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PDBsum entry 1a0f

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1a0f
Jmol
Contents
Protein chains
201 a.a. *
Ligands
GTS ×2
Waters ×174
* Residue conservation analysis
PDB id:
1a0f
Name: Transferase
Title: Crystal structure of glutathione s-transferase from escherichia coli complexed with glutathionesulfonic acid
Structure: Glutathione s-transferase. Chain: a, b. Fragment: glutathione-binding domain. Synonym: gst, glutathione transferase. Engineered: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: gst. Expressed in: escherichia coli k12. Expression_system_taxid: 83333.
Biol. unit: Dimer (from PDB file)
Resolution:
2.10Å     R-factor:   0.183     R-free:   0.245
Authors: M.Nishida,S.Harada,S.Noguchi,H.Inoue,K.Takahashi,Y.Satow
Key ref:
M.Nishida et al. (1998). Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106. J Mol Biol, 281, 135-147. PubMed id: 9680481 DOI: 10.1006/jmbi.1998.1927
Date:
29-Nov-97     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A9D2  (GSTA_ECOLI) -  Glutathione S-transferase GstA
Seq:
Struc:
201 a.a.
201 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 86.00% 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     xenobiotic catabolic process   1 term 
  Biochemical function     transferase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.1927 J Mol Biol 281:135-147 (1998)
PubMed id: 9680481  
 
 
Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106.
M.Nishida, S.Harada, S.Noguchi, Y.Satow, H.Inoue, K.Takahashi.
 
