The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine

Journal of Biological Chemistry

Volumn 286, Issue 20, 2011, Pages 17658-17664

  Cottrell, Joseph W ^a   Scott, Lincoln G ^b   Fedor, Martha J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b Cassia LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; CATALYTIC ACTIVITY; DIVALENT METAL CATIONS; HAIRPIN RIBOZYME; PH DEPENDENCE; PH-DEPENDENT; PHOSPHODIESTER BONDS; RIBOZYMES; SELF-CLEAVAGE; TRANSITION STATE;

CATALYST ACTIVITY; GENE EXPRESSION; IONIZATION; PHOSPHORUS; RNA;

CATALYSIS;

8 AZAADENOSINE; ADENOSINE; HAIRPIN RIBOZYME; RIBOZYME; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; FLUORESCENCE; IONIZATION; PH; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTON TRANSPORT;

ADENOSINE; BACTERIA; CATALYSIS; CATALYTIC DOMAIN; HUMANS; HYDROGEN-ION CONCENTRATION; RNA, CATALYTIC; STRUCTURE-ACTIVITY RELATIONSHIP;

BACTERIA (MICROORGANISMS);

EID: 79955954695     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.234906     Document Type: Article

References (56)

1. Fedor, M. J. (2009) Annu. Rev. Biophys. 38, 271-299
2. Hampel, A., and Cowan, J. A. (1997) Chem. Biol. 4, 513-517
3. Nesbitt, S., Hegg, L. A., and Fedor, M. J. (1997) Chem. Biol. 4, 619-630
4. Young, K. J., Gill, F., and Grasby, J. A. (1997) Nucleic Acids Res. 25, 3760-3766
5. Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) Chem. Biol. 5, 587-595
6. Rupert, P. B., and Ferré-D'Amaré, A. R. (2001) Nature 410, 780-786
7. Rupert, P. B., Massey, A. P., Sigurdsson, S. T., and Ferré- D'Amaré, A. R. (2002) Science 298, 1421-1424
8. Torelli, A. T., Krucinska, J., and Wedekind, J. E. (2007) RNA 13, 1052-1070
9. Raines, R. T. (1998) Chem. Rev. 98, 1045-1066
10. Kuzmin, Y. I., Da Costa, C. P., Cottrell, J. W., and Fedor, M. J. (2005) J. Mol. Biol. 349, 989-1010
11. Tolman, R. (1938) The Principles of Statistical Mechanics, Oxford University Press, London
12. Saenger, W. (1984) Principles of Nucleic Acid Structure, pp. 107-110, Springer-Verlag, New York
13. Bevilacqua, P. C., Brown, T. S., Nakano, S., and Yajima, R. (2004) Biopolymers 73, 90-109
14. Moody, E. M., Lecomte, J. T., and Bevilacqua, P. C. (2005) RNA 11, 157-172
15. Tang, C. L., Alexov, E., Pyle, A. M., and Honig, B. (2007) J. Mol. Biol. 366, 1475-1496
16. Spitale, R. C., Volpini, R., Heller, M. G., Krucinska, J., Cristalli, G., and Wedekind, J. E. (2009) J. Am. Chem. Soc. 131, 6093-6095
17. Suydam, I. T., Levandoski, S. D., and Strobel, S. A. (2010) Biochemistry 49, 3723-3732
18. Kuzmin, Y. I., Da Costa, C. P., and Fedor, M. J. (2004) J. Mol. Biol. 340, 233-251
19. Liu, L., Cottrell, J. W., Scott, L. G., and Fedor, M. J. (2009) Nat. Chem. Biol. 5, 351-357
20. Jencks, W. P. (1969) Catalysis in Chemistry and Enzymology, pp. 163-242, Dover Publications, Inc., New York
21. Mlýnský, V., Banás, P., Hollas, D., Réblová, K., Walter, N. G., Sponer, J., and Otyepka, M. (2010) J. Phys. Chem. B 114, 6642-6652
22. Ditzler, M. A., Sponer, J., and Walter, N. G. (2009) RNA 15, 560-575
23. Nam, K., Gao, J., and York, D. M. (2008) RNA 14, 1501-1507
