Matching active site and substrate structures for an RNA editing reaction

Journal of the American Chemical Society

Volumn 131, Issue 33, 2009, Pages 11882-11891

  Pokharel, Subhash ^b   Jayalath, Prasanna ^a   Maydanovych, Olena ^b   Goodman, Rena A ^a   Wang, Selina C ^a   Tantillo, Dean J ^a   Beal, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ACTIVE SITE RESIDUES; ADENOSINE DEAMINASES; AMINO ACID RESIDUES; ENZYME ACTIVE SITES; GLUTAMATE RECEPTOR; INHIBITORY EFFECT; INOSINE; NUCLEOTIDE BINDING; PHOSPHORAMIDITES; PRE-MRNA; PROPARGYL ALCOHOL; RNA EDITING; RNA SUBSTRATE; S.CEREVISIAE; STRUCTURE/ACTIVITY RELATIONSHIP; SUBSTRATE STRUCTURE;

AMINES; AMINO ACIDS; BINDING SITES; BROMINE; ENZYMES; FUNCTIONAL GROUPS; HYDROGEN; IODINE; NUCLEIC ACIDS; NUCLEOTIDES; ORGANIC ACIDS; ORGANIC POLYMERS; REACTION KINETICS; RNA;

SUBSTRATES;

ADENOSINE DEAMINASE; BROMINE; HYDROGEN; IODINE; RNA;

ARTICLE; GENE EXPRESSION; GENE MUTATION; NONHUMAN; RNA EDITING; SACCHAROMYCES CEREVISIAE; SONOGASHIRA REACTION;

ADENOSINE DEAMINASE; BASE SEQUENCE; CATALYTIC DOMAIN; DEOXYADENOSINES; HUMANS; LIGANDS; MODELS, MOLECULAR; OLIGONUCLEOTIDES; RNA; RNA EDITING;

EID: 69049117276     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja9034076     Document Type: Article

References (74)

