3GTU

LIGAND-FREE HETERODIMERIC HUMAN GLUTATHIONE S-TRANSFERASE M2-3 (EC 2.5.1.18), MONOCLINIC CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An asparagine-phenylalanine substitution accounts for catalytic differences between hGSTM3-3 and other human class mu glutathione S-transferases.

Patskovsky, Y.V.Patskovska, L.N.Listowsky, I.

(1999) Biochemistry 38: 16187-16194

  • DOI: 10.1021/bi991714t
  • Primary Citation of Related Structures:  
    3GTU, 4GTU

  • PubMed Abstract: 
  • The hGSTM3 subunit, which is preferentially expressed in germ-line cells, has the greatest sequence divergence among the human mu class glutathione S-transferases. To determine a structural basis for the catalytic differences between hGSTM3-3 and other mu class enzymes, chimeric proteins were designed by modular interchange of the divergent C-terminal domains of hGSTM3 and hGSTM5 subunits ...

    The hGSTM3 subunit, which is preferentially expressed in germ-line cells, has the greatest sequence divergence among the human mu class glutathione S-transferases. To determine a structural basis for the catalytic differences between hGSTM3-3 and other mu class enzymes, chimeric proteins were designed by modular interchange of the divergent C-terminal domains of hGSTM3 and hGSTM5 subunits. Replacement of 24 residues of the C-terminal segment of either subunit produced chimeric enzymes with catalytic properties that reflected those of the wild-type enzyme from which the C-terminus had been derived. Deletion of the tripeptide C-terminal extension found only in the hGSTM3 subunit had no effect on catalysis. The crystal structure determined for a ligand-free hGSTM3 subunit indicates that an Asn212 residue of the C-terminal domain is near a hydrophobic cluster of side chains formed in part by Ile13, Leu16, Leu114, Ile115, Tyr119, Ile211, and Trp218. Accordingly, a series of point mutations were introduced into the hGSTM3 subunit, and it was indeed determined that a Y119F mutation considerably enhanced the turnover rate of the enzyme for nucleophilic aromatic substitution reactions. A more striking effect was observed for a double mutant (Y119F/N212F) which had a k(cat)/K(m)(CDNB) value of 7.6 x 10(5) s(-)(1) M(-)(1) as compared to 4.9 x 10(3) s(-)(1) M(-)(1) for the wild-type hGSTM3-3 enzyme. The presence of a polar Asn212 in place of a Phe residue found in the cognate position of other mu class glutathione S-transferases, therefore, has a marked influence on catalysis by hGSTM3-3.


    Related Citations: 
    • Crystal Structure of Human Class Mu Glutathione Transferase Gstm2-2. Effects of Lattice Packing on Conformational Heterogeneity
      Raghunathan, S., Chandross, R.J., Kretsinger, R.H., Allison, T.J., Penington, C.J., Rule, G.S.
      (1994) J Mol Biol 238: 815
    • Cloning, Expression, and Characterization of a Class-Mu Glutathione Transferase from Human Muscle, the Product of the Gst4 Locus
      Vorachek, W.R., Pearson, W.R., Rule, G.S.
      (1991) Proc Natl Acad Sci U S A 88: 4443
    • A Distinct Human Testis and Brain Mu-Class Glutathione S-Transferase. Molecular Cloning and Characterization of a Form Present Even in Individuals Lacking Hepatic Type Mu Isoenzymes
      Campbell, E., Takahashi, Y., Abramovitz, M., Peretz, M., Listowsky, I.
      (1990) J Biol Chem 265: 9188

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTATHIONE S-TRANSFERASEA, C217Homo sapiensMutation(s): 0 
Gene Names: GSTM2GSTM3GST4
EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P28161 (Homo sapiens)
Explore P28161 
Go to UniProtKB:  P28161
PHAROS:  P28161
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28161
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTATHIONE S-TRANSFERASEB, D224Homo sapiensMutation(s): 0 
Gene Names: GSTM2GSTM3GST5
EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P21266 (Homo sapiens)
Explore P21266 
Go to UniProtKB:  P21266
PHAROS:  P21266
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21266
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.97α = 90
b = 102.747β = 95.8
c = 103.977γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-29
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance