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PDBsum entry 6gsu

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protein ligands Protein-protein interface(s) links
Transferase PDB id
6gsu
Jmol
Contents
Protein chains
217 a.a. *
Ligands
SO4 ×3
GPS ×2
Waters ×323
* Residue conservation analysis
PDB id:
6gsu
Name: Transferase
Title: First-sphere and second-sphere electrostatic effects in the site of a class mu glutathione transferase
Structure: Mu class glutathione s-transferase of isoenzyme 3 chain: a, b. Synonym: rat gst. Engineered: yes. Mutation: yes
Source: Rattus rattus. Black rat. Organism_taxid: 10117. Organ: liver. Gene: cdna insert of clone pgt33mx. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.175    
Authors: G.Xiao,X.Ji,R.N.Armstrong,G.L.Gilliland
Key ref:
G.Xiao et al. (1996). First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase. Biochemistry, 35, 4753-4765. PubMed id: 8664265 DOI: 10.1021/bi960189k
Date:
26-Jan-96     Release date:   08-Nov-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04905  (GSTM1_RAT) -  Glutathione S-transferase Mu 1
Seq:
Struc:
218 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 = GPS)
matches with 57.14% 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     extracellular region   3 terms 
  Biological process     metabolic process   12 terms 
  Biochemical function     transferase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi960189k Biochemistry 35:4753-4765 (1996)
PubMed id: 8664265  
 
 
First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase.
G.Xiao, S.Liu, X.Ji, W.W.Johnson, J.Chen, J.F.Parsons, W.J.Stevens, G.L.Gilliland, R.N.Armstrong.
 
