3FYG

CRYSTAL STRUCTURE OF TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational changes in the crystal structure of rat glutathione transferase M1-1 with global substitution of 3-fluorotyrosine for tyrosine.

Xiao, G.Parsons, J.F.Tesh, K.Armstrong, R.N.Gilliland, G.L.

(1998) J.Mol.Biol. 281: 323-339

  • DOI: 10.1006/jmbi.1998.1935

  • PubMed Abstract: 
  • The structure of the tetradeca-(3-fluorotyrosyl) M1-1 GSH transferase (3-FTyr GSH transferase), a protein in which tyrosine residues are globally substituted by 3-fluorotyrosines has been determined at 2.2 A resolution. This variant was produced to s ...

    The structure of the tetradeca-(3-fluorotyrosyl) M1-1 GSH transferase (3-FTyr GSH transferase), a protein in which tyrosine residues are globally substituted by 3-fluorotyrosines has been determined at 2.2 A resolution. This variant was produced to study the effect on the enzymatic mechanism and the structure was undertaken to assess how the presence of the 3-fluorotyrosyl residue influences the protein conformation and hence its function. Although fluorinated amino acid residues have frequently been used in biochemical and NMR investigations of proteins, no structure of a protein that has been globally substituted with a fluorinated amino acid has previously been reported. Thus, this structure represents the first crystal structure of such a protein containing a library of 14 (28 crystallographically distinct) microenvironments from which the nature of the interactions of fluorine atoms with the rest of the protein can be evaluated. Numerous conformational changes are observed in the protein structure as a result of substitution of 3-fluorotyrosine for tyrosine. The results of the comparison of the crystal structure of the fluorinated protein with the native enzyme reveal that conformational changes are observed for most of the 3-fluorotyrosines. The largest differences are seen for residues where the fluorine, the OH, or both are directly involved in interactions with other regions of the protein or with a symmetry-related molecule. The fluorine atoms of the 3-fluorotyrosine interact primarily through hydrogen bonds with other residues and water molecules. In several cases, the conformation of a 3-fluorotyrosine is different in one of the monomers of the enzyme from that observed in the other, including different hydrogen-bonding patterns. Altered conformations can be related to differences in the crystal packing interactions of the two monomers in the asymmetric unit. The fluorine atom on the active-site Tyr6 is located near the S atom of the thioether product (9R,10R)-9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene and creates a different pattern of interactions between 3-fluorotyrosine 6 and the S atom. Studies of these interactions help explain why 3-FTyr GSH transferase exhibits spectral and kinetic properties distinct from the native GSH transferase.


    Related Citations: 
    • Second-Sphere Electrostatic Effects in the Active Site of Glutathione S-Transferase. Observation of an on-Facet Hydrogen Bond between the Side Chain of Threonine 13 and the Pi-Cloud of Tyrosine 6 and its Influence on Catalysis
      Liu, S.,Ji, X.,Gilliland, G.L.,Stevens, W.J.,Armstrong, R.N.
      (1993) J.Am.Chem.Soc. 115: 7910
    • Contribution of Tyrosine 6 to the Catalytic Mechanism of Isoenzyme 3-3 of Glutathione S-Transferase
      Liu, S.,Zhang, P.,Ji, X.,Johnson, W.W.,Gilliland, G.L.,Armstrong, R.N.
      (1992) J.Biol.Chem. 267: 4296
    • The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2-A Resolution
      Ji, X.,Zhang, P.,Armstrong, R.N.,Gilliland, G.L.
      (1992) Biochemistry 31: 10169
    • Proton Configuration in the Ground State and Transition State of a Glutathione Transferase-Catalyzed Reaction Inferred from the Properties of Tetradeca(3-Fluorotyrosyl)Glutathione Transferase
      Parsons, J.F.,Armstrong, R.N.
      (1996) J.Am.Chem.Soc. 118: 2295
    • Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene
      Ji, X.,Johnson, W.W.,Sesay, M.A.,Dickert, L.,Prasad, S.M.,Ammon, H.L.,Armstrong, R.N.,Gilliland, G.L.
      (1994) Biochemistry 33: 1043
    • Snapshots Along the Reaction Coordinate of an Snar Reaction Catalyzed by Glutathione Transferase
      Ji, X.,Armstrong, R.N.,Gilliland, G.L.
      (1993) Biochemistry 32: 12949


    Organizational Affiliation

    Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute, and of the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MU CLASS TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE OF ISOENZYME
A, B
217Rattus norvegicusMutation(s): 13 
Gene Names: Gstm1
EC: 2.5.1.18
Find proteins for P04905 (Rattus norvegicus)
Go to UniProtKB:  P04905
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GPR
Query on GPR

Download SDF File 
Download CCD File 
A, B
(9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE
C24 H27 N3 O7 S
JNNIZILNBMPOAC-MOXQZVSFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YOF
Query on YOF
A, B
L-PEPTIDE LINKINGC9 H10 F N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.430α = 90.00
b = 88.420β = 90.00
c = 57.260γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
TNTrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-01
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance