Comparative structural analysis of a novel glutathione S-transferase (Atu5508) from Agrobacterium tumefaciens at 2.0 Å resolution

Proteins: Structure, Function and Genetics

Volumn 65, Issue 3, 2006, Pages 527-537

  Kosloff, Mickey ^a   Han, Gye Won ^b,c   Sri Krishna, S ^b,d,e   Schwarzenbacher, Robert ^b,e   Fasnacht, Marc ^a,f   Elsliger, Marc André ^b,c   Abdubek, Polat ^b,g   Agarwalla, Sanjay ^b,g   Ambing, Eileen ^b,g   Astakhova, Tamara ^b,e   Axelrod, Herbert L ^b,h   Canaves, Jaume M ^b,e   Carlton, Dennis ^b,c   Chiu, Hsiu Ju ^b,h   Clayton, Thomas ^b,c   DiDonato, Michael ^b,g   Duan, Lian ^b,e   Feuerhelm, Julie ^b,g   Grittini, Carina ^b,c   Grzechnik, Slawomir K ^b,e   Hale, Joanna ^b,g   Hampton, Eric ^b,g   Haugen, Justin ^b,g   Jaroszewski, Lukasz ^b,d,e   Jin, Kevin K ^b,h   Johnson, Hope ^b,c   Klock, Heath E ^b,g   Knuth, Mark W ^b,g   Koesema, Eric ^b,g   Kreusch, Andreas ^b,g   Kuhn, Peter ^b,c   Levin, Inna ^b,h   McMullan, Daniel ^b,g   Miller, Mitchell D ^b,h   Morse, Andrew T ^b,e   Moy, Kin ^b,c   Nigoghossian, Edward ^b,g   Okach, Linda ^b,g   Oommachen, Silvya ^b,h   Page, Rebecca ^b,c   Paulsen, Jessica ^b,g   Quijano, Kevin ^b,g   Reyes, Ron ^b,h   Rife, Christopher L ^b,h   Sims, Eric ^b,c   Spraggon, Glen ^b,g   Sridhar, Vandana ^b,c   Stevens, Raymond C ^b,c   Van Den Bedem, Henry ^b,h   Velasquez, Jeff ^b,c   White, Aprilfawn ^b,g   Wolf, Guenter ^b,h   Xu, Qingping ^b,h   Hodgson, Keith O ^b,h   Wooley, John ^b,e   Deacon, Ashley M ^b,h   Godzik, Adam ^b,d,e   Lesley, Scott A ^b,c,g   Wilson, Ian A ^b,c   more..

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b Joint Center for Structural Genomics   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d BURNHAM INSTITUTE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^g GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^h SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

Active site; Consensus sequence; Dimer interface; Glutathione transferase; JCSG; Local structural motif; Specificity; Structural genomics; X ray crystallography

Indexed keywords

GLUTATHIONE TRANSFERASE;

ARTICLE; CONSENSUS SEQUENCE; CRYSTAL STRUCTURE; DETOXIFICATION; DIMERIZATION; ENZYME ACTIVE SITE; ENZYME STRUCTURE; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN ENGINEERING; RHIZOBIUM RADIOBACTER; SEQUENCE ANALYSIS; SOIL BACTERIUM; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; GLUTATHIONE TRANSFERASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RHIZOBIUM RADIOBACTER;

AGROBACTERIUM TUMEFACIENS; BACTERIA (MICROORGANISMS);

EID: 33750178803     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21130     Document Type: Article

