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PDBsum entry 2j9h

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Transferase PDB id
2j9h
Jmol
Contents
Protein chain
209 a.a. *
Ligands
GTX ×2
Waters ×45
* Residue conservation analysis
PDB id:
2j9h
Name: Transferase
Title: Crystal structure of human glutathione-s-transferase p1-1 cys-free mutant in complex with s-hexylglutathione at 2.4 a resolution
Structure: Glutathione s-transferase p. Chain: a, b. Synonym: glutathione-s-transferase p1-1, gst class-pi, gstp1-1. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.4Å     R-factor:   0.253     R-free:   0.310
Authors: K.Tars,U.M.Hegazy,U.Hellman,B.Mannervik
Key ref:
U.M.Hegazy et al. (2008). Modulating catalytic activity by unnatural amino acid residues in a GSH-binding loop of GST P1-1. J Mol Biol, 376, 811-826. PubMed id: 18177897 DOI: 10.1016/j.jmb.2007.12.013
Date:
08-Nov-06     Release date:   14-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09211  (GSTP1_HUMAN) -  Glutathione S-transferase P
Seq:
Struc:
210 a.a.
209 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 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 = GTX)
matches with 76.00% similarity
= HX
+ R-S-glutathione
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     TRAF2-GSTP1 complex   9 terms 
  Biological process     metabolic process   31 terms 
  Biochemical function     S-nitrosoglutathione binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2007.12.013 J Mol Biol 376:811-826 (2008)
PubMed id: 18177897  
 
 
Modulating catalytic activity by unnatural amino acid residues in a GSH-binding loop of GST P1-1.
U.M.Hegazy, K.Tars, U.Hellman, B.Mannervik.
 
  ABSTRACT  
 
The loop following helix alpha2 in glutathione transferase P1-1 has two conserved residues, Cys48 and Tyr50, important for glutathione (GSH) binding and catalytic activity. Chemical modification of Cys48 thwarts the catalytic activity of the enzyme, and mutation of Tyr50 generally decreases the k(cat) value and the affinity for GSH in a differential manner. Cys48 and Tyr50 were targeted by site-specific mutations and chemical modifications in order to investigate how the alpha2 loop modulates GSH binding and catalysis. Mutation of Cys48 into Ala increased K(M)(GSH) 24-fold and decreased the binding energy of GSH by 1.5 kcal/mol. Furthermore, the protein stability against thermal inactivation and chemical denaturation decreased. The crystal structure of the Cys-free variant was determined, and its similarity to the wild-type structure suggests that the mutation of Cys48 increases the flexibility of the alpha2 loop rather than dislocating the GSH-interacting residues. On the other hand, replacement of Tyr50 with Cys, producing mutant Y50C, increased the Gibbs free energy of the catalyzed reaction by 4.8 kcal/mol, lowered the affinity for S-hexyl glutathione by 2.2 kcal/mol, and decreased the thermal stability. The targeted alkylation of Cys50 in Y50C increased the affinity for GSH and protein stability. Characterization of the most active alkylated variants, S-n-butyl-, S-n-pentyl-, and S-cyclobutylmethyl-Y50C, indicated that the affinity for GSH is restored by stabilizing the alpha2 loop through positioning of the key residue into the lock structure of the neighboring subunit. In addition, k(cat) can be further modulated by varying the structure of the key residue side chain, which impinges on the rate-limiting step of catalysis.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Chemical reactions catalyzed by GST P1-1 variants. (a) Nucleophilic aromatic substitution reaction between GSH and CDNB, demonstrating the intermediate Meisenheimer complex in brackets and the end product GS-DNB. (b) Reversible formation of the Meisenheimer complex 1-(S-glutathionyl)-2,4,6-trinitrocyclohexadienate anion between glutathione and TNB, mimicking the formation of the intermediate in the conjugation of GSH with CDNB. The TNB σ-complex does not decompose into GS-TNB due to the lack of a good leaving group.
Figure 6.
Fig. 6. Comparison of position 48 and the surrounding residues of (a) wild-type human GST P1-1 and (b) the Cys-free mutant. Cys48 in the wild-type structure (a) occupies a hydrophobic pocket, formed by the side chains Trp39, Leu44, Leu53, Lys55, and Tyr64 of the same subunit. This interaction may stabilize the structure of the α2 loop. The positions of the side chains remain essentially unchanged in the Cys-free mutant (b), but removal of the Cys48 sulfur atom leaves an empty cavity, which may weaken the interaction and increase the mobility of the α2 loop. Alkylation of the Cys48 sulfur would displace the sulfur atom and alter the conformation of the α2 loop, thereby compromising binding of glutathione.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 376, 811-826) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20540076 I.Quesada-Soriano, L.J.Parker, A.Primavera, J.Wielens, J.K.Holien, J.M.Casas-Solvas, A.Vargas-Berenguel, A.M.Aguilera, M.Nuccetelli, A.P.Mazzetti, M.L.Bello, M.W.Parker, and L.García-Fuentes (2011).
Diuretic drug binding to human glutathione transferase P1-1: potential role of Cys-101 revealed in the double mutant C47S/Y108V.
  J Mol Recognit, 24, 220-234.
PDB codes: 3km6 3kmo
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