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Structure and function of residue 104 and water molecules in the xenobiotic substrate-binding site in human glutathione S-transferase P1-1.

Ji X, Blaszczyk J, Xiao B, O'Donnell R, Hu X, Herzog C, Singh SV, Zimniak P
Biochemistry 38 10231-8 (1999)
Related entries: 1gss, 1pgt, 2pgt, 4pgt

Cited: 27 times
EuropePMC logo PMID: 10441116

Abstract

Two variants of human class pi glutathione (GSH) S-transferase 1-1 with either isoleucine or valine in position 104 (hGSTP1-1[I104] and hGSTP1-1[V104]) have distinct activity toward (+)-anti-7, 8-dihydroxy-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-anti-BPDE]. To elucidate their structure-function relationship, we determined the crystal structures of the two variants in complex with GSBpd, the GSH conjugate of (+)-anti-BPDE, at 2.1 and 2.0 A resolution, respectively. The crystal structures reveal that residue 104 in the xenobiotic substrate-binding site (H-site) dictates the binding modes of the product molecule GSBpd with the following three consequences. First, the distance between the hydroxyl group of Y7 and the sulfur atom of GSBpd is 5.9 A in the hGSTP1-1[I104].GSBpd complex versus 3.2 A in the V104 variant. Second, one of the hydroxyl groups of GSBpd forms a direct hydrogen bond with R13 in hGSTP1-1[V104].GSBpd; in contrast, this hydrogen bond is not observed in the I104 complex. Third, in the hydrophilic portion of the H-site of the I104 complex, five H-site water molecules [Ji, X., et al. (1997) Biochemistry 36, 9690-9702] are observed, whereas in the V104 complex, two of the five have been displaced by the Bpd moiety of GSBpd. Although there is no direct hydrogen bond between Y108 (OH) and the hydroxyl groups of GSBpd, indirect hydrogen bonds mediated by water molecules are observed in both complexes, supporting the previously suggested role of the hydroxyl group of Y108 as an electrophilic participant in the addition of GSH to epoxides.

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  2. Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking. Fukunishi Y, Nakamura H. Pharmaceuticals (Basel) 5 1332-1345 (2012)
  3. A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Omagari K, Mitomo D, Kubota S, Nakamura H, Fukunishi Y. Adv Appl Bioinform Chem 1 19-28 (2008)


Reviews citing this publication (2)

  1. Glutathione transferases: a structural perspective. Oakley A. Drug Metab Rev 43 138-151 (2011)
  2. Glutathione S-transferase genotypes and cancer risk. Parl FF. Cancer Lett 221 123-129 (2005)

Articles citing this publication (22)