  ABSTRACT  
 
The activation of the thiol of glutathione (GSH) bound in the active site of the class mu glutathione transferase M1-1 from rat involves a hydrogen-bonding network that includes a direct (first-sphere) interaction between the hydroxyl group of Y6 and the sulfur of GSH and second-sphere interactions involving a hydrogen bond between the main-chain amide N-H of L12 and the hydroxyl group of Y6 and an on-face hydrogen bond between the hydroxyl group of T13 and the pi-electron cloud of Y6 (i.e., T13-OH---pi-Y6-OH--- -SG). The functions of these hydrogen bonds have been examined with a combination of site-specific mutagenesis and X-ray crystallography. The hydroxyl group of Y6 has a normal pKa of about 10 even though it is shielded from solvent and is in a largely hydrophobic environment. The apparent pKa of GSH in the binary Y6F.GSH complex is increased by 1.6 log units, and the reactivity of the enzyme-bound nucleophile is reduced. The catalytic properties of the Y6L mutant are identical to those of Y6F, suggesting that the weakly polar on-edge interaction between the aromatic ring and sulfur has no influence on catalysis. The refined three-dimensional structure of the Y6F mutant in complex with GSH shows no major structural perturbation of the protein other than a change in the coordination environment of the sulfur. Removal of the second-sphere influence of the on-face hydrogen bond between the hydroxyl groups T13 as in the T13V and T13A mutants elevates the pKa of enzyme-bound GSH by about 0.7 pKa units. Crystal structures of these mutants show that structural changes in the active site are minor and suggest that the changes in pKa of E.GSH are due to the presence or absence of the on-face hydrogen bond. The T13S mutant has a completely different side-chain hydrogen-bonding geometry than T13 in the native enzyme and catalytic properties similar to the T13A and T13V mutants consistent with the absence of an on-face hydrogen bond. The gamma-methyl group of T13 is essential in enforcing the on-face hydrogen bond geometry and preventing the hydroxyl group from forming more favorable conventional hydrogen bonds.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
18703268 N.Kinsley, Y.Sayed, S.Mosebi, R.N.Armstrong, and H.W.Dirr (2008).
Characterization of the binding of 8-anilinonaphthalene sulfonate to rat class Mu GST M1-1.
  Biophys Chem, 137, 100-104.  
18689687 P.Verdino, C.Aldag, D.Hilvert, and I.A.Wilson (2008).
Closely related antibody receptors exploit fundamentally different strategies for steroid recognition.
  Proc Natl Acad Sci U S A, 105, 11725-11730.
PDB codes: 2o5x 2o5y 2o5z
17682821 B.Blanchette, X.Feng, and B.R.Singh (2007).
Marine glutathione S-transferases.
  Mar Biotechnol (NY), 9, 513-542.  
16672236 J.L.Hearne, and R.F.Colman (2006).
Contribution of the mu loop to the structure and function of rat glutathione transferase M1-1.
  Protein Sci, 15, 1277-1289.  
16154081 F.Angelucci, P.Baiocco, M.Brunori, L.Gourlay, V.Morea, and A.Bellelli (2005).
Insights into the catalytic mechanism of glutathione S-transferase: the lesson from Schistosoma haematobium.
  Structure, 13, 1241-1246.  
16021597 R.Villar, M.J.Gil, J.I.García, and V.Martínez-Merino (2005).
Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs?
  J Comput Chem, 26, 1347-1358.  
15549710 C.A.Contreras-Vergara, C.Harris-Valle, R.R.Sotelo-Mundo, and G.Yepiz-Plascencia (2004).
A mu-class glutathione S-transferase from the marine shrimp Litopenaeus vannamei: molecular cloning and active-site structural modeling.
  J Biochem Mol Toxicol, 18, 245-252.  
11297419 B.S.Nieslanik, C.Ibarra, and W.M.Atkins (2001).
The C-terminus of glutathione S-transferase A1-1 is required for entropically-driven ligand binding.
  Biochemistry, 40, 3536-3543.  
10737945 J.U.Flanagan, W.King, M.W.Parker, P.G.Board, and G.Chelvanayagam (2000).
Ab initio calculations on hidden modulators of theta class glutathione transferase activity.
  Proteins, 39, 235-243.  
10883816 M.Ishigai, J.I.Langridge, R.S.Bordoli, and S.J.Gaskell (2000).
Noncovalent associations of glutathione S-transferase and ligands: a study using electrospray quadrupole/time-of-flight mass spectrometry.
  J Am Soc Mass Spectrom, 11, 606-614.  
  10716187 Z.Szeltner, V.Renner, and L.Polgár (2000).
Substrate- and pH-dependent contribution of oxyanion binding site to the catalysis of prolyl oligopeptidase, a paradigm of the serine oligopeptidase family.
  Protein Sci, 9, 353-360.  
10587450 A.Gustafsson, M.Etahadieh, P.Jemth, and B.Mannervik (1999).
The C-terminal region of human glutathione transferase A1-1 affects the rate of glutathione binding and the ionization of the active-site Tyr9.
  Biochemistry, 38, 16268-16275.  
  10548058 D.L.Sackett, S.B.Ruvinov, and J.Thompson (1999).
N5-(L-1-carboxyethyl)-L-ornithine synthase: physical and spectral characterization of the enzyme and its unusual low pKa fluorescent tyrosine residues.
  Protein Sci, 8, 2121-2129.  
9930979 Y.V.Patskovsky, L.N.Patskovska, and I.Listowsky (1999).
Functions of His107 in the catalytic mechanism of human glutathione S-transferase hGSTM1a-1a.
  Biochemistry, 38, 1193-1202.
PDB code: 1gtu
9572843 J.F.Parsons, G.Xiao, G.L.Gilliland, and R.N.Armstrong (1998).
Enzymes harboring unnatural amino acids: mechanistic and structural analysis of the enhanced catalytic activity of a glutathione transferase containing 5-fluorotryptophan.
  Biochemistry, 37, 6286-6294.
PDB code: 5fwg
9761928 L.N.Patskovska, A.A.Fedorov, Y.V.Patskovsky, S.C.Almo, and I.Listowsky (1998).
Expression, crystallization and preliminary X-ray analysis of ligand-free human glutathione S-transferase M2-2.
  Acta Crystallogr D Biol Crystallogr, 54, 458-460.  
9760231 R.L.Krauth-Siegel, L.D.Arscott, A.Schönleben-Janas, R.H.Schirmer, and C.H.Williams (1998).
Role of active site tyrosine residues in catalysis by human glutathione reductase.
  Biochemistry, 37, 13968-13977.  
8810897 E.C.Dietze, C.Ibarra, M.J.Dabrowski, A.Bird, and W.M.Atkins (1996).
Rational modulation of the catalytic activity of A1-1 glutathione S-transferase: evidence for incorporation of an on-face (pi...HO-Ar) hydrogen bond at tyrosine-9.
  Biochemistry, 35, 11938-11944.  
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 codes are shown on the right.