Model for general acid-base catalysis by the hammerhead ribozyme: PH-activity relationships of G8 and G12 variants at the putative active site

Biochemistry

Volumn 44, Issue 21, 2005, Pages 7864-7870

  Han, Joonhee ^a   Burke, John M ^a  

^a UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACID-BASE CATALYSIS; NUCLEOBASE SUBSTITUTION; PHOTOCHEMICAL CROSS-LINKING; PROTONATION;

CATALYSIS; CROSSLINKING; ORGANIC ACIDS; PH EFFECTS; PHOTOCHEMICAL REACTIONS; SUBSTITUTION REACTIONS;

ENZYMES;

2' HYDROXYL; 2,6 DIAMINOPURINE; 5' OXYGEN; HAMMERHEAD RIBOZYME; HYDROXYL GROUP; NUCLEIC ACID BASE; OXYGEN DERIVATIVE; UNCLASSIFIED DRUG;

ACID BASE BALANCE; ARTICLE; CATALYSIS; CHEMICAL MODEL; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CROSS LINKING; ENZYME ACTIVE SITE; ENZYME KINETICS; NONHUMAN; PH; PHOTOCHEMISTRY; PRIORITY JOURNAL; PROTON TRANSPORT;

BINDING SITES; CATALYSIS; CONSERVED SEQUENCE; DNA FOOTPRINTING; GUANOSINE; HYDROGEN-ION CONCENTRATION; HYDROLYSIS; HYDROXYL RADICAL; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; SUBSTRATE SPECIFICITY;

EID: 19644391548     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047941z     Document Type: Article

References (49)