  1. Structure of a Drosophila sigma class glutathione S-transferase reveals a novel active site topography suited for lipid peroxidation products. Agianian B, Tucker PA, Schouten A, Leonard K, Bullard B, Gros P. J Mol Biol 326 151-165 (2003)
  2. Allelic variants of the human glutathione S-transferase P1 gene confer differential cytoprotection against anticancer agents in Escherichia coli. Ishimoto TM, Ali-Osman F. Pharmacogenetics 12 543-553 (2002)
  3. Glutathione S-transferases mu 1, theta 1, pi 1, alpha 1 and mu 3 genetic polymorphisms and the risk of colorectal and gastric cancers in humans. Martínez C, Martín F, Fernández JM, García-Martín E, Sastre J, Díaz-Rubio M, Agúndez JA, Ladero JM. Pharmacogenomics 7 711-718 (2006)
  4. The crystal structures of glutathione S-transferases isozymes 1-3 and 1-4 from Anopheles dirus species B. Oakley AJ, Harnnoi T, Udomsinprasert R, Jirajaroenrat K, Ketterman AJ, Wilce MC. Protein Sci 10 2176-2185 (2001)
  5. Liver disease in pediatric patients with cystic fibrosis is associated with glutathione S-transferase P1 polymorphism. Henrion-Caude A, Flamant C, Roussey M, Housset C, Flahault A, Fryer AA, Chadelat K, Strange RC, Clement A. Hepatology 36 913-917 (2002)
  6. Activity of allelic variants of Pi class human glutathione S-transferase toward chlorambucil. Pandya U, Srivastava SK, Singhal SS, Pal A, Awasthi S, Zimniak P, Awasthi YC, Singh SV. Biochem Biophys Res Commun 278 258-262 (2000)
  7. Glutathione-S-transferase M1, M3, P1 and T1 polymorphisms and severity of lung disease in children with cystic fibrosis. Flamant C, Henrion-Caude A, Boëlle PY, Brémont F, Brouard J, Delaisi B, Duhamel JF, Marguet C, Roussey M, Miesch MC, Boulé M, Strange RC, Clement A. Pharmacogenetics 14 295-301 (2004)
  8. The anti-cancer drug chlorambucil as a substrate for the human polymorphic enzyme glutathione transferase P1-1: kinetic properties and crystallographic characterisation of allelic variants. Parker LJ, Ciccone S, Italiano LC, Primavera A, Oakley AJ, Morton CJ, Hancock NC, Bello ML, Parker MW. J Mol Biol 380 131-144 (2008)
  9. Thermodynamics of the ligandin function of human class Alpha glutathione transferase A1-1: energetics of organic anion ligand binding. Sayed Y, Hornby JA, Lopez M, Dirr H. Biochem J 363 341-346 (2002)
  10. Molecular cloning of CYP4 and GSTpi homologues in the scallop Chlamys farreri and its expression in response to benzo[a]pyrene exposure. Miao J, Pan L, Liu N, Xu C, Zhang L. Mar Genomics 4 99-108 (2011)
  11. Genetic biomarkers for hepatocellular cancer risk in a caucasian population. De Mattia E, Cecchin E, Polesel J, Bignucolo A, Roncato R, Lupo F, Crovatto M, Buonadonna A, Tiribelli C, Toffoli G. World J Gastroenterol 23 6674-6684 (2017)
  12. Effect of human glutathione S-transferase hGSTP1-1 polymorphism on the detoxification of reactive metabolites of clozapine, diclofenac and acetaminophen. Dragovic S, Venkataraman H, Begheijn S, Vermeulen NP, Commandeur JN. Toxicol Lett 224 272-281 (2014)
  13. Interaction between glutathione-S-transferase polymorphisms, smoking habit, and HPV infection in cervical cancer risk. Palma S, Novelli F, Padua L, Venuti A, Prignano G, Mariani L, Cozzi R, Tirindelli D, Testa A. J Cancer Res Clin Oncol 136 1101-1109 (2010)
  14. Expression patterns and novel splicing variants of glutathione-S-transferase isoenzymes of human lung and hepatocyte cell lines. Bauer M, Herbarth O, Aust G, Hengstler JG, Dotzauer A, Graebsch C, Schmuecking E. Cell Tissue Res 324 423-432 (2006)
  15. Catalytically active monomer of glutathione S-transferase pi and key residues involved in the electrostatic interaction between subunits. Huang YC, Misquitta S, Blond SY, Adams E, Colman RF. J Biol Chem 283 32880-32888 (2008)
  16. Isoenzyme- and allozyme-specific inhibitors: 2,2'-dihydroxybenzophenones and their carbonyl N-analogues that discriminate between human glutathione transferase A1-1 and P1-1 allozymes. Pouliou FM, Thireou TN, Eliopoulos EE, Tsoungas PG, Labrou NE, Clonis YD. Chem Biol Drug Des 86 1055-1063 (2015)
  17. Association between susceptibility to advanced pelvic organ prolapse and glutathione S-transferase P1 Ile105Val polymorphism. Kim JY, Kim EJ, Jeon MJ, Kim R, Lee MW, Kim SW. Eur J Obstet Gynecol Reprod Biol 175 205-208 (2014)
  18. Glutathione S-transferases pi 1, alpha 1 and M3 genetic polymorphisms and the risk of hepatocellular carcinoma in humans. Ladero JM, Martínez C, Fernández JM, Martín F, García-Martín E, Ropero P, Villegas A, Díaz-Rubio M, Agúndez JA. Pharmacogenomics 8 895-899 (2007)
  19. Energy landscape of a GSTP1 polymorph linked with cytological function decay in response to chemical stressors. Basharat Z, Yasmin A. Gene 609 19-27 (2017)
  20. Arg-158 is critical in both binding the substrate and stabilizing the transition-state oxyanion for the enzymatic reaction of malonamidase E2. Yun YS, Lee W, Shin S, Oh BH, Choi KY. J Biol Chem 281 40057-40064 (2006)
  21. Assembly of ligands interaction models for glutathione-S-transferases from Plasmodium falciparum, human and mouse using enzyme kinetics and molecular docking. Al-Qattan MN, Mordi MN, Mansor SM. Comput Biol Chem 64 237-249 (2016)
  22. Association of glutathione S-transferase polymorphisms with the severity of mustard lung. Dastjerdi AH, Behboudi H, Kianmehr Z, Taravati A, Naghizadeh MM, Kaboudanian Ardestani S, Ghazanfari T. Bioimpacts 7 255-261 (2017)


Related citations provided by authors (3)

  1. 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.. Ji X, Tordova M, O'Donnell R, Parsons JF, Hayden JB, Gilliland GL, Zimniak P Biochemistry 36 9690-702 (1997)
  2. Naturally occurring human glutathione S-transferase GSTP1-1 isoforms with isoleucine and valine in position 104 differ in enzymic properties.. Zimniak P, Nanduri B, Pikuła S, Bandorowicz-Pikuła J, Singhal SS, Srivastava SK, Awasthi S, Awasthi YC Eur J Biochem 224 893-9 (1994)
  3. Three-dimensional structure of class pi glutathione S-transferase from human placenta in complex with S-hexylglutathione at 2.8 A resolution.. Reinemer P, Dirr HW, Ladenstein R, Huber R, Lo Bello M, Federici G, Parker MW J Mol Biol 227 214-26 (1992)

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