1E6B | pdb_00001e6b

Crystal structure of a Zeta class glutathione S-transferase from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.234 (Depositor) 
  • R-Value Work: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1E6B

This is version 1.3 of the entry. See complete history

Literature

The Structure of a Zeta Class Glutathione S-Transferase from Arabidopsis Thaliana: Characterisation of a Gst with Novel Active-Site Architecture and a Putative Role in Tyrosine Catabolism.

Thom, R.Dixon, D.P.Edwards, R.Cole, D.J.Lapthorn, A.J.

(2001) J Mol Biology 308: 949

  • DOI: https://doi.org/10.1006/jmbi.2001.4638
  • Primary Citation Related Structures: 
    1E6B

  • PubMed Abstract: 

    The cis-trans isomerisation of maleylacetoacetate to fumarylacetoacetate is the penultimate step in the tyrosine/phenylalanine catabolic pathway and has recently been shown to be catalysed by glutathione S-transferase enzymes belonging to the zeta class. Given this primary metabolic role it is unsurprising that zeta class glutathione S-transferases are well conserved over a considerable period of evolution, being found in vertebrates, plants, insects and fungi. The structure of this glutathione S-transferase, cloned from Arabidopsis thaliana, has been solved by single isomorphous replacement with anomalous scattering and refined to a final crystallographic R-factor of 19.6% using data from 25.0 A to 1.65 A. The zeta class enzyme adopts the canonical glutathione S-transferase fold and forms a homodimer with each subunit consisting of 221 residues. In agreement with structures of glutathione S-transferases from the theta and phi classes, a serine residue (Ser17) is present in the active site, at a position that would allow it to stabilise the thiolate anion of glutathione. Site-directed mutagenesis of this residue confirms its importance in catalysis. In addition, the role of a highly conserved cysteine residue (Cys19) present in the active site of the zeta class glutathione S-transferase enzymes is discussed.


  • Organizational Affiliation
    • Department of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.

Macromolecule Content 

  • Total Structure Weight: 24.99 kDa 
  • Atom Count: 1,683 
  • Modeled Residue Count: 194 
  • Deposited Residue Count: 221 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUTATHIONE S-TRANSFERASE221Arabidopsis thalianaMutation(s): 0 
EC: 2.5.1.18 (PDB Primary Data), 5.2.1 (UniProt)
UniProt
Find proteins for Q9ZVQ3 (Arabidopsis thaliana)
Explore Q9ZVQ3 
Go to UniProtKB:  Q9ZVQ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZVQ3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BME

Query on BME



Download:Ideal Coordinates CCD File
B [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.234 (Depositor) 
  • R-Value Work:  0.196 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.164α = 90
b = 75.164β = 90
c = 140.52γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Structure summary