1. Cooper, T. A.; Wan, L.; Dreyfuss, G. Cell 2009, 136, 777-793.
2. Soret, J.; Bakkour, N.; Maire, S.; Durand, S. b.; Zekri, L.; Gabut, M.; Fic, W.; Divita, G.; Rivalle, C.; Dauzonne, D.; Nguyen, C. H.; Jeanteur, P.; Tazi, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 8764-8769.
3. Elmen, J.; Lindow, M.; Schutz, S.; Lawrence, M.; Petri, A.; Obad, S.; Lindholm, M.; Hedtjarn, M.; Hansen, H. F.; Berger, U.; Gullans, S.; Kearney, P.; Sarnow, P.; Straarup, E. M.; Kauppinen, S. Nature 2008, 452, 896-899.
4. Bhuiya, M. W.; Rittery, E. M.; Bernard A. Brown, I. In RNA and DNA Editing; Harold, C. S., Ed.; Wiley-Interscience: Hoboken, NJ, 2008; pp 340-368.
5. Jepson, J. E. C.; Reenan, R. A. Biochim. Biophys. Acta, Gene Regul. Mech. 2008, 1779, 459-470.
6. Li, J. B.; Levanon, E. Y.; Yoon, J.-K.; Aach, J.; Xie, B.; LeProust, E.; Zhang, K.; Gao, Y.; Church, G. M. Science 2009, 324, 1210-1213.
7. Higuchi, M.; Single, F. N.; Koehler, M.; Sommer, B.; Sprengel, R.; Seeburg, P. H. Cell 1993, 75, 1361-70.
8. Burns, C. M.; Chu, H.; Rueter, S. M.; Hutchinson, L. K.; Canton, H.; Sanders-Bush, E.; Emeson, R. B. Nature 1997, 387, 303-308.
9. Bhalla, T.; Rosenthal, J. J. C.; Holmgren, M.; Reenan, R. Nat. Struct. Mol. Biol. 2004, 11, 950-956.
10. Higuchi, M.; Maas, S.; Single, F. N.; Hartner, J.; Rozov, A.; Burnashev, N.; Feldmeyer, D.; Sprengel, R.; Seeburg, P. H. Nature 2000, 406, 78-81.
11. Palladino, M. J.; Keegan, L. P.; O'Connell, M. A.; Reenan, R. A. Cell 2000, 102, 437-449.
12. Tonkin, L. A.; Saccomanno, L.; Morse, D. P.; Brodigan, T.; Krause, M.; Bass, B. L. EMBO J. 2002, 21, 6025-6035.
13. Wang, Q.; Khillan, J.; Gadue, P.; Nishikura, K. Science 2000, 290, 1765-1768.
14. Kishore, S.; Stamm, S. Science 2006, 311, 230-232.
15. Cenci, C.; Barzotti, R.; Galeano, F.; Corbelli, S.; Rota, R.; Massimi, L.; Di Rocco, C.; O'Connell, M. A.; Gallo, A. J. Biol. Chem. 2008, 283, 7251-7260.
16. Yi-Brunozzi, H. Y.; Easterwood, L. M.; Kamilar, G. M.; Beal, P. A. Nucleic Acids Res. 1999, 27, 2912-2917.
17. Easterwood, L. M.; Veliz, E. A.; Beal, P. A. J. Am. Chem. Soc. 2000, 122, 11537-11538.
18. Stephens, O. M.; Yi-Brunozzi, H. Y.; Beal, P. A. Biochemistry 2000, 39, 12243-12251.
19. Veliz, E. A.; Stephens, O. M.; Beal, P. A. Org. Lett. 2001, 3, 2969-2972.
20. Yi-Brunozzi, H. Y.; Stephens, O. M.; Beal, P. A. J. Biol. Chem. 2001, 276, 37827-37833.
21. Cho, D.-S. C.; Yang, W.; Lee, J. T.; Shiekhattar, R.; Murray, J. M.; Nishikura, K. J. Biol. Chem. 2003, 278, 17093-17102.
22. Gallo, A.; Keegan, L. P.; Ring, G. M.; O'Connell, M. A. EMBO J. 2003, 22, 3421-3430.
23. Veliz, E. A.; Easterwood, L. M.; Beal, P. A. J. Am. Chem. Soc. 2003, 125, 10867-10876.
24. Dawson, T. R.; Sansam, C. L.; Emeson, R. B. J. Biol. Chem. 2004, 279, 4941-4951.
25. Haudenschild, B. L.; Maydanovych, O.; Veliz, E. A.; Macbeth, M. R.; Bass, B. L.; Beal, P. A. J. Am. Chem. Soc. 2004, 126, 11213-11219.
26. Macbeth, M. R.; Lingam, A. T.; Bass, B. L. RNA 2004, 10, 1563-1571.
27. Stephens, O. M.; Haudenschild, B. L.; Beal, P. A. Chem. Biol. 2004, 11, 1239-1250.
28. Macbeth, M. R.; Schubert, H. L.; VanDemark, A. P.; Lingam, A. T.; Hill, C. P.; Bass, B. L. Science 2005, 309, 1534-1539.
29. Maydanovych, O.; Beal, P. A. Chem. Rev. 2006, 106, 3397-3411.
30. Pokharel, S.; Beal, P. A. ACS Chem. Biol. 2006, 1, 761-765.
31. Stefl, R.; Xu, M.; Skrisovska, L.; Emeson, R. B.; Allain, F. H.-T. Structure 2006, 14, 345-355.
32. Maydanovych, O.; Easterwood, L. M.; Cui, T.; Veliz, E. A.; Pokharel, S.; Beal, P. A. Methods Enzymol. 2007, 424, 369-86.
33. Bass, B. L.; Weintraub, H. Cell 1987, 48, 607-13.
