Probing general acid catalysis in the hammerhead ribozyme

Journal of the American Chemical Society

Volumn 131, Issue 3, 2009, Pages 1135-1143

  Thomas, Jason M ^a   Perrin, David M ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; BASE CATALYST; CATALYTIC MECHANISMS; CATALYTIC ROLE; COFACTOR; COMPUTATIONAL STUDIES; DIVALENT METAL CATIONS; FUNCTIONAL CHARACTERIZATION; GENERAL ACID CATALYSIS; LEAVING GROUPS; LEWIS ACID; NATURAL SUBSTRATES; PHOSPHODIESTER; PHOSPHOROTHIOATE; RIBOZYME; SIMPLE METHOD; TRANSITION STATE;

ACIDS; CATALYSIS; FUNCTIONAL GROUPS; MEATS; NUCLEIC ACIDS; PROTON TRANSFER; QUANTUM CHEMISTRY; RNA;

SUBSTRATES;

5 PHOSPHOROTHIOATE; ANION; ESTER DERIVATIVE; HAMMERHEAD RIBOZYME; LEWIS ACID; OLIGONUCLEOTIDE; PHOSPHOROTHIOIC ACID DERIVATIVE; RIBO PHOSPHODIESTER; UNCLASSIFIED DRUG; ACID; RIBOZYME;

AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; ENZYME STRUCTURE; GENE MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PH MEASUREMENT; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN MODIFICATION; SCHISTOSOMA MANSONI; ANIMAL; CHEMISTRY; ENZYME SPECIFICITY; METABOLISM; MOLECULAR GENETICS; PH;

ACIDS; ANIMALS; BASE SEQUENCE; CATALYSIS; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; RNA, CATALYTIC; SCHISTOSOMA MANSONI; SUBSTRATE SPECIFICITY;

EID: 61749098364     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja807790e     Document Type: Article

References (61)

