Functional analysis of hairpin ribozyme active site architecture

Journal of Biological Chemistry

Volumn 282, Issue 18, 2007, Pages 13498-13507

  Cottrell, Joseph W ^a   Kuzmin, Yaroslav I ^a,b   Fedor, Martha J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b LOBACHEVSKY STATE UNIVERSITY OF NIZHNY NOVGOROD   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYST ACTIVITY; HYDROGEN BONDS; NUCLEOTIDES; RNA;

ACTIVE SITE; BIOCHEMICAL ANALYSES; RIBOZYME;

ENZYMES;

HYDROGEN; NUCLEIC ACID BASE; OXYGEN; PHOSPHATE; RIBOZYME; PLANT RNA;

ARTICLE; CATALYSIS; CHEMICAL ANALYSIS; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME MECHANISM; ENZYME STABILITY; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN MODIFICATION; SUBSTITUTION REACTION; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; RNA, PLANT;

EID: 34250367504     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M700451200     Document Type: Article

References (43)

1. Fedor, M. J. (2000) J. Mol. Biol. 297, 269-291
2. Rupert, P. B., and Ferré-D'Amaré, A. R. (2001) Nature 410, 780-786
3. Rupert, P. B., Massey, A. P., Sigurdsson, S. T., and Ferré- D'Amaré, A. R. (2002) Science 298, 1421-1424
4. Alam, S., Grum-Tokars, V., Krucinska, J., Kundracik, M. L., and Wedekind, J. E. (2005) Biochemistry 44, 14396-14408
5. Salter, J., Krucinska, J., Alam, S., Grum-Tokars, V., and Wedekind, J. E. (2006) Biochemistry 45, 686-700
6. Fedor, M. J., and Williamson, J. R. (2005) Nat. Rev. Mol. Cell. Biol. 6, 399-412
7. Hampel, A., and Tritz, R. (1989) Biochemistry 28, 4929-4933
8. Pinard, R., Lambert, D., Walter, N. G., Heckman, J. E., Major, F., and Burke, J. M. (1999) Biochemistry 38, 16035-16039
9. Page, M. I., and Jencks, W. P. (1971) Proc. Natl. Acad. Sci. U. S. A. 68, 1678-1683
10. Grasby, J. A., Mersmann, K., Singh, M., and Gait, M. J. (1995) Biochemistry 34, 4068-4076
11. Shippy, R., Siwkowski, A., and Hampel, A. (1998) Biochemistry 37, 564-570
12. Lebruska, L. L., Kuzmine, I. I., and Fedor, M. J. (2002) Chem. Biol. 9, 465-473
13. Nesbitt, S. M., Erlacher, H. A., and Fedor, M. J. (1999) J. Mol. Biol. 286, 1009-1024
14. Fedor, M. J. (1999) Biochemistry 38, 11040-11050
15. Donahue, C. P., Yadava, R. S., Nesbitt, S. M., and Fedor, M. J. (2000) J. Mol. Biol. 295, 693-707
16. Yadava, R. S., Choi, A. J., Lebruska, L. L., and Fedor, M. J. (2001) J. Mol. Biol. 309, 893-902
17. Kuzmin, Y. I., DaCosta, C. P., Cottrell, J., and Fedor, M. J. (2005) J. Mol. Biol. 349, 989-1010
18. Kuzmin, Y. I., Da Costa, C. P., and Fedor, M. J. (2004) J. Mol. Biol. 340, 233-251
19. Walter, N. G., Burke, J. M., and Millar, D. P. (1999) Nat. Struct. Biol. 6, 544-549
20. Walter, N. G., Hampel, K. J., Brown, K. M., and Burke, J. M. (1998) EMBO J. 17, 2378-2391
21. Zhao, Z., Wilson, T., Maxwell, K., and Lilley, D. (2000) RNA 6, 1833-1846
22. Murchie, A. I., Thomson, J. B., Walter, F., and Lilley, D. M. (1998) Mol. Cell 1, 873-881
23. Klostermeier, D., and Millar, D. P. (2001) Biochemistry 40, 11211-11218
24. England, T. E., and Uhlenbeck, O. C. (1978) Biochemistry 17, 2069-2076
25. Hegg, L. A., and Fedor, M. J. (1995) Biochemistry 34, 15813-15828
26. Fedor, M. J. (2004) Methods Mol. Biol. 252, 19-32
27. Fersht, A. R. (1988) Biochemistry 27, 1577-1580
28. Wilson, T. J., Zhao, Z. Y., Maxwell, K., Kontogiannis, L., and Lilley, D. M. (2001) Biochemistry 40, 2291-2302
29. Klostermeier, D., and Millar, D. P. (2002) Biochemistry 41, 14095-14102
30. Chowrira, B. M., Berzal-Herranz, A., and Burke, J. M. (1991) Nature 354, 320-322
31. Freier, S., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., and Turner, D. H. (1986) Proc. Natl. Acad. Sci. U. S. A. 83, 9373-9377
32. Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) J. Mol. Biol. 288, 911-940
33. Canny, M. D., Jucker, F. M., and Pardi, A. (2007) Biochemistry 46, 3824-3834
34. De la Pena, M., Gago, S., and Flores, R. (2003) EMBO J. 22, 5561-5570
35. Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S. D. (2003) Nat. Struct. Biol. 10, 708-712
36. Martick, M., and Scott, W. G. (2006) Cell 126, 309-320
37. Hertel, K. J., Herschlag, D., and Uhlenbeck, O. C. (1994) Biochemistry 33, 3374-3385
38. Pyle, A. M., and Cech, T. R. (1991) Nature 350, 628-631
39. Silverman, S. K., and Cech, T. R. (1999) Biochemistry 38, 8691-8702
40. Schmidt, S., Beigelman, L., Karpeisky, A., Usman, N., Sorensen, U. S., and Gait, M. J. (1996) Nucleic Acids Res. 24, 573-581
41. Ryder, S. P., and Strobel, S. A. (1999) J. Mol. Biol. 291, 295-311
42. Saenger, W. (1984) Principles of Nucleic Acid Structure, pp. 55-65, Springer-Verlag, New York
43. Lubini, P., Zurcher, W., and Egli, M. (1994) Chem. Biol. 1, 39-45