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PDBsum entry 1axd

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protein ligands Protein-protein interface(s) links
Transferase/transferase inhibitor PDB id
1axd
Jmol
Contents
Protein chains
209 a.a. *
Ligands
GGL-CYW-GLY ×2
Waters ×570
* Residue conservation analysis
PDB id:
1axd
Name: Transferase/transferase inhibitor
Title: Structure of glutathione s-transferase-i bound with the liga lactoylglutathione
Structure: Glutathione s-transferase i. Chain: a, b. Engineered: yes. Lactoylglutathione. Chain: c, d
Source: Zea mays. Organism_taxid: 4577. Variant: mutin. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.174    
Authors: T.Neuefeind,R.Huber,H.Dasenbrock,L.Prade,B.Bieseler
Key ref:
T.Neuefeind et al. (1997). Crystal structure of herbicide-detoxifying maize glutathione S-transferase-I in complex with lactoylglutathione: evidence for an induced-fit mechanism. J Mol Biol, 274, 446-453. PubMed id: 9417926 DOI: 10.1006/jmbi.1997.1402
Date:
15-Oct-97     Release date:   28-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P12653  (GSTF1_MAIZE) -  Glutathione S-transferase 1
Seq:
Struc:
214 a.a.
209 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 = GGL)
matches with 45.00% similarity
= HX
+ R-S-glutathione
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     transferase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1997.1402 J Mol Biol 274:446-453 (1997)
PubMed id: 9417926  
 
 
Crystal structure of herbicide-detoxifying maize glutathione S-transferase-I in complex with lactoylglutathione: evidence for an induced-fit mechanism.
T.Neuefeind, R.Huber, H.Dasenbrock, L.Prade, B.Bieseler.
 
  ABSTRACT  
 
Glutathione S-transferases (GSTs) -I and -III are involved in herbicide metabolism in maize and have been intensively studied. Starting with plant tissue from Zea mays var. mutin recombinant GST-I was prepared by heterologous expression in Escherichia coli. The enzyme was crystallized in the presence of lactoylglutathione, a ligand formerly never observed in a GST structure and known as an intermediate of the pharmacologically relevant glyoxalase system. The crystal structure of GST-I has been determined at 2.5 A resolution and exhibits the GST-typical dimer of two identical subunits, each consisting of 214 residues. Compared with other plant GSTs the three-dimensional structure of GST-I primarily shows structural differences in the hydrophobic substrate binding site, the linker segment and the C-terminal region. Furthermore, a comparison of the ligand-bound GST-I structure with the apo structure of GST-III indicates the movement of a ten-residue loop upon binding of the ligand to the active site. This is the first structure-based evidence for an induced fit mechanism of glutathione S-transferases, which has previously been postulated for class pi enzymes. Together with GST-III, GST-I may explain herbicide resistance and selectivity in maize as well as in other agronomic relevant crops.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Stereo ribbon representation of the GST-I monomer bound with the inhibitor lactoylglutathione. Helices (H) are drawn as red spirals, β-strands (S) as blue arrows. The Figure was made with MOLSCRIPT [Kraulis 1991]. (b) Ribbon representation of the GST-I dimer along the local dyad. The Figure was made with RASTER3D [Merrit and Murphy 1994].
Figure 3.
Figure 3. (a) Model of the inhibitor lactoylglutathione (magenta) and its next neighbors in the active site of maize GST-I with an overlayed 2 F[o]—F[c]map contoured at 1σ. (b) Superposition of the active site of maize GST-I (red) complexed with lactoylglutathione (magenta) and maize GST-III (blue). (c) Superposition of maize GST-I (red) and A. thaliana GST (green) complexed with the productively bound inhibitor S-hexylglutathione (yellow).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 274, 446-453) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20177697 A.Vertommen, B.Panis, R.Swennen, and S.C.Carpentier (2010).
Evaluation of chloroform/methanol extraction to facilitate the study of membrane proteins of non-model plants.
  Planta, 231, 1113-1125.  
20135200 S.Banerjee, and R.Goswami (2010).
GST profile expression study in some selected plants: in silico approach.
  Mol Cell Biochem, 336, 109-126.  
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
19851333 X.X.Ma, Y.L.Jiang, Y.X.He, R.Bao, Y.Chen, and C.Z.Zhou (2009).
Structures of yeast glutathione-S-transferase Gtt2 reveal a new catalytic type of GST family.
  EMBO Rep, 10, 1320-1326.
PDB codes: 3erf 3erg 3ibh
18343821 K.J.Kim, M.C.Park, S.J.Choi, Y.S.Oh, E.C.Choi, H.J.Cho, M.H.Kim, S.H.Kim, D.W.Kim, S.Kim, and B.S.Kang (2008).
Determination of three-dimensional structure and residues of the novel tumor suppressor AIMP3/p18 required for the interaction with ATM.
  J Biol Chem, 283, 14032-14040.
PDB code: 2uz8
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.  
18836188 S.Conn, C.Curtin, A.Bézier, C.Franco, and W.Zhang (2008).
Purification, molecular cloning, and characterization of glutathione S-transferases (GSTs) from pigmented Vitis vinifera L. cell suspension cultures as putative anthocyanin transport proteins.
  J Exp Bot, 59, 3621-3634.  
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.  
16923014 E.Goulas, M.Schubert, T.Kieselbach, L.A.Kleczkowski, P.Gardeström, W.Schröder, and V.Hurry (2006).
The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature.
  Plant J, 47, 720-734.  
15906083 N.E.Labrou, M.Karavangeli, A.Tsaftaris, and Y.D.Clonis (2005).
Kinetic analysis of maize glutathione S-transferase I catalysing the detoxification from chloroacetanilide herbicides.
  Planta, 222, 91-97.  
15317585 G.A.Kotzia, and N.E.Labrou (2004).
S-(2,3-dichlorotriazinyl)glutathione. A new affinity label for probing the structure and function of glutathione transferases.
  Eur J Biochem, 271, 3503-3511.  
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
15122630 P.Jeschke (2004).
The unique role of fluorine in the design of active ingredients for modern crop protection.
  Chembiochem, 5, 571-589.  
12692133 D.P.Dixon, A.G.McEwen, A.J.Lapthorn, and R.Edwards (2003).
Forced evolution of a herbicide detoxifying glutathione transferase.
  J Biol Chem, 278, 23930-23935.
PDB code: 1oyj
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
  11897031 D.P.Dixon, A.Lapthorn, and R.Edwards (2002).
Plant glutathione transferases.
  Genome Biol, 3, REVIEWS3004.  
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
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.  
10451545 L.Stella, M.Nicotra, G.Ricci, N.Rosato, and E.E.Di Iorio (1999).
Molecular dynamics simulations of human glutathione transferase P1-1: analysis of the induced-fit mechanism by GSH binding.
  Proteins, 37, 1-9.  
9665696 A.J.Oakley, M.Lo Bello, G.Ricci, G.Federici, and M.W.Parker (1998).
Evidence for an induced-fit mechanism operating in pi class glutathione transferases.
  Biochemistry, 37, 9912-9917.
PDB codes: 14gs 16gs
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.  
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
9818188 R.N.Armstrong (1998).
Mechanistic imperatives for the evolution of glutathione transferases.
  Curr Opin Chem Biol, 2, 618-623.  
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.