3GST

STRUCTURE 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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 1043-1052

  • Primary Citation of Related Structures:  2GST

  • PubMed Abstract: 
  • The three-dimensional structures of isoenzyme 3-3 of glutathione (GSH) transferase complexed with (9R,10R)- and (9S,10S)-9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene [(9R,10R)-2 and (9S,10S)-2], which are the products of the addition of GSH ...

    The three-dimensional structures of isoenzyme 3-3 of glutathione (GSH) transferase complexed with (9R,10R)- and (9S,10S)-9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene [(9R,10R)-2 and (9S,10S)-2], which are the products of the addition of GSH to phenanthrene 9,10-oxide, have been determined at resolutions of 1.9 and 1.8 A, respectively. The structures indicate that the xenobiotic substrate binding site is a hydrophobic cavity defined by the side chains of Y6, W7, V9, and L12 from domain I (the GSH binding domain) and I111, Y115, F208, and S209 in domain II of the protein. All of these residues are located in variable-sequence regions of the primary structure of class mu isoenzymes. Three of the eight residues (V9, I111, and S209) of isoenzyme 3-3 that are in direct van der Waals contact with the dihydrophenanthrenyl portion of the products are mutated (V9I, I111A, and S209A) in the related isoenzyme 4-4. These three residues are implicated in control of the stereoselectivity of the class mu isoenzymes. The hydroxyl group of Y115 is found to be hydrogen-bonded to the 10-hydroxyl group of (9S,10S)-2, a fact suggesting that this residue could act as an electrophile to stabilize the transition state for the addition of GSH to epoxides. The Y115F mutant isoenzyme 3-3 is about 100-fold less efficient than the native enzyme in catalyzing the addition of GSH to phenanthrene 9,10-oxide and about 50-fold less efficient in the Michael addition of GSH to 4-phenyl-3-buten-2-one. The side chain of Y115 is positioned so as to act as a general-acid catalytic group for two types of reactions that would benefit from electrophilic assistance. The results are consistent with the notion that domain II, which harbors most of the variability in primary structure, plays a crucial role in defining the substrate specificity of class mu isoenzymes.


    Related Citations: 
    • Tyrosine 115 Participates Both in Chemical and Physical Steps of the Catalytic Mechanism of a Glutathione S-Transferase
      Johnson, W.W.,Liu, S.,Ji, X.,Gilliland, G.L.,Armstrong, R.N.
      (1993) J.Biol.Chem. 268: 11508
    • The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2 Angstroms Resolution
      Ji, X.,Zhang, P.,Armstrong, R.N.,Gilliland, G.L.
      (1992) Biochemistry 31: 10169
    • Contribution of Tyrosine 6 to the Catalytic Mechanism of Isoenzyme 3-3 of Glutathione S-Transferase
      Liu, S.,Zhang, P.,Ji, X.,Johnson, W.W.,Gilliland, G.L.,Armstrong, R.N.
      (1992) J.Biol.Chem. 267: 4296


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland, College Park 20742.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE S-TRANSFERASE
A, B
217Rattus norvegicusGene Names: Gstm1
EC: 2.5.1.18
Find proteins for P04905 (Rattus norvegicus)
Go to UniProtKB:  P04905
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GPR
Query on GPR

Download SDF File 
Download CCD File 
A, B
(9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE
C24 H27 N3 O7 S
JNNIZILNBMPOAC-MOXQZVSFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GPRKi: 190 nM BINDINGMOAD
GPRKi: 190 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.240α = 90.00
b = 69.440β = 106.01
c = 81.280γ = 90.00
Software Package:
Software NamePurpose
GPRLSArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other