34. Doyle, M.; Jantsch, M. F. J. Cell Biol. 2003, 161, 309-319.
35. Melcher, T.; Maas, S.; Herb, A.; Sprengel, R.; Seeburg, P. H.; Higuchi, M. Nature 1996, 379, 460-4.
36. Kim, U.; Wang, Y.; Sanford, T.; Zeng, Y.; Nishikura, K. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 11457-61.
37. Carter, C. W., Jr. Biochimie 1995, 77, 92-8.
38. Betts, L.; Xiang, S.; Short, S. A.; Wolfenden, R.; Carter, C. W., Jr. J. Mol. Biol. 1994, 235, 635-56.
39. Maydanovych, O.; Beal, P. A. Org. Lett. 2006, 8, 3753-3756.
40. Jayalath, P.; Pokharel, S.; Veliz, E.; Beal, P. A. Nucleosides, Nucleotides, Nucleic Acids 2009, 28, 78-88.
41. Luo, M.; Schramm, V. L. J. Am. Chem. Soc. 2008, 130, 2649-2655.
42. Erion, M. D.; Reddy, M. R. J. Am. Chem. Soc. 1998, 120, 3295-3304.
43. Evans, B.; Wolfenden, R. Biochemistry 1973, 12, 392-398.
44. Agarwal, R. P.; Sagar, S. M.; Parks, R. E., Jr. Biochem. Pharmacol. 1975, 24, 693-701.
45. Albert, A. Adv. Heterocycl. Chem. 1976, 20, 117-43.
46. Shewach, D. S.; Krawczyk, S. H.; Acevedo, O. L.; Townsend, L. B. Biochem. Pharmacol. 1992, 44, 1697-700.
47. Hernandez, S.; Ford, H.; Marquez, V. E. Bioorg. Med. Chem. 2002, 10, 2723-2730.
48. Clemons, P. A.; Gladstone, B. G.; Seth, A.; Chao, E. D.; Foley, M. A.; Schreiber, S. L. Chem. Biol. 2002, 9, 49-61.
49. Kraybill, B. C.; Elkin, L. L.; Blethrow, J. D.; Morgan, D. O.; Shokat, K. M. J. Am. Chem. Soc. 2002, 124, 12118-12128.
50. Shah, K.; Shokat, K. M. Chem. Biol. 2002, 9, 35-47.
51. Belshaw, P. J.; Schreiber, S. L. J. Am. Chem. Soc. 1997, 119, 1805-1806.
52. Lin, Q.; Jiang, F.; Schultz, P. G.; Gray, N. S. J. Am. Chem. Soc. 2001, 123, 11608-11613.
53. Verdine, G. L.; Norman, D. P. G. Annu. Rev. Biochem. 2003, 72, 337-366.
54. Jiang, Y. L.; Krosky, D. J.; Seiple, L.; Stivers, J. T. J. Am. Chem. Soc. 2005, 127, 17412-17420.
55. Wilson, D. K.; Rudolph, F. B.; Quiocho, F. A. Science 1991, 252, 1278-84.
56. Frederiksen, S. Arch. Biochem. Biophys. 1966, 113, 383-388.
57. Seela, F.; Xu, K. Org. Biomol. Chem. 2007, 5, 3034-3045.
58. Luyten, I.; Thibaudeau, C.; Chattopadhyaya, J. J. Org. Chem. 1997, 62, 8800-8808.
59. Jeong, L. S.; Buenger, G.; McCormack, J. J.; Cooney, D. A.; Hao, Z.; Marquez, V. E. J. Med. Chem. 1998, 41, 2572-2578.
60. Marquez, V. E.; Russ, P.; Alonso, R.; Siddiqui, M. A.; Hernandez, S.; George, C.; Nicklaus, M. C.; Dai, F.; Ford, H., Jr. HelV. Chim. Acta 1999, 82, 2119-2129.
61. Ford, H., Jr.; Dai, F.; Mu, L.; Siddiqui, M. A.; Nicklaus, M. C.; Anderson, L.; Marquez, V. E.; Barchi, J. J. Biochemistry 2000, 39, 2581-2592.
62. Seela, F.; Zulauf, M.; Debelak, H. Helv. Chim. Acta 2000, 83, 1437-1453.
63. Hernandez, S.; Ford, H.; Marquez, V. E. Bioorg. Med. Chem. 2002, 10, 2723-2730.
64. Seela, F.; Zulauf, M. J. Chem. Soc., Perkin Trans. 1 1999, 479-488.
65. Peng, X.; Li, H.; Seela, F. Nucleic Acids Res. 2006, 34, 5987-6000.
66. Pangborn, A. B.; Giardello, M. A.; Grubbs, R. H.; Rosen, R. K.; Timmers, F. J. Organometallics 1996, 15, 1518-20.
67. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
68. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B: Solid Sate 1988, 37, 785-789.
69. Stephens, P. J.; Devlin, F. J.; Cabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623-11627.
70. Barone, V.; Cossi, M. J. J. Phys. Chem. A 1998, 102, 1995-2001.
71. Barone, V.; Cossi, M.; Tomasi, J. J. Comput. Chem. 1998, 19, 404-417.
72. Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 270-283.
73. Takano, Y.; Houk, K. N. J. Chem. Theory Comput. 2005, 1, 70-77.
74. Frisch, M. J.; et al. Gaussian03; Gaussian, Inc.