3FYG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1006/jmbi.1998.1935
  • Primary Citation of Related Structures:  
    3FYG

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MU CLASS TETRADECA-(3-FLUOROTYROSYL)-GLUTATHIONE S-TRANSFERASE OF ISOENZYME
A, B
217Rattus norvegicusMutation(s): 13 
Gene Names: CDNA INSERT OF CLONE PGT33M
EC: 2.5.1.18
UniProt
Find proteins for P04905 (Rattus norvegicus)
Explore P04905 
Go to UniProtKB:  P04905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04905
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YOF
Query on YOF
A, B
L-PEPTIDE LINKINGC9 H10 F N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.43α = 90
b = 88.42β = 90
c = 57.26γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-01
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-09
    Changes: Refinement description
  • Version 1.5: 2024-11-06
    Changes: Data collection, Structure summary