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PDBsum entry 1c72

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1c72
Jmol PyMol
Contents
Protein chains
217 a.a. *
Ligands
EPY ×4
Waters ×158
* Residue conservation analysis
PDB id:
1c72
Name: Transferase
Title: Tyr115, gln165 and trp209 contribute to the 1,2-epoxy-3-(p- nitrophenoxy)propane conjugating activities of glutathione s-transferase cgstm1-1
Structure: Protein (glutathione s-transferase). Chain: a, b, c, d. Synonym: gsts. Engineered: yes. Other_details: 1,2-epoxy-3-(p-nitrophenoxy)propane
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.190     R-free:   0.280
Authors: M.K.Chern,T.C.Wu,C.H.Hsieh,C.C.Chou,L.F.Liu,I.C.Kuan, Y.H.Yeh,C.D.Hsiao,M.F.Tam
Key ref:
M.K.Chern et al. (2000). Tyr115, gln165 and trp209 contribute to the 1, 2-epoxy-3-(p-nitrophenoxy)propane-conjugating activity of glutathione S-transferase cGSTM1-1. J Mol Biol, 300, 1257-1269. PubMed id: 10903867 DOI: 10.1006/jmbi.2000.3904
Date:
02-Feb-00     Release date:   30-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P20136  (GSTM2_CHICK) -  Glutathione S-transferase 2
Seq:
Struc:
220 a.a.
217 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 = EPY)
matches with 58.00% 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     cytoplasm   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     transferase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3904 J Mol Biol 300:1257-1269 (2000)
PubMed id: 10903867  
 
 
Tyr115, gln165 and trp209 contribute to the 1, 2-epoxy-3-(p-nitrophenoxy)propane-conjugating activity of glutathione S-transferase cGSTM1-1.
M.K.Chern, T.C.Wu, C.H.Hsieh, C.C.Chou, L.F.Liu, I.C.Kuan, Y.H.Yeh, C.D.Hsiao, M.F.Tam.
 
  ABSTRACT  
 
We investigated the epoxidase activity of a class mu glutathione S-transferase (cGSTM1-1), using 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP) as substrate. Trp209 on the C-terminal tail, Arg107 on the alpha4 helix, Asp161 and Gln165 on the alpha6 helix of cGSTM1-1 were selected for mutagenesis and kinetic studies. A hydrophobic side-chain at residue 209 is needed for the epoxidase activity of cGSTM1-1. Replacing Trp209 with histidine, isoleucine or proline resulted in a fivefold to 28-fold decrease in the k(cat)(app) of the enzyme, while a modest 25 % decrease in the k(cat)(app) was observed for the W209F mutant. The rGSTM1-1 enzyme has serine at the correponding position. The k(cat)(app) of the S209W mutant is 2. 5-fold higher than that of the wild-type rGSTM1-1. A charged residue is needed at position 107 of cGSTM1-1. The K(m)(app)(GSH) of the R107L mutant is 38-fold lower than that of the wild-type enzyme. On the contrary, the R107E mutant has a K(m)(app)(GSH) and a k(cat)(app) that are 11-fold and 35 % lower than those of the wild-type cGSTM1-1. The substitutions of Gln165 with Glu or Leu have minimal effect on the affinity of the mutants towards GSH or EPNP. However, a discernible reduction in k(cat)(app) was observed. Asp161 is involved in maintaining the structural integrity of the enzyme. The K(m)(app)(GSH) of the D161L mutant is 616-fold higher than that of the wild-type enzyme. In the hydrogen/deuterium exchange experiments, this mutant has the highest level of deuteration among all the proteins tested.We also elucidated the structure of cGSTM1-1 co-crystallized with the glutathionyl-conjugated 1, 2-epoxy-3-(p-nitrophenoxy)propane (EPNP) at 2.8 A resolution. The product found in the active site was 1-hydroxy-2-(S-glutathionyl)-3-(p-nitrophenoxy)propane, instead of the conventional 2-hydroxy isomer. The EPNP moiety orients towards Arg107 and Gln165 in dimer AB, and protrudes into a hydrophobic region formed by the loop connecting beta1 and alpha1 and part of the C-terminal tail in dimer CD. The phenoxyl ring forms strong ring stacking with the Trp209 side-chain in dimer CD. We hypothesize that these two conformations represent the EPNP moiety close to the initial and final stages of the reaction mechanism, respectively.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The residue-deleted (GS-EPNP) 2|F[o]| -|F[c]| density maps with the final refined model superimposed. The maps are contoured at 1.0 s: (a) and (b) correspond to subunit A and C, respectively.
Figure 4.
Figure 4. Possible reaction mechanism of EPNP conjugation on cGSTM1-1. G-S -, the thiolate anion of glutathione.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 1257-1269) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20489719 V.T.Bhat, A.M.Caniard, T.Luksch, R.Brenk, D.J.Campopiano, and M.F.Greaney (2010).
Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry.
  Nat Chem, 2, 490-497.  
16385005 N.Hiller, K.Fritz-Wolf, M.Deponte, W.Wende, H.Zimmermann, and K.Becker (2006).
Plasmodium falciparum glutathione S-transferase--structural and mechanistic studies on ligand binding and enzyme inhibition.
  Protein Sci, 15, 281-289.
PDB code: 2aaw
15685230 I.Encío, D.J.Morré, R.Villar, M.J.Gil, and V.Martínez-Merino (2005).
Benzo[b]thiophenesulphonamide 1,1-dioxide derivatives inhibit tNOX activity in a redox state-dependent manner.
  Br J Cancer, 92, 690-695.  
15596504 T.Haliloglu, O.Keskin, B.Ma, and R.Nussinov (2005).
How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
  Biophys J, 88, 1552-1559.  
14623980 K.Fritz-Wolf, A.Becker, S.Rahlfs, P.Harwaldt, R.H.Schirmer, W.Kabsch, and K.Becker (2003).
X-ray structure of glutathione S-transferase from the malarial parasite Plasmodium falciparum.
  Proc Natl Acad Sci U S A, 100, 13821-13826.
PDB code: 1okt
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 code is shown on the right.

 

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