24. Wierzchowski, J., Wielgus-Kutrowska, B., and Shugar, D. (1996) Biochim. Biophys. Acta 1290, 9-17
25. Ryder, S. P., Oyelere, A. K., Padilla, J. L., Klostermeier, D., Millar, D. P., and Strobel, S. A. (2001) RNA 7, 1454-1463
26. Fedor, M. J. (1999) Biochemistry 38, 11040-11050
27. Lebruska, L. L., Kuzmine, I. I., and Fedor, M. J. (2002) Chem. Biol. 9, 465-473
28. Yadava, R. S., Choi, A. J., Lebruska, L. L., and Fedor, M. J. (2001) J. Mol. Biol. 309, 893-902
29. Uhlenbeck, O. C., and Cameron, V. (1977) Nucleic Acids Res. 4, 85-98
30. Milligan, J. F., and Uhlenbeck, O. C. (1989) Methods Enzymol. 180, 51-62
31. Siwkowski, A., Shippy, R., and Hampel, A. (1997) Biochemistry 36, 3930-3940
32. Kochetkov, N. K., and Budovskii, E. I. (1971) in Organic Chemistry of Nucleic Acids (Kochetkov, N. K., and Budovskii, E. I., eds) pp. 148-165, Plenum Press, New York
33. Da Costa, C. P., Fedor, M. J., and Scott, L. G. (2007) J. Am. Chem. Soc. 129, 3426-3432
34. Ward, D. C., Reich, E., and Stryer, L. (1969) J. Biol. Chem. 244, 1228-1237
35. Millar, D. P. (1996) Curr. Opin. Struct. Biol. 6, 322-326
36. Jean, J. M., and Hall, K. B. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 37-41
37. Clauwaert, J., and Stockx, J. (1968) Z. Naturforsch. B 23, 25-30
38. Puglisi, J. D., Wyatt, J. R., and Tinoco, I., Jr. (1990) Biochemistry 29, 4215-4226
39. Cai, Z., and Tinoco, I., Jr. (1996) Biochemistry 35, 6026-6036
40. Ravindranathan, S., Butcher, S. E., and Feigon, J. (2000) Biochemistry 39, 16026-16032
41. Wadkins, T. S., Shih, I., Perrotta, A. T., and Been, M. D. (2001) J. Mol. Biol. 305, 1045-1055
42. Lupták, A., Ferré-D'Amaré, A. R., Zhou, K., Zilm, K. W., and Doudna, J. A. (2001) J. Am. Chem. Soc. 123, 8447-8452
43. Shih, I. H., and Been, M. D. (2002) Annu. Rev. Biochem. 71, 887-917
44. Bevilacqua, P. C. (2003) Biochemistry 42, 2259-2265
45. Bevilacqua, P. C., Brown, T. S., Chadalavada, D., Lecomte, J., Moody, E., and Nakano, S. I. (2005) Biochem. Soc. Trans. 33, 466-470
46. Bevilacqua, P. C., and Yajima, R. (2006) Curr. Opin. Chem. Biol. 10, 455-464
47. Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335-13342
48. Guo, M., Spitale, R. C., Volpini, R., Krucinska, J., Cristalli, G., Carey, P. R., and Wedekind, J. E. (2009) J. Am. Chem. Soc. 131, 12908-12909
49. Chen, J. H., Gong, B., Bevilacqua, P. C., Carey, P. R., and Golden, B. L. (2009) Biochemistry 48, 1498-1507
50. Gong, B., Chen, J. H., Bevilacqua, P. C., Golden, B. L., and Carey, P. R. (2009) Biochemistry 48, 11961-11970
51. Gong, B., Chen, J. H., Yajima, R., Chen, Y., Chase, E., Chadalavada, D. M., Golden, B. L., Carey, P. R., and Bevilacqua, P. C. (2009) Methods 49, 101-111
52. Ryder, S. P., and Strobel, S. A. (1999) J. Mol. Biol. 291, 295-311
53. Rogstad, K. N., Jang, Y. H., Sowers, L. C., and Goddard, W. A., 3rd (2003) Chem. Res. Toxicol. 16, 1455-1462
54. Pinard, R., Lambert, D., Walter, N. G., Heckman, J. E., Major, F., and Burke, J. M. (1999) Biochemistry 38, 16035-16039
55. Walter, N. G., Burke, J. M., and Millar, D. P. (1999) Nat. Struct. Biol. 6, 544-549
56. Nesbitt, S. M., Erlacher, H. A., and Fedor, M. J. (1999) J. Mol. Biol. 286, 1009-1024