  ABSTRACT  
 
Cytosolic glutathione S-transferase is a family of multi-functional enzymes involved in the detoxification of a large variety of xenobiotic and endobiotic compounds through glutathione conjugation. The three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate, N-(N-L-gamma-glutamyl-3-sulfo-L-alanyl)-glycine, has been determined by the multiple isomorphous replacement method and refined to a crystallographic R factor of 0.183 at 2.1 A resolution.The E. coli enzyme is a globular homodimer with dimensions of 58 Ax56 Ax52 A. Each subunit, consisting of a polypeptide of 201 amino acid residues, is divided into a smaller N-terminal domain (residues 1 to 80) and a larger C-terminal one (residues 89 to 201). The core of the N-terminal domain is constructed by a four-stranded beta-sheet and two alpha-helices, and that of the C-terminal one is constructed by a right-handed bundle of four alpha-helices. Glutathione sulfonate, a competitive inhibitor against glutathione, is bound in a cleft between the N and C-terminal domains. Therefore, the E. coli enzyme conserves overall constructions common to the eukaryotic enzymes, in its polypeptide fold, dimeric assembly, and glutathione-binding site. In the case of the eukaryotic enzymes, tyrosine and serine residues near the N terminus are located in the proximity of the sulfur atom of the bound glutathione, and are proposed to be catalytically essential. In the E. coli enzyme, Tyr5 and Ser11 corresponding to these residues are not involved in the interaction with the inhibitor, although they are located in the vicinity of catalytic site. Instead, Cys10 N and His106 Nepsilon2 atoms are hydrogen-bonded to the sulfonate group of the inhibitor. On the basis of this structural study, Cys10 and His106 are ascribed to the catalytic residues that are distinctive from the family of the eukaryotic enzymes. We propose that glutathione S-transferases have diverged from a common origin and acquired different catalytic apparatuses in the process of evolution.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Schematic drawing for interactions between E. coli GST and glutathione sulfonate. Water molecules located in the GSH-bind- ing site are shown as Wat. Hydro- gen bonds are drawn as broken lines, and their distances are given in Å . Residues from the accompa- nying subunit are indicated by asterisks.
Figure 7.
Figure 7. Stereo views of the cata- lytic site of E. coli GST superposed on the structures of eukaryotic theta and alpha GSTs. The ligand molecules, glutathione sulfonate in E. coli GST, S-hexyl-glutathione in theta GST from A. thaliana (Reinemer et al., 1996), and S-ben- zyl-glutathione in human GST alpha 1-1 (Sinning et al., 1993), and the C a atoms of the enzymes are superposed in the Figure. The structure for the liganded E. coli GST is colored red, and those for the theta (a) and alpha (b) GSTs are in green and blue, respectively. Residues from the accompanying subunit are shown by asterisks. The ligand molecules are in light colors. Hydrogen bonds formed in the catalytic site of E. coli and alpha are drawn as dotted lines.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 281, 135-147) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20663851 L.Federici, M.Masulli, C.Di Ilio, and N.Allocati (2010).
Characterization of the hydrophobic substrate-binding site of the bacterial beta class glutathione transferase from Proteus mirabilis.
  Protein Eng Des Sel, 23, 743-750.  
20388120 L.Xun, S.M.Belchik, R.Xun, Y.Huang, H.Zhou, E.Sanchez, C.Kang, and P.G.Board (2010).
S-Glutathionyl-(chloro)hydroquinone reductases: a novel class of glutathione transferases.
  Biochem J, 428, 419-427.  
20080536 T.W.Lin, P.J.Hsieh, C.L.Lin, Y.Y.Fang, J.X.Yang, C.C.Tsai, P.L.Chiang, C.Y.Pan, and Y.T.Chen (2010).
Label-free detection of protein-protein interactions using a calmodulin-modified nanowire transistor.
  Proc Natl Acad Sci U S A, 107, 1047-1052.  
19668857 J.K.Takimoto, K.L.Adams, Z.Xiang, and L.Wang (2009).
Improving orthogonal tRNA-synthetase recognition for efficient unnatural amino acid incorporation and application in mammalian cells.
  Mol Biosyst, 5, 931-934.  
19016852 N.Allocati, L.Federici, M.Masulli, and C.Di Ilio (2009).
Glutathione transferases in bacteria.
  FEBS J, 276, 58-75.  
  18540073 B.Remmerie, K.Vandenbroucke, L.De Smet, W.Carpentier, D.De Vos, J.Stout, J.Van Beeumen, and S.N.Savvides (2008).
Expression, purification, crystallization and structure determination of two glutathione S-transferase-like proteins from Shewanella oneidensis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 548-553.  
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
18076047 N.Allocati, L.Federici, M.Masulli, B.Favaloro, and C.Di Ilio (2008).
Cysteine 10 is critical for the activity of Ochrobactrum anthropi glutathione transferase and its mutation to alanine causes the preferential binding of glutathione to the H-site.
  Proteins, 71, 16-23.
PDB code: 2pvq
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.  
17213657 E.Masai, Y.Katayama, and M.Fukuda (2007).
Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds.
  Biosci Biotechnol Biochem, 71, 1.  
16920719 E.I.Tocheva, P.D.Fortin, L.D.Eltis, and M.E.Murphy (2006).
Structures of ternary complexes of BphK, a bacterial glutathione S-transferase that reductively dechlorinates polychlorinated biphenyl metabolites.
  J Biol Chem, 281, 30933-30940.
PDB codes: 2dsa 2gdr
17139087 H.Simader, M.Hothorn, and D.Suck (2006).
Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold.
  Acta Crystallogr D Biol Crystallogr, 62, 1510-1519.
PDB codes: 2hqt 2hra
17008712 J.L.Pan, and J.C.Bardwell (2006).
The origami of thioredoxin-like folds.
  Protein Sci, 15, 2217-2227.  
15735307 A.M.Hansen, Y.Gu, M.Li, M.Andrykovitch, D.S.Waugh, D.J.Jin, and X.Ji (2005).
Structural basis for the function of stringent starvation protein a as a transcription factor.
  J Biol Chem, 280, 17380-17391.
PDB code: 1yy7
16081649 J.Li, Z.Xia, and J.Ding (2005).
Thioredoxin-like domain of human kappa class glutathione transferase reveals sequence homology and structure similarity to the theta class enzyme.
  Protein Sci, 14, 2361-2369.
PDB code: 1yzx
15475348 K.P.Lim, and W.Hong (2004).
Human Nischarin/imidazoline receptor antisera-selected protein is targeted to the endosomes by a combined action of a PX domain and a coiled-coil region.
  J Biol Chem, 279, 54770-54782.  
14635120 C.L.Rife, J.F.Parsons, G.Xiao, G.L.Gilliland, and R.N.Armstrong (2003).
Conserved structural elements in glutathione transferase homologues encoded in the genome of Escherichia coli.
  Proteins, 53, 777-782.
PDB code: 1n2a
12438698 A.Kentsis, R.E.Gordon, and K.L.Borden (2002).
Control of biochemical reactions through supramolecular RING domain self-assembly.
  Proc Natl Acad Sci U S A, 99, 15404-15409.  
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.  
11342133 L.Bousset, H.Belrhali, J.Janin, R.Melki, and S.Morera (2001).
Structure of the globular region of the prion protein Ure2 from the yeast Saccharomyces cerevisiae.
  Structure, 9, 39-46.
PDB codes: 1g6w 1g6y
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
  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.  
10476062 Van Hop D, A.Gaikwad, B.S.Yadav, M.K.Reddy, S.Sopory, and S.K.Mukherjee (1999).
Suppression of pea nuclear topoisomerase I enzyme activity by pea PCNA.
  Plant J, 19, 153-162.  
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.