3F6D

Crystal Structure of a Genetically Modified Delta Class GST (adGSTD4-4) from Anopheles dirus, F123A, in Complex with S-Hexyl Glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural contributions of delta class glutathione transferase active-site residues to catalysis

Wongsantichon, J.Robinson, R.C.Ketterman, A.J.

(2010) Biochem.J. 428: 25-32

  • DOI: 10.1042/BJ20091939
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GST (glutathione transferase) is a dimeric enzyme recognized for biotransformation of xenobiotics and endogenous toxic compounds. In the present study, residues forming the hydrophobic substrate-binding site (H-site) of a Delta class enzyme were inve ...

    GST (glutathione transferase) is a dimeric enzyme recognized for biotransformation of xenobiotics and endogenous toxic compounds. In the present study, residues forming the hydrophobic substrate-binding site (H-site) of a Delta class enzyme were investigated in detail for the first time by site-directed mutagenesis and crystallographic studies. Enzyme kinetics reveal that Tyr111 indirectly stabilizes GSH binding, Tyr119 modulates hydrophobic substrate binding and Phe123 indirectly modulates catalysis. Mutations at Tyr111 and Phe123 also showed evidence for positive co-operativity for GSH and 1-chloro-2,4-dinitrobenzene respectively, strongly suggesting a role for these residues in manipulating subunit-subunit communication. In the present paper we report crystal structures of the wild-type enzyme, and two mutants, in complex with S-hexylglutathione. This study has identified an aromatic 'zipper' in the H-site contributing a network of aromatic pi-pi interactions. Several residues of the cluster directly interact with the hydrophobic substrate, whereas others indirectly maintain conformational stability of the dimeric structure through the C-terminal domain (domain II). The Y119E mutant structure shows major main-chain rearrangement of domain II. This reorganization is moderated through the 'zipper' that contributes to the H-site remodelling, thus illustrating a role in co-substrate binding modulation. The F123A structure shows molecular rearrangement of the H-site in one subunit, but not the other, explaining weakened hydrophobic substrate binding and kinetic co-operativity effects of Phe123 mutations. The three crystal structures provide comprehensive evidence of the aromatic 'zipper' residues having an impact upon protein stability, catalysis and specificity. Consequently, 'zipper' residues appear to modulate and co-ordinate substrate processing through permissive flexing.


    Organizational Affiliation

    Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione transferase GST1-4
A, B
219Anopheles dirusMutation(s): 1 
Find proteins for Q9GN60 (Anopheles dirus)
Go to UniProtKB:  Q9GN60
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 49.692α = 90.00
b = 49.692β = 90.00
c = 272.943γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance