol.Biol. 227: 214
    • Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene
      Ji, X.,Johnson, W.W.,Sesay, M.A.,Dickert, L.,Prasad, S.M.,Ammon, H.L.,Armstrong, R.N.,Gilliland, G.L.
      (1994) Biochemistry 33: 1043
    • Naturally Occurring Human Glutathione S-Transferase Gstp1-1 Isoforms with Isoleucine and Valine in Position 104 Differ in Enzymic Properties
      Zimniak, P.,Nanduri, B.,Pikula, S.,Bandorowicz-Pikula, J.,Singhal, S.S.,Srivastava, S.K.,Awasthi, S.,Awasthi, Y.C.
      (1994) Eur.J.Biochem. 224: 893


    Organizational Affiliation

    ABL-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE S-TRANSFERASE
A, B
210Homo sapiensGene Names: GSTP1 (FAEES3, GST3)
EC: 2.5.1.18
Find proteins for P09211 (Homo sapiens)
Go to Gene View: GSTP1
Go to UniProtKB:  P09211
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
GTX
Query on GTX

Download SDF File 
Download CCD File 
A, B
S-HEXYLGLUTATHIONE
C16 H30 N3 O6 S
HXJDWCWJDCOHDG-RYUDHWBXSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.390α = 90.00
b = 90.800β = 98.08
c = 69.150γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
GPRLSArefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-02-17 
  • Released Date: 1997-09-04 
  • Deposition Author(s): Ji, X.

Revision History 

  • Version 1.0: 1997-09-04
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance