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PDBsum entry 1gnw

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1gnw
Jmol
Contents
Protein chains
210 a.a. *
Ligands
GTX ×4
Waters ×660
* Residue conservation analysis
PDB id:
1gnw
Name: Transferase
Title: Structure of glutathione s-transferase
Structure: Glutathione s-transferase. Chain: a, b. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.175    
Authors: P.Reinemer,L.Prade,P.Hof,T.Neuefeind,R.Huber,K.Palme, H.D.Bartunik,B.Bieseler
Key ref:
P.Reinemer et al. (1996). Three-dimensional structure of glutathione S-transferase from Arabidopsis thaliana at 2.2 A resolution: structural characterization of herbicide-conjugating plant glutathione S-transferases and a novel active site architecture. J Mol Biol, 255, 289-309. PubMed id: 8551521 DOI: 10.1006/jmbi.1996.0024
Date:
15-Sep-96     Release date:   17-Sep-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P46422  (GSTF2_ARATH) -  Glutathione S-transferase F2
Seq:
Struc:
212 a.a.
210 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 = 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     apoplast   11 terms 
  Biological process     response to stress   12 terms 
  Biochemical function     camalexin binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1996.0024 J Mol Biol 255:289-309 (1996)
PubMed id: 8551521  
 
 
Three-dimensional structure of glutathione S-transferase from Arabidopsis thaliana at 2.2 A resolution: structural characterization of herbicide-conjugating plant glutathione S-transferases and a novel active site architecture.
P.Reinemer, L.Prade, P.Hof, T.Neuefeind, R.Huber, R.Zettl, K.Palme, J.Schell, I.Koelln, H.D.Bartunik, B.Bieseler.
 
  ABSTRACT  
 
Glutathione S-transferases (GST) are a family of multifunctional enzymes involved in the metabolization of a broad variety of xenobiotics and reactive endogenous compounds. The interest in plant glutathione S-transferases may be attributed to their agronomic value, since it has been demonstrated that glutathione conjugation for a variety of herbicides is the major resistance and selectivity factor in plants. The three-dimensional structure of glutathione S-transferase from the plant Arabidopsis thaliana has been solved by multiple isomorphous replacement and multiwavelength anomalous dispersion techniques at 3 A resolution and refined to a final crystallographic R-factor of 17.5% using data from 8 to 2.2 A resolution. The enzyme forms a dimer of two identical subunits each consisting of 211 residues. Each subunit is characterized by the GST-typical modular structure with two spatially distinct domains. Domain I consists of a central four-stranded beta-sheet flanked on one side by two alpha-helices and on the other side by an irregular segment containing three short 3(10)-helices, while domain II is entirely helical. The dimeric molecule is globular with a prominent large cavity formed between the two subunits. The active site is located in a cleft situated between domains I and II and each subunit binds two molecules of a competitive inhibitor S-hexylglutathione. Both hexyl moieties are oriented parallel and fill the H-subsite of the enzyme's active site. The glutathione peptide of one inhibitor, termed productive binding, occupies the G-subsite with multiple interactions similar to those observed for other glutathione S-transferases, while the glutathione backbone of the second inhibitor, termed unproductive binding, exhibits only weak interactions mediated by two polar contacts. A most striking difference from the mammalian glutathione S-transferases, which share a conserved catalytic tyrosine residue, is the lack of this tyrosine in the active site of the plant glutathione S-transferase.
 
  Selected figure(s)  
 
Figure 9.
Figure 9. A schematic represen- tation of the binding of the gluta- thione peptid of the productively bound inhibitor to the G-subsite of A. thaliana glutathone S-trans- ferase's active site.
Figure 10.
Figure 10. Superimposition of A. thaliana and mammalian glutathione S-transferase monomers complexed with their ligands; red, A. thaliana glutathione S-transferase; black, pi class isoenzyme (pGSTPI-1); ble, mu class isoenzyme (rGSTM3-3); and reen, alpha class isoenzyme (hGSTAI-1).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 255, 289-309) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21428697 A.Oakley (2011).
Glutathione transferases: a structural perspective.
  Drug Metab Rev, 43, 138-151.  
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.  
21054438 X.Li, P.Gao, D.Cui, L.Wu, I.Parkin, R.Saberianfar, R.Menassa, H.Pan, N.Westcott, and M.Y.Gruber (2011).
The Arabidopsis tt19-4 mutant differentially accumulates proanthocyanidin and anthocyanin through a 3' amino acid substitution in glutathione S-transferase.
  Plant Cell Environ, 34, 374-388.  
20135200 S.Banerjee, and R.Goswami (2010).
GST profile expression study in some selected plants: in silico approach.
  Mol Cell Biochem, 336, 109-126.  
19520850 D.P.Dixon, and R.Edwards (2009).
Selective binding of glutathione conjugates of Fatty Acid derivatives by plant glutathione transferases.
  J Biol Chem, 284, 21249-21256.  
18691867 P.Kapoli, I.A.Axarli, D.Platis, M.Fragoulaki, M.Paine, J.Hemingway, J.Vontas, and N.E.Labrou (2008).
Engineering sensitive glutathione transferase for the detection of xenobiotics.
  Biosens Bioelectron, 24, 498-503.  
17932678 S.G.Kim, S.T.Kim, S.Y.Kang, Y.Wang, W.Kim, and K.Y.Kang (2008).
Proteomic analysis of reactive oxygen species (ROS)-related proteins in rice roots.
  Plant Cell Rep, 27, 363-375.  
18670133 Z.Li, X.Wang, J.Ma, G.Zhang, and Z.Ma (2008).
Cloning and characterization of a tau glutathione S-transferase subunit encoding gene in Gossypium hirsutum.
  Genes Genet Syst, 83, 219-225.  
17682821 B.Blanchette, X.Feng, and B.R.Singh (2007).
Marine glutathione S-transferases.
  Mar Biotechnol (NY), 9, 513-542.  
17284839 K.Yamamoto, H.Fujii, Y.Aso, Y.Banno, and K.Koga (2007).
Expression and characterization of a sigma-class glutathione S-transferase of the fall webworm, Hyphantria cunea.
  Biosci Biotechnol Biochem, 71, 553-560.  
17488842 Y.S.Chung, W.H.Lee, C.Y.Tang, and C.L.Lu (2007).
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints.
  Nucleic Acids Res, 35, W639-W644.  
16538523 E.Nutricati, A.Miceli, F.Blando, and L.De Bellis (2006).
Characterization of two Arabidopsis thaliana glutathione S-transferases.
  Plant Cell Rep, 25, 997.  
14617075 A.P.Smith, S.D.Nourizadeh, W.A.Peer, J.Xu, A.Bandyopadhyay, A.S.Murphy, and P.B.Goldsbrough (2003).
Arabidopsis AtGSTF2 is regulated by ethylene and auxin, and encodes a glutathione S-transferase that interacts with flavonoids.
  Plant J, 36, 433-442.  
12972429 M.G.Jeppesen, P.Ortiz, W.Shepard, T.G.Kinzy, J.Nyborg, and G.R.Andersen (2003).
The crystal structure of the glutathione S-transferase-like domain of elongation factor 1Bgamma from Saccharomyces cerevisiae.
  J Biol Chem, 278, 47190-47198.
PDB code: 1nhy
11889135 A.M.Caccuri, G.Antonini, N.Allocati, C.Di Ilio, F.De Maria, F.Innocenti, M.W.Parker, M.Masulli, M.Lo Bello, P.Turella, G.Federici, and G.Ricci (2002).
GSTB1-1 from Proteus mirabilis: a snapshot of an enzyme in the evolutionary pathway from a redox enzyme to a conjugating enzyme.
  J Biol Chem, 277, 18777-18784.  
  11897031 D.P.Dixon, A.Lapthorn, and R.Edwards (2002).
Plant glutathione transferases.
  Genome Biol, 3, REVIEWS3004.  
12207667 M.W.Bianchi, C.Roux, and N.Vartanian (2002).
Drought regulation of GST8, encoding the Arabidopsis homologue of ParC/Nt107 glutathione transferase/peroxidase.
  Physiol Plant, 116, 96.  
11604524 A.J.Oakley, T.Harnnoi, R.Udomsinprasert, K.Jirajaroenrat, A.J.Ketterman, and M.C.Wilce (2001).
The crystal structures of glutathione S-transferases isozymes 1-3 and 1-4 from Anopheles dirus species B.
  Protein Sci, 10, 2176-2185.
PDB codes: 1jlv 1jlw
11327815 G.Polekhina, P.G.Board, A.C.Blackburn, and M.W.Parker (2001).
Crystal structure of maleylacetoacetate isomerase/glutathione transferase zeta reveals the molecular basis for its remarkable catalytic promiscuity.
  Biochemistry, 40, 1567-1576.
PDB code: 1fw1
11453988 N.E.Labrou, L.V.Mello, and Y.D.Clonis (2001).
The conserved Asn49 of maize glutathione S-transferase I modulates substrate binding, catalysis and intersubunit communication.
  Eur J Biochem, 268, 3950-3957.  
