Two decades of RNA catalysis

Chemistry and Biology

Volumn 9, Issue 9, 2002, Pages 961-969

  DeRose, Victoria J ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE SEQUENCE; CATALYSIS; INTRONS; KINETICS; METALS; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; SPLICEOSOMES;

EID: 0036753229     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(02)00217-X     Document Type: Review

References (35)

1. Kruger K., Grabowski P., Zaug A., Sands J., Gottschling D., Cech T. Self-splicing RNA. autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena Cell. 31:1982;147-157.
2. Guerrier-Takada C., Gardiner K., Marsh T., Pace N., Altman S. The RNA moiety of ribonucleases P is the catalytic subunit of the enzyme. Cell. 35:1983;849-857.
3. Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A. The structural basis of ribosome activity in peptide bond synthesis. Science. 5481:2000;920-930.
4. Muth G.W., Ortoleva-Donnelly L., Strobel S.A. A single adenosine with a neutral pKa in the ribosomal peptidyl transerase center. Science. 289:2000;947-950.
5. Valadkhan S., Manley J.L. Splicing-related catalysis by protein-free snRNAs. Nature. 6857:2001;701-707.
6. Wilson D.S., Szostak J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68:1999;611-647.
7. Narlikar G., Herschlag D. Mechanistic aspects of enzymatic catalysis. lessons from comparison of RNA and protein enzymes Annu. Rev. Biochem. 66:1997;19-59.
8. Warashina M., Takagi Y., Stec W.J., Taira K. Differences among mechanisms of ribozyme-catalyzed reactions. Curr. Opin. Biotechnol. 11:2001;354-362.
9. Doudna J.A., Cech T.R. The chemical repertoire of natural ribozymes. Nature. 418:2002;222-228.
10. Butcher S.E. Structure and function of the small ribozymes. Curr. Opin. Struct. Biol. 3:2001;315-320.
11. Wedekind J., McKay D. Crystal structure of a lead-dependent ribozyme revealing metal binding sites revelant to catalysis. Nat. Struct. Biol. 6:1999;261-268.
12. Scott W.G. RNA structure, metal ions, and catalysis. Curr. Opin. Chem. Biol. 6:1999;705-709.
13. Hunsicker L.M., DeRose V.J. Activities and relative affinities of divalent metals in unmodified and phosphorothioate-substituted hammerhead ribozymes. J. Inorg. Biochem. 80:2000;271-281.
14. Pontius B.W., Lott W.B., von Hippel P.H. Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism. Proc. Natl. Acad. Sci. USA. 94:1999;2290-2294.
15. Zhuang X., Kim H., Pereira M., Babcock H., Walter N., Chu S. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:2002;1473-1476.
16. +- mediated reactions catalyzed by a hammerhead ribozyme. J. Am. Chem. Soc. 124:2002;3850-3852.
17. Wang S.L., Karbstein K., Peracchi A., Beigelman L., Herschlag D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry. 73:1999;14363-14378.
18. Maderia M., Hunsicker L.M., DeRose V.J. Metal-phosphate interactions in the hammerhead ribozyme observed by P-31 NMR and phosphorothioate substitutions. Biochemistry. 40:2000;12113-12120.
19. Murray J., Dunham C., Scott W. A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction. J. Mol. Biol. 2:2002;121-130.
20. O'Rear J.L., Wang S.L., Feig A.L., Beigelman L., Uhlenbeck O.C., Herschlag D. Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA. 4:2001;537-545.
21. Rupert P.B., Ferre-D'Amare A.R. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature. 6830:2001;780-786.
22. Pinard R., Hampel K., Heckman J., Lambert D., Chan P., Major F., Burke J. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J. 22:2001;6434-6442.
23. Lebruska L., Kuzmine I., Fedor M. Rescue of an abasic hairpin ribozyme by cationic nucleobases. evidence for a novel mechanism of RNA catalysis Chem. Biol. 9:2002;465-473.
24. Ferre-D'Amare A.R., Zhou K.H., Doudna J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature. 6702:1998;567-574.
25. Nakano D.M., Chadalavada D.M., Bevilacqua P.C. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science. 287:2000;1493-1497.
26. 2+-containing solutions. J. Am. Chem. Soc. 45:2001;11333-11334.
27. Luptak A., Ferre-D'Amare A.R., Zhou K.H., Zilm K.W., Doudna J.A. Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme. J. Am. Chem. Soc. 35:2001;8447-8452.
28. Pereira M.J.B., Harris D.A., Rueda D., Walter N.G. Reaction pathway of the trans-acting hepatitis delta virus ribozyme. A conformational change accompanies catalysis Biochemistry. 3:2002;730-740.
29. Golden B.L., Gooding A.R., Podell E.R., Cech T.R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science. 5387:1998;259-264.
30. Shan S., Kravchuk A.V., Piccirilli J.A., Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry. 17:2001;5161-5171.
31. Shan S., Yoshida A., Sun S., Piccirilli J.A., Herschlag D. Three metal ions at the active site of the Terahymena group I ribozyme. Proc. Natl. Acad. Sci. USA. 96:1999;12299-12304.
32. Szewczak A.A., Kosek A.B., Piccirilli J.A., Strobel S.A. Identification of an active site ligand for a group I ribozyme catalytic metal ion. Biochemistry. 41:2002;2516-2525.
33. Barta A., Dorner S., Polacek N. Mechanism of ribosomal peptide bond formation. Science. 291:2001;203-205.
34. Stuhlmann F., Jaschke A. Characterization of an RNA active site. interactions between a Diels-Alderase ribozyme and its substrates and products J. Am. Chem. Soc. 124:2002;3238-3244.
35. Hammann C., Lilley D.M.J. Folding and activity of the hammerhead ribozyme. Chem. Bio. Chem. 3:2002;690-700.