1. Heekman, J. E., Lambert, D., and Burke, J. M. (2005) Photocrosslinking detects a compact active structure of the hammerhead ribozyme, Biochemistry 44, 4148-4156.
2. Forster, A. C., and Symons, R. H. (1987) Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site, Cell 50, 9-16.
3. Uhlenbeck, O. C. (1987) A small catalytic oligoribonucleotide, Nature 328, 596-600.
4. Hutchins, C. J., Rathjen, P. D., Forster, A. C., and Symons, R. H. (1986) Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid, Nucleic Acids Res. 14, 3627-3640.
5. Prody, G. A., Bakos, J. T., Buzayan, J. M., Schneider, I. R., and Breuning, G. (1986) Autolytic processing of dimeric plant virus satellite RNA, Science 321, 1577-1580.
6. Bondensgaard, K., Mollova, E. T., and Pardi, A. (2002) The global conformation of the hammerhead ribozyme determined using residual dipolar couplings, Biochemistry 41, 11532-11542.
7. Derrick, W. B., Greef, C. H., Caruthers, M. H., and Uhlenbeck, O. C. (2000) Hammerhead cleavage of the phosphorodithioate linkage, Biochemistry 39, 4947-4954.
8. Gast, F. U., Amiri, K. M., and Hagerman, P. J. (1994) Interhelix geometry of stems I and II of a self-cleaving hammerhead RNA, Biochemistry 33, 1788-1796.
9. Hermann, T., Auffinger, P., and Westhof, E. (1998) Molecular dynamics investigations of hammerhead ribozyme RNA, Eur. Biophys. J. 27, 153-165.
10. Penedo, J. C., Wilson, T. J., Jayasena, S. D., Khvorova, A., and Lilley, D. M. (2004) Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements, RNA 10, 880-888.
11. Pley, H. W., Flaherty, K. M., and McKay, D. B. (1994) Three-dimensional structure of a hammerhead ribozyme, Nature 372, 68-74.
12. 2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core, Biochemistry 42, 9924-9936.
13. Salehi-Ashtiani, K., and Szostak, J. W. (2001) In vitro evolution suggests multiple origins for the hammerhead ribozyme, Nature 414, 82-84.
14. Scott, W. G., Finch, J. T., and Klug, A. (1995) The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage, Cell 81, 991-1002.
15. Tuschl, T., Gohlke, C., Jovin, T. M., Westhof, E., and Eckstein, F. (1994) A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements, Science 266, 785-789.
16. Wedekind, J. E., and McKay, D. B. (1998) Cristallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis, Annu. Rev. Biophys. Biomol. Struct. 27, 475-502.
17. Takagi, Y., Warashina, M., Stec, W. J., Yoshinari, K., and Taira, K. (2001) Recent advances in the elucidation of the mechanisms of action of ribozymes, Nucleic Acids Res. 29, 1815-1834.
18. Roberts, G. C., Dennis, E. A., Meadows, D. H., Cohen, J. S., and Jardetzky, O. (1969) The mechanism of action of ribonuclease, Proc. Natl. Acad. Sci. U.S.A. 62, 1151-1158.
19. Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone, Chem. Biol. 5, 587-595.
20. Curtis, E. A., and Bartel, D. P. (2001) The hammerhead cleavage reaction in monovalent cations, RNA 7, 546-552.
21. O'Rear, J. L., Wang, S., Feig, A. L., Beigelman, L., Uhlenbeck, O. C., and Herschlag, D. (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations, RNA 7, 537-545.
22. Hampel, K. J., and Burke, J. M. (2003) Solvent protection of the hammerhead ribozyme in the ground state: evidence for a cation-assisted conformational change leading to catalysis, Biochemistry 42, 4421-4429.
23. Bassi, G. S., Mollegaard, N. E., Murchie, A. I., von Kitzing, E., and Lilley, D. M. (1995) Ionic interactions and the global conformations of the hammerhead ribozyme, Nat. Struct. Biol. 2, 45-55.
24. Maderia, M., Hunsicker, L. M., and DeRose, V. J. (2000) Metalphosphate interactions in the hammerhead ribozyme observed by 31P NMR and phosphorothioate substitutions, Biochemistry 39, 12113-12120.
25. Scott, W. G. (2001) Ribozyme catalysis via orbital steering, J. Mol. Biol. 311, 989-999.
26. Murray, J. B., Dunham, C. M., and Scott, W. G. (2002) A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction, J. Mol. Biol. 315, 121-130.
27. Wang, S., Karbstein, K., Peracchi, A., Beigelman, L., and Herschlag, D. (1999) Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate, Biochemistry 38, 14363-14378.
28. Blount, K. F., Grover, N. L., Mokier, V., Beigelman, L., and Uhlenbeck, O. C. (2002) Steric interference modification of the hammerhead ribozyme, Chem. Biol. 9, 1009-1016.
29. Blount, K. F., and Uhlenbeck, O. C. (2005) The Structure-Function Dilemma of the Hammerhead Ribozyme, Annu. Rev. Biophys. Biomol. Struct., in press.
30. Canny, M. D., Jucker, F. M., Kellogg, E., Khvorova, A., Jayasena, S. D., and Pardi, A. (2004) Fast cleavage kinetics of a natural hammerhead ribozyme, J. Am. Chem. Soc. 126, 10848-10849.
31. Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S. D. (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity, Nat. Struct. Biol. 10, 708-712.
32. Bevilacqua, P. C. (2003) Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme, Biochemistry 42, 2259-2265.
33. Pinard, R., Hampel, K. J., Heckman, J. E., Lambert, D., Chan, P. A., Major, F., and Burke, J. M. (2001) Functional involvement of G8 in the hairpin ribozyme cleavage mechanism, EMBO J. 20, 6434-6442.
34. Rupert, P. B., and Ferre-D'Amare, A. R. (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis, Nature 410, 780-786.
35. Rupert, P. B., Massey, A. P., Sigurdsson, S. T., and Ferre-D'Amare, A. R. (2002) Transition state stabilization by a catalytic RNA, Science 298, 1421-1424.
36. Dahm, S. C., Derrick, W. B., and Uhlenbeck, O. C. (1993) Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism, Biochemistry 32, 13040-13045.
37. Walter, N. G., Yang, N., and Burke, J. M. (2000) Probing nonselective cation binding in the hairpin ribozyme with Tb(III), J. Mol. Biol. 298, 539-555.
38. Butcher, S. E., and Burke, J. M. (1994) A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules is essential for catalytic function of the hairpin ribozyme, Biochemistry 33, 992-999.
39. Hampel, K. J., Walter, N. G., and Burke, J. M. ( 1998) The solvent-protected core of the hairpin ribozyme-substrate complex, Biochemistry 37, 14672-14682.
40. McKay, D. B. (1996) Structure and function of the hammerhead ribozyme: an unfinished story, RNA 2, 395-403.
41. Ruffner, D. E., Stormo, G. D., and Uhlenbeck, O. C. (1990) Sequence requirements of the hammerhead RNA self-cleavage reaction, Biochemistry 29, 10695-10702.
42. Bassi, G. S., Murchie, A. I., and Lilley, D. M. (1996) The ion-induced folding of the hammerhead ribozyme: core sequence changes that perturb folding into the active conformation, RNA 2, 756-768.
43. Bassi, G. S., Mollegaard, N. E., Murchie, A. I., and Lilley, D. M. (1999) RNA folding and misfolding of the hammerhead ribozyme, Biochemistry 38, 3345-3354.
44. Hertel, K. J., Herschlag, D., and Uhlenbeck, O. C. (1994) A kinetic and thermodynamic framework for the hammerhead ribozyme reaction, Biochemistry 33, 3374-3385.
45. Nesbitt, S., Hegg, L. A., and Fedor, M. J. (1997) An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis, Chem. Biol. 4, 619-630.
46. Clouet-d'Orval, B., and Uhlenbeck, O. C. (1997) Hammerhead ribozymes with a faster cleavage rate, Biochemistry 36, 9087-9092.
47. Celander, D. W., and Cech, T. R. (1991) Visualizing the higher order folding of a catalytic RNA molecule, Science 251, 401-407.
48. Hertel, K. J., Pardi, A., Uhlenbeck, O. C., Koizumi, M., Ohtsuka, E., Uesugi, S., Cedergren, R., Eckstein, F., Gerlach, W. L., Hodgson, R., et al. (1992) Numbering system for the hammerhead, Nucleic Acids Res. 20, 3252.
49. Lebruska, L. L., Kuzmine, I.I., and Fedor, M. J. (2002) Rescue of an abasic hairpin ribozyme by cationic nucleobases. Evidence for a novel mechanism of RNA catalysis, Chem. Biol. 9, 465-473.