2F3M

Structure of human GLUTATHIONE S-TRANSFERASE M1A-1A complexed with 1-(S-(GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXADIENATE ANION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Transition state model and mechanism of nucleophilic aromatic substitution reactions catalyzed by human glutathione S-transferase M1a-1a.

Patskovsky, Y.Patskovska, L.Almo, S.C.Listowsky, I.

(2006) Biochemistry 45: 3852-3862

  • DOI: 10.1021/bi051823+
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An active site His107 residue distinguishes human glutathione S-transferase hGSTM1-1 from other mammalian Mu-class GSTs. The crystal structure of hGSTM1a-1a with bound glutathione (GSH) was solved to 1.9 A resolution, and site-directed mutagenesis su ...

    An active site His107 residue distinguishes human glutathione S-transferase hGSTM1-1 from other mammalian Mu-class GSTs. The crystal structure of hGSTM1a-1a with bound glutathione (GSH) was solved to 1.9 A resolution, and site-directed mutagenesis supports the conclusion that a proton transfer occurs in which bound water at the catalytic site acts as a primary proton acceptor from the GSH thiol group to transfer the proton to His107. The structure of the second substrate-binding site (H-site) was determined from hGSTM1a-1a complexed with 1-glutathionyl-2,4-dinitrobenzene (GS-DNB) formed by a reaction in the crystal between GSH and 1-chloro-2,4-dinitrobenzene (CDNB). In that structure, the GSH-binding site (G-site) is occupied by the GSH moiety of the product in the same configuration as that of the enzyme-GSH complex, and the dinitrobenzene ring is anchored between the side chains of Tyr6, Leu12, His107, Met108, and Tyr115. This orientation suggested a distinct transition state that was substantiated from the structure of hGSTM1a-1a complexed with transition state analogue 1-S-(glutathionyl)-2,4,6-trinitrocyclohexadienate (Meisenheimer complex). Kinetic data for GSTM1a-1a indicate that kcat(CDNB) for the reaction is more than 3 times greater than kcat(FDNB), even though the nonenzymatic second-order rate constant is more than 50-fold greater for 1-fluoro-2,4-dinitrobenzene (FDNB), and the product is the same for both substrates. In addition, Km(FDNB) is about 20 times less than Km(CDNB). The results are consistent with a mechanism in which the formation of the transition state is rate-limiting in the nucleophilic aromatic substitution reactions. Data obtained with active-site mutants support transition states in which Tyr115, Tyr6, and His107 side chains are involved in the stabilization of the Meisenheimer complex via interactions with the ortho nitro group of CDNB or FDNB and provide insight into the means by which GSTs adapt to accommodate different substrates.


    Related Citations: 
    • Function of His107 in the Catalytic Mechanism of Human Glutathione S-Transferase Hgstm1A-1A
      Patskovsky, Y.V.,Patskovska, L.N.,Listowsky, I.
      (1999) Biochemistry 38: 1193


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione S-transferase Mu 1
A, B, C, D, E, F
218Homo sapiensMutation(s): 0 
Gene Names: GSTM1 (GST1)
EC: 2.5.1.18
Find proteins for P09488 (Homo sapiens)
Go to Gene View: GSTM1
Go to UniProtKB:  P09488
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTD
Query on GTD

Download SDF File 
Download CCD File 
A, B, C, D, E, F
1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE
(S)-2-AMINO-5-((R)-1-(CARBOXYMETHYLAMINO)-1-OXO-3-(2,4,6-TRINITROCYCLOHEXA-2,5-DIENYLTHIO)PROPAN-2-YLAMINO)-5-OXOPENTANOIC ACID
C16 H20 N6 O12 S
VQUXYLXGOSJDJJ-OSGJSWLFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.233 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.965α = 120.53
b = 93.096β = 106.19
c = 92.998γ = 89.97
Software Package:
Software NamePurpose
MOLREPphasing
CCP4model building
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description