Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme

Nucleic Acids Research

Volumn 25, Issue 17, 1997, Pages 3421-3427

  Hermann, Thomas ^a   Auffinger, Pascal ^a   Scott, William G ^b   Westhof, Eric ^a  

^a CNRS   (France)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROXIDE; MAGNESIUM ION; PHOSPHATE; RIBOSE; RIBOZYME;

ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; SIMULATION;

BINDING SITES; CRYSTALLIZATION; ELECTROCHEMISTRY; FREEZING; HYDROXIDES; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC;

EID: 0030849184     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/25.17.3421     Document Type: Article

References (42)

1. Uhlenbeck, O. (1987) Nature, 328, 596-600.
2. McKay, D.B. (1996) RNA, 2, 395-403.
3. Scott, W.G. and Klug, A. (1996) Trends Biochem. Sci., 21, 220-224.
4. Dahm, S.C., Derrick, W.B. and Uhlenbeck, O.C. (1993) Biochemistry, 32, 13040-13045.
5. Thomson, J.B., Tuschl, T. and Eckstein, F. (1996) In Eckstein, F. and Lilley, D.M.J. (eds), Catalytic RNA, Springer, Berlin, pp. 173-196.
6. Scott, W.G., Murray, J.B., Arnold, J.R.P., Stoddard, B.L. and Klug, A. (1996) Science, 274, 2065-2069.
7. Scott, W.G., Finch, J.T. and Klug, A. (1995) Cell, 81, 991-1002.
8. Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994) Nature, 372, 68-74.
9. Setlik, R.F., Shibata, M., Sarma, R.H., Sarma, M.H., Kazim, A.L., Ornstein, R.L., Tomasi, T.B. and Rein, R.J. (1995) Biomol. Struct. Dynam., 13, 515-522.
10. Birikh, K.R., Heaton, P.A. and Eckstein, F. (1997) Eur. J. Biochem., 245, 1-16.
11. Zhou, D.M., Usman, N., Wincott, F.E., Matulic-Adamic, J., Orita, M., Zhang, L.H., Komiyama, M., Kumar, P.K.R. and Taira, K. (1996) J. Am. Chem. Soc., 118, 5862-5866.
12. Zhou, D.M., Kumar, P.K.R., Zhang, L.H. and Taira, K. (1996) J. Am. Chem. Soc., 118, 8969-8970.
13. Pontius, B.W., Lott, W.B. and von Hippel, P.H. (1997), Proc. Natl. Acad. Sci. USA, 94, 2290-2294.
14. Allen, M.P. and Tildesley, D.J. (1987) Computer Simulation of Liquids. Clarendon, Oxford.
15. Auffinger, P. and Westhof, E. (1996) Biophys. J., 71, 940-954.
16. Auffinger, P., Louise-May, S. and Westhof, E. (1997) Faraday Discuss., 103, 151-174.
17. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., DeBolt, S., Ferguson, D., Seibel, G., Singh, U.C., Weiner, P.K. and Kollman, P.A. (1994) AMBER 4.1, San Francisco.
18. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. (1995) J. Am. Chem. Soc., 117, 5179-5197.
19. Åqvist, J.J. (1990) J. Phys. Chem., 94, 8021-8024.
20. Lee, H., Darden, T.A. and Pedersen, L.G.(1995) J. Chem. Phys., 102, 3830-3834.
21. Berendsen, H.J.C., Grigera, J.R. and Straatsma, T.P. (1987) J. Phys. Chem., 97, 6269-6271.
22. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) J. Comput. Phys., 23, 327-336.
23. Darden, T.A., York, D. and Pedersen, L.G. (1993) J. Chem. Phys., 98, 10089-10092.
24. Pullman, A., Pullman, B. and Lavery, R. (1983) In Pullman, B. and Jortner J. (eds), Nucleic Acids: The Vectors of Life, Reidel, Dordrecht, pp. 75-88.
25. Cotton, F.A. and Wilkinson, G. (1988) Advanced Inorganic Chemistry. Wiley, New York.
26. Gorun, S.M. and Lippard S.J. (1986) Nature, 319, 666-668.
27. Wilcox, D.E. (1996) Chem. Rev., 96, 2435-2458.
28. Salminen, T., Käpylä, J., Heikinheimo, P., Kankare, J., Goldman, A., Heinonen, J., Baykov, A.A., Coopermann, B.S. and Lahti, R. (1995) Biochemistry, 34, 782-791.
29. Goldberg, J., Huang, B., Kwon, Y., Greengard, P., Nairn, A. and Kuriyan, J. (1995) Nature, 376, 745-753.
30. Larsen, T.M., Wedekind, J.E., Rayment, I. and Reed, G.H. (1996) Biochemistry, 35, 4349-4358.
31. Beese, L.S. and Steitz, T.A. (1991) EMBO J., 10, 25-33.
32. Steitz, T.A. (1993) Current Opin. Struct. Biol., 3, 31-38.
33. Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. and Kraut, J. (1994) Science, 264, 1891-1903.
34. Baykov, A.A., Alexandrov, A.P. and Smirnova, I.N. (1992) Arch. Biochem. Biophys., 294, 238-243.
35. Partono, S. and Lewin, A.S. (1990) Nucleic Acids Res., 19, 605-609.
36. Cech, T. (1993). In Gesteland, R.F. and Atkins, J.F. (eds), The RNA world, Cold Spring Harbor Laboratory Press, New York, pp. 239-269.
37. Streicher, B., Westhof, E. and Schroeder, R. (1996) EMBO J., 15, 2556-2564.
38. Mei, H.Y. Kaaret, T.W. and Bruice, T.C. (1989) Proc. Natl. Acad. Sci. USA, 86, 9727-9731.
39. Long, D.M., LaRiviere, F.J. and Uhlenbeck, O.C. (1995) Biochemistry, 34, 14435-14440.
40. Baes, C.F. and Mesmer, R.E. (1976) The Hydrolysis of Cations. Wiley, New York.
41. Delarue, M., Poch, O., Tordo, N., Moras, D. and Argos, P. (1990) Protein Engng., 3, 461-467.
42. Sousa, R. (1996) Trends Biochem. Sci., 21, 186-190.