The structural basis of hammerhead ribozyme self-cleavage

Cell

Volumn 92, Issue 5, 1998, Pages 665-673

  Murray, James B ^a   Terwey, Daniel P ^a   Maloney, Lara ^b   Karpeisky, Alexander ^b   Usman, Nassim ^b   Beigelman, Leonid ^b   Scott, William G ^a  

^a INDIANA UNIVERSITY   (United States)

^b Sirna Therapeutics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOZYME;

ARTICLE; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME DEGRADATION; ENZYME MECHANISM; NONHUMAN; PRIORITY JOURNAL; RNA CLEAVAGE; SHARK; X RAY CRYSTALLOGRAPHY;

CHONDRICHTHYES;

EID: 0032489357     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81134-4     Document Type: Article

References (41)

1. Amiri, K.M., and Hagerman, P. (1996). The global conformation of an active hammerhead RNA during the process of self-cleavage. J. Mol. Biol. 261, 125-134.
2. Bassi, G.S., Murchie, A.I.H., and Lilley, D.M.J. (1996). The ion-induced folding of the hammerhead ribozyme: core sequence changes that perturb folding into the active conformation. RNA 2, 756-768.
3. Bassi, G.S., Murchie, A.I.H., Walter,F., Clegg, R.M.,and Lilley, D.M.J. (1997). Ion-induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study. EMBO J., 16, 7481-7489.
4. Beigelman, L., Karpeisky, A., and Usman, N. (1995). Synthesis of 5′-C-methyl-D-allo-and L-tallo-ribonucleoside 3′-O-phosphoramidites and their incorporation into hammerhead ribozymes. Nucleosides Nucleotides 14, 901-905.
5. Bolduc, J.M., Dyer, D.H., Scott, W.G., Singer, P., Sweet, R.M., Koshland, Jr., D.E., and Stoddard, B.L. (1995). Mutagenesis and laue structures of enzyme intermediates: isocitrate dehydrogenase. Science 268, 1312-1317.
6. Brown, R.S., Dewan, J.C., and Klug, A. (1985). Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA. Biochemistry 24, 4785-4801.
7. Brünger, A.T. (1993). X-PLOR 3.1: A System for Crystallography and NMR (New Haven, CT: Yale University Press).
8. Clouet-Dorval, B., and Uhlenbeck, O.C. (1996). Kinetic characterization of two I/II format hammerhead ribozymes. RNA 2, 483-491.
9. Collaborative Computational Project, Number 4 (CCP4) (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763.
10. Dahm, S., and Uhlenbeck, O.C. (1991). Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30, 9464-9469.
11. Dahm, S., 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.
12. Feig, A., Scott, W.G., and Uhlenbeck, O.C. (1998). Inhibition of the hammerhead ribozyme cleavage reaction by site-specific binding of Tb(III). Science 279, 81-84.
13. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857.
14. Herman, T., Auffinger, P., Scott, W.G., and Westhof, E. (1997). Evidence fora hydroxide ion bridging tow magnesium ions at the active site of the hammerhead ribozyme. Nucleic Acids Res. 25, 3421-3427.
15. Herman, T., Auffinger, P., and Westhof, E. (1998). Molecular dynamics investigations on the hammerhead ribozyme RNA. Eur. J. Biophys., in press.
16. Hertel, K.J., Herschlag, D., and Uhlenbeck, O.C. (1994). A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry 33, 3374-3385.
17. Hodel, A., Kim, S.-H., and Brünger, A.T. (1992). Model bias in macro-molecular crystal structures, Acta Crystallogr. A48, 851-859.
18. Jones, T.A., and Kjeldgaard, M. (1997). O Version 6.1.0 (Dept. of Mol. Biol., BMC, Uppsala Univ., Sweden, and Dept. of Chem., Aarhus Univ., Denmark).
19. 2+ binding. Biochemistry 30, 5145-5150.
20. McKay, D.B. (1996). Structure and function of the hammerhead ribozyme: an unfinished story. RNA 2, 395-403.
21. Moffat, K., and Henderson, R. (1995). Freeze-trapping of reaction intermediates. Curr. Opin. Struct. Biol. 5, 656-661.
22. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
23. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A.T., and Berman, H.M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr. D52, 57-69.
24. Pearson, R.G. (1963). Hard and soft acids and bases. J. Am. Chem. Soc. 85, 3533-3539.
25. Peracchi, A., Beigelman, L., Scott, E.G., Uhlenbeck, O.C., and Herschlag, D. (1997). Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J. Biol. Chem. 272, 26822-26826.
26. Pley, H.W., Flaherty, K.M., and McKay, D.B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74.
27. Read, R.J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140-149.
28. Scott, W.G., and Klug, A. (1996). Ribozymes: structure and mechanism in RNA catalysis. Trends Biochem. Sci. 21, 220-224.
29. 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.
30. Scott, W.G., Murray, J.B., Arnold, J.R.P., Stoddard, B.L., and Klug, A. (1996). Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274, 2065-2069.
31. Sigurdsson, S.-T., Tuschl, T., and Eckstein, F. (1995). Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme. RNA 1, 575-583.
32. Simorre, J.-P., Legault, P., Hangar, A.B., Michiels, P., and Pardi, A. (1997). A conformational change in the catalytic core of the hammerhead ribozyme upon cleavage of an RNA substrate. Biochemistry 36, 518-525.
33. Slim, G., and Gait, M.J. (1991). Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucleic Acids Res. 19, 1183-1188.
34. Steitz, T.A., and Steitz, J.A. (1993). A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA 90, 6498-6502.
35. Symons, R.H. (1992). Small catalytic RNAs. Annu. Rev. Biochem. 61, 641-671.
36. Thomson, J.B., Tuschl, T., and Eckstein, F. (1996). The hammerhead ribozyme. In Nucleic Acids and Molecular Biology, Vol 10., F. Eckstein and D.M.J. Lilley, eds. (Berlin: Springer-Verlag), pp. 173-196.
37. Uchimaru, T., Tanabe, K., Shimayama, T., Uebayasi, M., and Taira, K. (1993). Theoretical analyses on the role of metal cations in RNA cleavage processes. Nucleic Acids Symp. Ser. 29, 179-180.
38. Uhlenbeck, O.C. (1987). A small catalytic oligoribonucleotide. Nature 328, 596-600.
39. van Tol, H., Buzayan, J.M., Feldstein, P.A., Eckstein, F., and Bruening, G. (1990). Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration. Nucleic Acids Res. 18, 1971-1975.
40. Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Sweedler, D., Gonzalez, C., Scaringe, S., and Usman, N. (1995). Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res. 23, 2677-2684.
41. Zaug, A.J., and Cech, T.R. (1986). The intervening sequence RNA of Tetrahymena is an enzyme. Science 231, 470-475.