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PDBsum entry 2vo4

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2vo4
Jmol
Contents
Protein chains
219 a.a. *
Ligands
GTB ×2
4NM ×2
GOL ×2
Waters ×430
* Residue conservation analysis
PDB id:
2vo4
Name: Transferase
Title: Glutathione transferase from glycine max
Structure: 2,4-d inducible glutathione s-transferase. Chain: a, b. Synonym: glutathione-s-transferase, gsta. Ec: 2.5.1.18
Source: Glycine max. Soybean. Organism_taxid: 3847
Resolution:
1.75Å     R-factor:   0.197     R-free:   0.243
Authors: I.Axarli,P.Dhavala,A.C.Papageorgiou,N.E.Labrou
Key ref:
I.Axarli et al. (2009). Crystallographic and Functional Characterization of the Fluorodifen-inducible Glutathione Transferase from Glycine max Reveals an Active Site Topography Suited for Diphenylether Herbicides and a Novel L-site. J Mol Biol, 385, 984. PubMed id: 19014949 DOI: 10.1016/j.jmb.2008.10.084
Date:
08-Feb-08     Release date:   02-Dec-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O49235  (O49235_SOYBN) -  2,4-D inducible glutathione S-transferase
Seq:
Struc:
219 a.a.
219 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.5.1.18  - Glutathione transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RX + glutathione = HX + R-S-glutathione
RX
+
glutathione
Bound ligand (Het Group name = GTB)
matches with 66.67% similarity
= HX
+ R-S-glutathione
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     transferase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2008.10.084 J Mol Biol 385:984 (2009)
PubMed id: 19014949  
 
 
Crystallographic and Functional Characterization of the Fluorodifen-inducible Glutathione Transferase from Glycine max Reveals an Active Site Topography Suited for Diphenylether Herbicides and a Novel L-site.
I.Axarli, P.Dhavala, A.C.Papageorgiou, N.E.Labrou.
 
  ABSTRACT  
 
Glutathione transferases (GSTs) from the tau class (GSTU) are unique to plants and have important roles in stress tolerance and the detoxification of herbicides in crops and weeds. A fluorodifen-induced GST isoezyme (GmGSTU4-4) belonging to the tau class was purified from Glycine max by affinity chromatography. This isoenzyme was cloned and expressed in Escherichia coli, and its structural and catalytic properties were investigated. The structure of GmGSTU4-4 was determined at 1.75 A resolution in complex with S-(p-nitrobenzyl)-glutathione (Nb-GSH). The enzyme adopts the canonical GST fold but with a number of functionally important differences. Compared with other plant GSTs, the three-dimensional structure of GmGSTU4-4 primarily shows structural differences in the hydrphobic substrate binding site, the linker segment and the C-terminal region. The X-ray structure identifies key amino acid residues in the hydrophobic binding site (H-site) and provides insights into the substrate specificity and catalytic mechanism of the enzyme. The isoenzyme was highly active in conjugating the diphenylether herbicide fluorodifen. A possible reaction pathway involving the conjugation of glutathione with fluorodifen is described based on site-directed mutagenesis and molecular modeling studies. A serine residue (Ser13) is present in the active site, at a position that would allow it to stabilise the thiolate anion of glutathione and enhance its nucleophilicity. Tyr107 and Arg111 present in the active site are important structural moieties that modulate the catalytic efficiency and specificity of the enzyme, and participate in k(cat) regulation by affecting the rate-limiting step of the catalytic reaction. A hitherto undescribed ligand-binding site (L-site) located in a surface pocket of the enzyme was also found. This site is formed by conserved residues, suggesting it may have an important functional role in the transfer and delivery of bound ligands, presumably to specific protein receptors.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. (a) A cartoon representation of GmGSTU4-4 monomer coloured from blue (N-terminus) to red (C-terminus). Secondary structure elements are labelled. The inhibitor Nb-GSH is represented as a stick and coloured according to atom type. (b) A ribbon diagram of the dimeric GmGSTU4-4 structure, the twofold axis relating the two subunits is perpendicular to the plane of the page, with subunit A coloured green and subunit B is turquoise. The proposed lock-and-key residues are shown in stick representation and labelled, except Val, which is shown in a ball representation. The three salt bridges that are formed between residues Glu66 and Lys104′ and between Glu76 and side chains of Arg92′ and Arg96′ are also shown. The inhibitor Nb-GSH is represented as a stick and coloured according to atom type. The figure was produced using PyMol [http://pymol.sourceforge.net/].
Figure 6.
Fig. 6. The predicted mode of interaction between fluorodifen and GmGSTU4-4. The ligand is represented as a stick and coloured according to atom type. Mutated residues are represented as sticks.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 385, 984) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205172 C.L.Wang, and H.L.Yang (2011).
Conserved residues in the subunit interface of tau glutathione s-transferase affect catalytic and structural functions.
  J Integr Plant Biol, 53, 35-43.  
  21425939 I.Cummins, D.P.Dixon, S.Freitag-Pohl, M.Skipsey, and R.Edwards (2011).
Multiple roles for plant glutathione transferases in xenobiotic detoxification.
  Drug Metab Rev, 43, 266-280.  
20192743 S.B.Powles, and Q.Yu (2010).
Evolution in action: plants resistant to herbicides.
  Annu Rev Plant Biol, 61, 317-347.  
19538182 I.Axarli, P.Dhavala, A.C.Papageorgiou, and N.E.Labrou (2009).
Crystal structure of Glycine max glutathione transferase in complex with glutathione: investigation of the mechanism operating by the Tau class glutathione transferases.
  Biochem J, 422, 247-256.
PDB code: 3fhs
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