1. Pley, H. W.; Flaherty, K. M.; McKay, D. B. Nature 1994, 372, 68-74.
2. Scott, W. G.; Finch, J. T.; Klug, A. Cell 1995, 81, 991-1002.
3. Scott, W. G.; Murray, J. B.; Arnold, J. R.; Stoddard, B. L.; Klug, A. Science 1996, 274, 2065-2069.
4. Blount, K. F.; Uhlenbeck, O. C. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 415-440.
5. In particular, the work of Burke and coworkers should be noted as a clear illustration of the discrepancy between the results of functional experiments and minimal hammerhead crystal structures. Their findings correctly predicted the proximity of several ribozyme residues to the substrate cleavage site, as observed later in the S. mansoni crystal structure. See: (a) Heckman, J. E.; Lambert, D.; Burke, J. M. Biochemistry 2005, 44, 4148-4156.
6. (b) Lambert, D.; Heckman, J. E.; Burke, J. M. Biochemistry 2006, 45, 7140-7147.
7. (c) Han, J.; Burke, J. M. Biochemistry 2005, 44, 7864-7870.
8. Nelson, J. A.; Uhlenbeck, O. C. Mol. Cell 2006, 23, 447-450.
9. Nelson, J. A.; Uhlenbeck, O. C. RNA 2008, 14, 605-615.
10. Khvorova, A.; Lescoute, A.; Westhof, E.; Jayasena, S. D. Nat. Struct. Biol. 2003, 10, 708-712.
11. Canny, M. D.; Jucker, F. M.; Kellogg, E.; Khvorova, A.; Jayasena, S. D.; Pardi, A. J. Am. Chem. Soc. 2004, 126, 10848-10849.
12. Saksmerprome, V.; Roychowdhury-Saha, M.; Jayasena, S. D.; Khvorova, A.; Burke, D. H. RNA 2004, 10, 1916-1924.
13. Martick, M.; Scott, W. G. Cell 2006, 126, 309-320.
14. Martick, M.; Lee, T.-S.; York, D. M.; Scott, W. G. Chem. Biol. 2008, 15, 332-342.
15. Chi, Y.-I.; Martick, M.; Lares, M.; Kim, R.; Scott, W. G.; Kim, S.-H. PLoS Biol. 2008, 6, e234.
16. Thomas, J. M.; Perrin, D. M. J. Am. Chem. Soc. 2008, 130, 15467-15675.
17. Han, J.; Burke, J. M. Biochemistry 2005, 44, 7864-7870.
18. Hertel, K. J.; Herschlag, D. J. A.; Uhlenbeck, O. C. Biochemistry 1994, 33, 3374-3385.
19. Lee, T.-S.; Lopez, C. S.; Giambasu, G. M.; Martick, M.; Scott, W. G.; York, D. M. J. Am. Chem. Soc. 2008, 130, 3053-3064.
20. Lee, T.-S.; Silva-Lopez, C.; Martick, M.; Scott, W. G.; York, D. M. J. Chem. Theory Comput. 2007, 3, 325-327.
21. Murray, J. B.; Seyhan, A. A.; Walter, N. G.; Burke, J. M.; Scott, W. G. Chem. Biol. 1998, 5, 587-595.
22. Curtis, E. A.; Bartel, D. P. RNA 2001, 7, 546-552.
23. Peracchi, A.; Beigelman, L.; Scott, E. C.; Uhlenbeck, O. C.; Herschlag, D. J. Biol. Chem. 1997, 272, 26822-26826.
24. Wang, S.; Karbstein, K.; Peracchi, A.; Beigelman, L.; Herschlag, D. Biochemistry 1999, 38, 14363-14378.
25. Maderia, M.; Hunsicker, L. M.; DeRose, V. J. Biochemistry 2000, 39, 12113-12120.
26. Suzumura, K.; Yoshinari, K.; Tanaka, Y.; Takagi, Y.; Kasai, Y.; Warashina, M.; Kuwabara, T.; Orita, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 8230-8236.
27. Cunningham, L. A.; Li, J.; Lu, Y. J. Am. Chem. Soc. 1998, 120, 4518-4519.
28. Osborne, E. M.; Schaak, J. E.; Derose, V. J. WA 2005, 11, 187-196.
29. Murray, J. B.; Scott, W. G. J. Mol. Biol. 1999, 296, 33-41.
30. Roychowdhury-Saha, M.; Burke, D. H. IWA 2006, 12, 1846-1852.
31. Das, S. R.; Piccirilli, J. A. Nat. Chem. Biol. 2005, 1, 45-52.
32. Krogh, B. O.; Shuman, S. Mol. Cell 2000, 5, 1035-1041.
33. Piccirilli, J. A.; Vyle, J. S.; Caruthers, M. H.; Cech, T. R. Nature 1993, 361, 85-88.
34. Kuimelis, R. G.; McLaughlin, L. W. J. Am. Chem. Soc. 1995, 117, 11019-11020.
35. Zhou, D.-M.; Usman, N.; Wincott, F. E.; Matulic-Adamic, J.; Orita, M.; Zhang, L.-H.; Komiyama, M.; Kumar, P. K. R.; Taira, K. J. Am. Chem. Soc. 1996, 118, 5862-5866.
36. a nitrophenolate leaving group in place of the native alkoxide, has been reported to confirm that His119 performs general acid catalysis in RNaseA catalysis of RNA cleavage. See: Thompson, J. E.; Raines, R. T. J. Am. Chem. Soc. 1994, 116, 5467-5468.
37. Hondal, R. J.; Bruzik, K. S.; Zhao, Z.; Tsai, M.-D. J. Am. Chem. Soc. 1997, 119, 5477-5478.
38. Hondal, R. J.; Zhao, Z.; Riddle, S. R.; Kravchuk, A. V.; Liao, H.; Bruzik, K. S.; Tsai, M.-D. J. Am. Chem. Soc. 1997, 119, 9933-9934.
39. Kubiak, R. J.; Hondal, R. J.; Yue, X.; Tsai, M.-D.; Bruzik, K. S. J. Am. Chem. Soc. 1999, 121, 488-489.
40. Thomson, J. B.; Patel, B. K.; Jimenez, V.; Eckart, K.; Eckstein, F. J. Org. Chem. 1996, 61, 6273-6281.
41. Velikyan, I.; Acharya, S.; Trifonova, A.; Foldesi, A.; Chattopadhyaya, J. J. Am. Chem. Soc. 2001, 123, 2893-2894.
42. Lyne, P. D.; Karplus, M. J. Am. Chem. Soc. 2000, 122, 166-167.
43. Acharya, S.; Foldesi, A.; Chattopadhyaya, J. J. Org. Chem. 2003, 68, 1906-1910.
44. Milligan, J. F.; Groebe, D. R.; Witherell, G. W.; Uhlenbeck, O. C. Nucleic Acids Res. 1987, 15, 8783-8798.
45. Miller, G. P.; Kool, E. T. Org. Lett. 2002, 4, 3599-3601.
46. Zhang, B.; Cui, Z.; Sun, L. Ore. Lett. 2000, 3, 275-278.
47. Kuimelis, R. G.; McLaughlin, L. W. Biorg. Med. Chem. 1997, 5, 1051-1061.
48. Dittmer, D. C.; Ramsay, O. B.; Spalding, R. E. J. Org. Chem. 1963, 28, 1273-1278.
49. Kuimelis, R. G.; McLaughlin, L. W. Biochemistry 1996, 35, 5308-5317.
50. Biphasic cleavage kinetics were more apparent in the case of the S-link substrate. See Figures S3 and S4 in the Supporting Information for further explanation.
51. Kim, N.-K.; Murali, A.; DeRose, V. J. J. Am. Chem. Soc. 2005, 127, 14134-14135.
52. Canny, M. D.; Jucker, F. M.; Pardi, A. Biochemistry 2007, 46, 3826-3834.
53. Yang, J.-H.; Perreault, J.-P.; Labuda, D.; Usman, N.; Cedergren, R. Biochemistry 1990, 29, 11156-11160.
54. Soukup, G. A.; Breaker, R. R. RNA 1999, 5, 1308-1325.
55. Bevilacqua, P. C. Biochemistry 2003, 42, 2259-2265.
56. Pontius, B. W.; Lott, W. B.; von Hippel, P. H. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 2290-2294.
57. Zhou, D.-M.; Zhang, L.-H.; Taira, K. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 14343-14348.
58. Leclerc, F.; Karplus, M. J. Phys. Chem. B 2006, 110, 3395-3409.
59. Lee, T.-S.; York, D. M. J. Am. Chem. Soc. 2008, 130, 7168-7169.
60. a downward for O-link substrate cleavage by the HDV ribozyme. See: Das, S. R.; Piccirilli, J. A. Nat. Chem. Biol. 2005, 1, 45-52.
61. Sigel, R. K. O.; Pyle, A. M. Chem. Rev. 2007, 107, 97-113.