References (45)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
2. Salinas AE, Wong MG. Glutathione S-transferases-a review. Curr Med Chem 1999;6:279-309.
3. Sheehan D, Meade G, Foley VM, Dowd CA. Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily. Biochem J 2001;360:1-16.
4. Armstrong RN. Structure, catalytic mechanism, and evolution of the glutathione transferases. Chem Res Toxicol 1997;10:2-18.
5. Armstrong RN. Mechanistic imperatives for the evolution of glutathione transferases. Curr Opin Chem Biol 1998;2:618-623.
6. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA 2002;99:11664-11669.
7. Santarsiero BD, Yegian DT, Lee CC, Spraggon G, Gu J, Scheibe D, Uber DC, Cornell EW, Nordmeyer RA, Kolbe WF, Jin J, Jones AL, Jaklevic JM, Schultz PG, Stevens RC. An approach to rapid protein crystallization using nanodroplets. J Appl Crystallogr 2002;35:278-281.
8. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
9. Tickle IJ, Laskowski RA, Moss DS. Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of γB- and βB2-crystallin. Acta Crystallogr D Biol Crystallogr 1998;54:243-252.
10. Borek D, Minor W, Otwinowski Z. Measurement errors and their consequences in protein crystallography. Acta Crystallogr D Biol Crystallogr 2003;59:2031-2038.
11. Schneider TR, Sheldrick GM. Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 2002;58:1772-1779.
12. Bricogne G, Vonrhein C, Flensburg C, Schiltz M, Paciorek W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr D Biol Crystallogr 2003;59:2023-2030.
13. Terwilliger T. SOLVE and RESOLVE: automated structure solution, density modification and model building. J Synchrotron Radiat 2004;11:49-52.
14. Cohen SX, Morris RJ, Fernandez FJ, Ben Jelloul M, Kakaris M, Parthasarathy V, Lamzin VS, Kleywegt GJ, Perrakis A. Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr D Biol Crystallogr 2004;60:2222-2229.
15. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
16. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004;60:2126-2132.
17. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD. Automated and accurate deposition of structures solved by X-ray diffraction to the protein data bank. Acta Crystallogr D Biol Crystallogr 2004;60:1833-1839.
18. Davis IW, Murray LW, Richardson JS, Richardson DC. MOL-PROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 2004;32:W615-W619.
19. Vaguine AA, Richelle J, Wodak SJ. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 1999;55:191-205.
20. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990;8:52-56, 29.
21. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
22. Laskowski RA, Chistyakov VV, Thornton JM. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 2005;33:D266-D268.
23. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000;302:205-217.
24. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876-4882.
25. Page RD. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 1996;12:357, 358.
26. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 2004;32:D226-D229.
27. Tang CL, Xie L, Koh IY, Posy S, Alexov E, Honig B. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol 2003;334:1043-1062.
28. Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 2003;53(Suppl 6):S430-S435.
29. Petrey D, Honig B. GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol 2003;374:492-509.
30. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
31. Martin JL. Thioredoxin-a fold for all reasons. Structure 1995;3:245-250.
32. Qi Y, Grishin NV. Structural classification of thioredoxin-like fold proteins. Proteins 2005;58:376-388.
33. Holm L, Sander C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
34. Kong KH, Nishida M, Inoue H, Takahashi K. Tyrosine-7 is an essential residue for the catalytic activity of human class PI glutathione S-transferase: chemical modification and site-directed mutagenesis studies. Biochem Biophys Res Commun 1992;182:1122-1129.
35. Nathaniel C, Wallace LA, Burke J, Dirr HW. The role of an evolutionarily conserved cis-proline in the thioredoxin-like domain of human class α glutathione transferase A1-1. Biochem J 2003;372:241-246.
36. Fritz-Wolf K, Becker A, Rahlfs S, Harwaldt P, Schirmer RH, Kabsch W, Becker K. X-ray structure of glutathione S-transferase from the malarial parasite Plasmodium falciparum. Proc Natl Acad Sci USA 2003;100:13821-13826.
37. Abdalla AM, Bruns CM, Tainer JA, Mannervik B, Stenberg G. Design of a monomeric human glutathione transferase GSTP1, a structurally stable but catalytically inactive protein. Protein Eng 2002;15:827-834.
38. Sayed Y, Wallace LA, Dirr HW. The hydrophobic lock-and-key intersubunit motif of glutathione transferase A1-1: implications for catalysis, ligandin function and stability. FEBS Lett 2000;465:169-172.
39. Alves CS, Kuhnert DC, Sayed Y, Dirr HW. The intersubunit lock-and-key motif in human glutathione transferase A1-1: role of the key residues Met51 and Phe52 in function and dimer stability. Biochem J 2006;393:523-528.
40. Habig WH, Jakoby WB. Assays for differentiation of glutathione S-transferases. Methods Enzymol 1981;77:398-405.
41. Bjornestedt R, Stenberg G, Widersten M, Board PG, Sinning I, Jones TA, Mannervik B. Functional significance of arginine 15 in the active site of human class α glutathione transferase A1-1. J Mol Biol 1995;247:765-773.
42. Hiller N, Fritz-Wolf K, Deponte M, Wende W, Zimmermann H, Becker K. Plasmodium falciparum glutathione S-transferase-structural and mechanistic studies on ligand binding and enzyme inhibition. Protein Sci 2006;15:281-289.
43. Micaloni C, Kong GK, Mazzetti AP, Nuccetelli M, Antonini G, Stella L, McKinstry WJ, Polekhina G, Rossjohn J, Federici G, Ricci G, Parker MW, Lo Bello M. Engineering a new C-terminal tail in the H-site of human glutathione transferase P1-1: structural and functional consequences. J Mol Biol 2003;325:111-122.
44. Dirr HW, Wallace LA. Role of the C-terminal helix 9 in the stability and ligandin function of class α glutathione transferase A1-1. Biochemistry 1999;38:15631-15640.
45. Bruns CM, Hubatsch I, Ridderstrom M, Mannervik B, Tainer JA. Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products. J Mol Biol 1999;288:427-439.