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PDBsum entry 3fyg

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protein ligands Protein-protein interface(s) links
Transferase PDB id
3fyg
Jmol
Contents
Protein chains
217 a.a. *
Ligands
GPR ×2
Waters ×431
* Residue conservation analysis
PDB id:
3fyg
Name: Transferase
Title: Crystal structure of tetradeca-(3-fluorotyrosyl)- glutathione s-transferase
Structure: Mu class tetradeca-(3-fluorotyrosyl)-glutathione s-transferase of isoenzyme. Chain: a, b. Synonym: rat gst. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Cell_line: bl21. Organ: liver. Gene: cdna insert of clone pgt33m. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.170    
Authors: G.Xiao,J.F.Parsons,R.N.Armstrong,G.L.Gilliland
Key ref:
G.Xiao et al. (1998). Conformational changes in the crystal structure of rat glutathione transferase M1-1 with global substitution of 3-fluorotyrosine for tyrosine. J Mol Biol, 281, 323-339. PubMed id: 9698551 DOI: 10.1006/jmbi.1998.1935
Date:
07-Aug-97     Release date:   01-Jun-99    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04905  (GSTM1_RAT) -  Glutathione S-transferase Mu 1
Seq:
Struc:
218 a.a.
217 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     metabolic process   12 terms 
  Biochemical function     transferase activity     5 terms  

 

 
DOI no: 10.1006/jmbi.1998.1935 J Mol Biol 281:323-339 (1998)
PubMed id: 9698551  
 
 
Conformational changes in the crystal structure of rat glutathione transferase M1-1 with global substitution of 3-fluorotyrosine for tyrosine.
G.Xiao, J.F.Parsons, K.Tesh, R.N.Armstrong, G.L.Gilliland.
 
  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.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereoviews of the 3FYG 2Fo - Fc map (pink) contoured at 1.2 s for (a) 3-FTyr166 and (b) 3-FTyr154, both from subunit A. The residue is colored according to atom type, with the fluorine atom colored orange.
Figure 4.
Figure 4. A superposition of 3-FTyr6 and the GPR pro- duct of 3FYG and corresponding groups in 3GST drawn using TURBO-FRODO (Roussel et al., 1996). Atoms and bonds of 3FYG are colored according to atom type; those of 3GST are shown in pink.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 281, 323-339) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20734112 J.L.Kitevski-LeBlanc, F.Evanics, and R.Scott Prosser (2010).
Optimizing ¹⁹F NMR protein spectroscopy by fractional biosynthetic labeling.
  J Biomol NMR, 48, 113-121.  
20401735 J.L.Kitevski-Leblanc, F.Evanics, and R.Scott Prosser (2010).
Approaches to the assignment of (19)F resonances from 3-fluorophenylalanine labeled calmodulin using solution state NMR.
  J Biomol NMR, 47, 113-123.  
19655092 J.L.Kitevski-LeBlanc, F.Evanics, and R.S.Prosser (2009).
Approaches for the measurement of solvent exposure in proteins by 19F NMR.
  J Biomol NMR, 45, 255-264.  
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
17915350 G.Cornilescu, E.B.Hadley, M.G.Woll, J.L.Markley, S.H.Gellman, and C.C.Cornilescu (2007).
Solution structure of a small protein containing a fluorinated side chain in the core.
  Protein Sci, 16, 2089.  
16131667 X.Wang, P.Mercier, P.J.Letourneau, and B.D.Sykes (2005).
Effects of Phe-to-Trp mutation and fluorotryptophan incorporation on the solution structure of cardiac troponin C, and analysis of its suitability as a potential probe for in situ NMR studies.
  Protein Sci, 14, 2447-2460.
PDB codes: 2jt0 2jt3 2jt8 2jtz
15122645 J.H.Bae, P.Paramita Pal, L.Moroder, R.Huber, and N.Budisa (2004).
Crystallographic evidence for isomeric chromophores in 3-fluorotyrosyl-green fluorescent protein.
  Chembiochem, 5, 720-722.
PDB code: 1rrx
12704087 D.A.Kraut, K.S.Carroll, and D.Herschlag (2003).
Challenges in enzyme mechanism and energetics.
  Annu Rev Biochem, 72, 517-571.  
11536360 M.A.Dominguez, K.C.Thornton, M.G.Melendez, and C.M.Dupureur (2001).
Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease.
  Proteins, 45, 55-61.  
10652317 Y.V.Patskovsky, L.N.Patskovska, and I.Listowsky (2000).
The enhanced affinity for thiolate anion and activation of enzyme-bound glutathione is governed by an arginine residue of human Mu class glutathione S-transferases.
  J Biol Chem, 275, 3296-3304.
PDB code: 2gtu
9818188 R.N.Armstrong (1998).
Mechanistic imperatives for the evolution of glutathione transferases.
  Curr Opin Chem Biol, 2, 618-623.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.