2GSR

Structure of porcine class pi glutathione s-transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Refined crystal structure of porcine class Pi glutathione S-transferase (pGST P1-1) at 2.1 A resolution.

Dirr, H.Reinemer, P.Huber, R.

(1994) J Mol Biol 243: 72-92

  • DOI: 10.1006/jmbi.1994.1631
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of class Pi glutathione S-transferase from porcine lung (pGST P1-1) in complex with glutathione sulphonate has been refined at 2.11 A resolution, to a crystallographic R-factor of 16.5% for 21, 165 unique reflections. The refine ...

    The crystal structure of class Pi glutathione S-transferase from porcine lung (pGST P1-1) in complex with glutathione sulphonate has been refined at 2.11 A resolution, to a crystallographic R-factor of 16.5% for 21, 165 unique reflections. The refined structure includes 3314 protein atoms, 46 inhibitor (glutathione sulphonate) atoms and 254 water molecules. The model shows good stereochemistry, with root-mean-square deviations from ideal bond lengths and bond angles of 0.011 A and 2.8 degrees, respectively. The estimated root-mean-square co-ordinate error is 0.2 A. The protein is a dimer assembled from identical subunits of 207 amino acid residues. The tertiary structure of the pGST P1 subunit is organized as two domains, the N-terminal domain (domain I, residues 1 to 74) and the larger C-terminal domain (domain II, residues 81 to 207). Glutathione sulphonate, a competitive inhibitor, binds to the G-site region (i.e. the glutathione-binding region) of the active site located on each subunit. Each G-site is, however, structurally dependent of the neighbouring subunit as structural elements forming a fully functional G-site are provided by both subunits, with domain I as the major supporting framework. A number of direct and water-mediated polar interactions are involved in sequestering the glutathione analogue at the G-site. The extended conformation assumed by the enzyme-bound inhibitor as well as the strategic interactions between inhibitor and protein, closely resemble those observed for the physiological substrate, reduced glutathione bound at the active site of class Mu glutathione S-transferase 3-3. Hydrogen bonding between the sulphonyl moiety of the inhibitor and the hydroxyl group of an evolutionary conserved tyrosine residue, Tyr7, provides the first direct structural evidence for a catalytic protein group in glutathione S-transferases that is involved in the activation of the substrate glutathione. The catalytic role for Tyr7 has subsequently been confirmed by mutagenesis and kinetic studies. Comparison of the known crystal structures for class Pi, class Mu and class Alpha isoenzymes, indicates that the cytosolic glutathione S-transferases share a common fold and that the structural features for catalysis are similar.


    Related Citations: 
    • The Three-Dimensional Structure of Class Pi Glutathione S-Transferase in Complex with Glutathione Sulfonate at 2.3 A Resolution
      Reinemer, P., Dirr, H.W., Ladenstein, R., Schaffer, J., Gallay, O., Huber, R.
      (1991) EMBO J 10: 1997

    Organizational Affiliation

    Abteilung Strukturforschung, Max-Planck-Institut fur Biochemie, Martinsried, FRG.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CLASS PI GST GLUTATHIONE S-TRANSFERASE
A, B
207Sus scrofaMutation(s): 0 
Gene Names: GSTP1
EC: 2.5.1.18
Find proteins for P80031 (Sus scrofa)
Go to UniProtKB:  P80031
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTS
Query on GTS

Download CCD File 
A, B
GLUTATHIONE SULFONIC ACID
C10 H17 N3 O9 S
QGWRMTHFAZVWAM-WDSKDSINSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GTSKi:  4000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.25α = 90
b = 82.53β = 90
c = 54.28γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2018-04-18
    Changes: Advisory, Data collection, Other