spacer
spacer

PDBsum entry 1m99

Go to PDB code: 
protein ligands links
Transferase PDB id
1m99
Jmol
Contents
Protein chain
216 a.a. *
Ligands
GTS
Waters ×118
* Residue conservation analysis
PDB id:
1m99
Name: Transferase
Title: Crystal structure of the 26 kda glutathione s-transferase fr schistosoma japonicum complexed with glutathione sulfonic a
Structure: Glutathione s-transferase 26kda. Chain: a. Synonym: gst 26, sj26 antigen. Engineered: yes
Source: Schistosoma japonicum. Organism_taxid: 6182. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.218     R-free:   0.261
Authors: R.M.F.Cardoso,D.S.Daniels,C.M.Bruns,J.A.Tainer
Key ref:
R.M.Cardoso et al. (2003). Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum. Proteins, 51, 137-146. PubMed id: 12596270 DOI: 10.1002/prot.10345
Date:
28-Jul-02     Release date:   04-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08515  (GST26_SCHJA) -  Glutathione S-transferase class-mu 26 kDa isozyme
Seq:
Struc:
218 a.a.
216 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 = GTS)
matches with 86.96% 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: 10.1002/prot.10345 Proteins 51:137-146 (2003)
PubMed id: 12596270  
 
 
Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum.
R.M.Cardoso, D.S.Daniels, C.M.Bruns, J.A.Tainer.
 
  ABSTRACT  
 
The 26-kDa glutathione S-transferase from Schistosoma japonicum (Sj26GST), a helminth worm that causes schistosomiasis, catalyzes the conjugation of glutathione with toxic secondary products of membrane lipid peroxidation. Crystal structures of Sj26GST in complex with glutathione sulfonate (Sj26GSTSLF), S-hexyl glutathione (Sj26GSTHEX), and S-2-iodobenzyl glutathione (Sj26GSTIBZ) allow characterization of the electrophile binding site (H site) of Sj26GST. The S-hexyl and S-2-iodobenzyl moieties of these product analogs bind in a pocket defined by side-chains from the beta1-alpha1 loop (Tyr7, Trp8, Ile10, Gly12, Leu13), helix alpha4 (Arg103, Tyr104, Ser107, Tyr111), and the C-terminal coil (Gln204, Gly205, Trp206, Gln207). Changes in the Ser107 and Gln204 dihedral angles make the H site more hydrophobic in the Sj26GSTHEX complex relative to the ligand-free structure. These structures, together with docking studies, indicate a possible binding mode of Sj26GST to its physiologic substrates 4-hydroxynon-2-enal (4HNE), trans-non-2-enal (NE), and ethacrynic acid (EA). In this binding mode, hydrogen bonds of Tyr111 and Gln207 to the carbonyl oxygen atoms of 4HNE, NE, and EA could orient the substrates and enhance their electrophilicity to promote conjugation with glutathione.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Binding of product analogs to the H and G sites of Sj26GST. A-weighted Fo - Fc electron density, contoured at 3.0 , is shown for the ligands (glutathione in brown, S-hexyl and S-2-iodobenzyl in yellow). Functionally important H site residues are shown in purple. (A) Glutathione sulfonate. Tyr7 and a water molecule participate in a hydrogen bond with the sulfonate. (B) S-hexyl glutathione. Tyr7, Gly12, Leu13, Arg103, Ser107, Tyr111, and Gln204 participate in the S-hexyl moiety binding to the H site. (C) S-2-Iodobenzyl glutathione. Tyr7, Leu13, Ser107, and Tyr111 participate in binding the 2-iodobenzyl moiety at the H site.
Figure 3.
Figure 3. Superposition of the Sj26GST and hGST A4-4 H sites. Functionally important H site residues of Sj26GST (pink trace and yellow side-chains) and hGST A4-4 (blue trace pink and green side-chains) are shown. The C-terminal coil of Sj26GST adopts an -helical structure in A4-4.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 51, 137-146) copyright 2003.  
  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.  
20331431 X.Chen, J.Liu, P.Yang, and D.Chen (2010).
Identifying functional residues in arabidopsis thaliana zeta class glutathione S-transferase through screening inactive point mutants.
  Biochemistry (Mosc), 75, 110-120.  
19409081 V.Kasam, J.Salzemann, M.Botha, A.Dacosta, G.Degliesposti, R.Isea, D.Kim, A.Maass, C.Kenyon, G.Rastelli, M.Hofmann-Apitius, and V.Breton (2009).
WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures.
  Malar J, 8, 88.  
  19052367 E.H.Jang, H.Park, A.K.Park, J.H.Moon, Y.M.Chi, and I.Y.Ahn (2008).
Crystallization and preliminary X-ray crystallographic studies of the rho-class glutathione S-transferase from the Antarctic clam Laternula elliptica.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1132-1134.  
17520145 Y.Tanaka, Y.Tsuruda, M.Nishi, N.Kamiya, and M.Goto (2007).
Exploring enzymatic catalysis at a solid surface: a case study with transglutaminase-mediated protein immobilization.
  Org Biomol Chem, 5, 1764-1770.  
  16511012 A.C.Rufer, L.Thiebach, K.Baer, H.W.Klein, and M.Hennig (2005).
X-ray structure of glutathione S-transferase from Schistosoma japonicum in a new crystal form reveals flexibility of the substrate-binding site.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 263-265.
PDB code: 1y6e
12972411 M.Perbandt, C.Burmeister, R.D.Walter, C.Betzel, and E.Liebau (2004).
Native and inhibited structure of a Mu class-related glutathione S-transferase from Plasmodium falciparum.
  J Biol Chem, 279, 1336-1342.
PDB codes: 1pa3 1q4j
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.