11171973 T.C.Umland, K.L.Taylor, S.Rhee, R.B.Wickner, and D.R.Davies (2001).
The crystal structure of the nitrogen regulation fragment of the yeast prion protein Ure2p.
  Proc Natl Acad Sci U S A, 98, 1459-1464.
PDB code: 1hqo
10673421 G.J.Palm, E.Billy, W.Filipowicz, and A.Wlodawer (2000).
Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology.
  Structure, 8, 13-23.
PDB codes: 1qmh 1qmi
  10548067 J.U.Flanagan, J.Rossjohn, M.W.Parker, P.G.Board, and G.Chelvanayagam (1999).
Mutagenic analysis of conserved arginine residues in and around the novel sulfate binding pocket of the human Theta class glutathione transferase T2-2.
  Protein Sci, 8, 2205-2212.  
10419539 L.W.Cheng, and O.Schneewind (1999).
Yersinia enterocolitica type III secretion. On the role of SycE in targeting YopE into HeLa cells.
  J Biol Chem, 274, 22102-22108.  
10610060 T.R.Santosh, M.Sreekala, and K.Lalitha (1999).
Oxidative stress during selenium deficiency in seedlings of Trigonella foenum-graecum and mitigation by mimosine Part II. Glutathione metabolism.
  Biol Trace Elem Res, 70, 209-222.  
10066594 D.P.Dixon, L.Cummins, D.J.Cole, and R.Edwards (1998).
Glutathione-mediated detoxification systems in plants.
  Curr Opin Plant Biol, 1, 258-266.  
9551553 J.Rossjohn, W.J.McKinstry, A.J.Oakley, D.Verger, J.Flanagan, G.Chelvanayagam, K.L.Tan, P.G.Board, and M.W.Parker (1998).
Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site.
  Structure, 6, 309-322.
PDB codes: 1ljr 2ljr 3ljr
9829702 J.U.Flanagan, J.Rossjohn, M.W.Parker, P.G.Board, and G.Chelvanayagam (1998).
A homology model for the human theta-class glutathione transferase T1-1.
  Proteins, 33, 444-454.  
9817846 L.Prade, R.Huber, and B.Bieseler (1998).
Structures of herbicides in complex with their detoxifying enzyme glutathione S-transferase - explanations for the selectivity of the enzyme in plants.
  Structure, 6, 1445-1452.
PDB codes: 1bx9 1bye
9485454 M.Nicotra, M.Paci, M.Sette, A.J.Oakley, M.W.Parker, M.Lo Bello, A.M.Caccuri, G.Federici, and G.Ricci (1998).
Solution structure of glutathione bound to human glutathione transferase P1-1: comparison of NMR measurements with the crystal structure.
  Biochemistry, 37, 3020-3027.  
9761841 W.J.McKinstry, A.J.Oakley, J.Rossjohn, D.Verger, K.L.Tan, P.G.Board, and M.W.Parker (1998).
Preliminary X-ray crystallographic studies of a newly defined human theta-class glutathione transferase.
  Acta Crystallogr D Biol Crystallogr, 54, 148-150.  
  9165073 D.Besse, N.Budisa, W.Karnbrock, C.Minks, H.J.Musiol, S.Pegoraro, F.Siedler, E.Weyher, and L.Moroder (1997).
Chalcogen-analogs of amino acids. Their use in X-ray crystallographic and folding studies of peptides and proteins.
  Biol Chem, 378, 211-218.  
9345628 K.Moffat, and Z.Ren (1997).
Synchrotron radiation applications to macromolecular crystallography.
  Curr Opin Struct Biol, 7, 689-696.  
  9165087 L.Prade, P.Hof, and B.Bieseler (1997).
Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification.
  Biol Chem, 378, 317-320.  
9351803 L.Prade, R.Huber, T.H.Manoharan, W.E.Fahl, and W.Reuter (1997).
Structures of class pi glutathione S-transferase from human placenta in complex with substrate, transition-state analogue and inhibitor.
  Structure, 5, 1287-1295.
PDB codes: 1aqv 1aqw 1aqx
  9045797 S.Vuilleumier (1997).
Bacterial glutathione S-transferases: what are they good for?
  J Bacteriol, 179, 1431-1441.  
  9165062 W.Baumeister, Z.Cejka, M.Kania, and E.Seemüller (1997).
The proteasome: a macromolecular assembly designed to confine proteolysis to a nanocompartment.
  Biol Chem, 378, 121-130.  
  9041642 W.Kaplan, P.Hüsler, H.Klump, J.Erhardt, N.Sluis-Cremer, and H.Dirr (1997).
Conformational stability of pGEX-expressed Schistosoma japonicum glutathione S-transferase: a detoxification enzyme and fusion-protein affinity tag.
  Protein Sci, 6, 399-406.  
9245401 X.Ji, M.Tordova, R.O'Donnell, J.F.Parsons, J.B.Hayden, G.L.Gilliland, and P.Zimniak (1997).
Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase.
  Biochemistry, 36, 9690-9702.
PDB codes: 1pgt 2pgt
8917446 N.Sluis-Cremer, N.N.Naidoo, W.H.Kaplan, T.H.Manoharan, W.E.Fahl, and H.W.Dirr (1996).
Determination of a binding site for a non-substrate ligand in mammalian cytosolic glutathione S-transferases by means of fluorescence-resonance energy transfer.
  Eur J Biochem, 241, 484-488.  
8706748 S.Vuilleumier, and T.Leisinger (1996).
Protein engineering studies of dichloromethane dehalogenase/glutathione S-transferase from Methylophilus sp. strain DM11. Ser12 but not Tyr6 is required for enzyme activity.
  Eur J Biochem, 239, 410-417.  
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.