Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site

Nature Structural Biology

Volumn 5, Issue 1, 1998, Pages 60-66

  Strobel, Scott A ^a   Ortoleva Donnelly, Lori ^a   Ryder, Sean P ^a   Gate, Jamie H ^a   Moncoeur, Eileen ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBOZYME;

ARTICLE; BASE PAIRING; INTRON; MOLECULAR INTERACTION; PRIORITY JOURNAL; RNA CONFORMATION; RNA PROCESSING; RNA SPLICING; RNA STRUCTURE; TETRAHYMENA;

ANIMALS; BINDING SITES; HYDROGEN BONDING; NUCLEIC ACID CONFORMATION; RNA SPLICING; RNA, CATALYTIC; RNA, PROTOZOAN; RNA, TRANSFER; TETRAHYMENA;

BACTERIA (MICROORGANISMS); TETRAHYMENA;

EID: 0031984645     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb0198-60     Document Type: Article

References (42)

1. Strobel, S.A. & Doudna, J.A. RNA Seeing Double: Close-Packing of Helices in RNA Tertiary Structure. Trends Biochem. Sci. 22, 262-266 (1997).
2. Gutell, R.R., Larsen, N. & Woese, C.R. Lessons from an Evolving rRNA: 16S and 235 rRNA Structures from a Comparative Perspective. Microbiol. Rev. 58, 10-26 (1994).
3. Michel, F. & Westhof, E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216, 585-610 (1990).
4. Strobel, S.A. & Cech, T.R. Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site. Science 267, 675-679 (1995).
5. Waring, R.B., Towner, P., Minter, S.J. & Davies, R.W. Splice-site selection by a self-splicing RNA of Tetrabymena. Nature 321, 133-139 (1986).
6. Been, M.D. & Cech, T.R. One binding site determines sequence specificity of tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. Cell 47, 207-216 (1986).
7. Zaug, A.J., Been, M.D. & Cech, T.R. The Tetrahymena ribozyme acts like an RNA restriction endonuclease. Nature 324, 429-433 (1986).
8. Herschlag, D. Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme Biochemistry 31, 1386-1399 (1992).
9. Bevilacqua, P.C., Kierzek, R., Johnson, K.A. & Turner, D.H. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods Science 258, 1355-1358 (1992).
10. Strobel, S.A. & Cech, T.R. Translocation of an RNA duplex on a ribozyme. Nature Struct. Biol. 1, 13-17 (1994).
11. Murphy, F.L. & Cech, T.R. Alteration of substrate specificity for the endoribonucleoytic cleavage of RNA by the Tetrahymena ribozyme. Proc. Natl. Acad. Sci. U.S.A. 86, 9218-9222 (1989).
12. Doudna, J.A. & Szostak, J.W. RNA-catalysed synthesis of complementary-strand RNA. Nature 339, 519-522 (1989).
13. Strobel, S.A. & Cech, T.R. Exocyclic amine of the conserved G-U pair at the cleavage site of the Tetrahymena ribozyme contributes to 5′-splice site selection and transition state stabilization. Biochemistry 35, 1201-1211 (1996)
14. Strobel, S.A. & Cech, T.R. Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme. Biochemistry 32, 13593-13604 (1993).
15. Wang, J.-F., Downs, W.D. & Cech, T.R. Movement of the guide sequence during RNA catalysis by a group I ribozyme. Science 260, 504-508 (1993).
16. Cate, J.H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678-1685 (1996).
17. Strobel, S.A. & Shetty, K. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc. Natl. Acad. Sci. USA 94, 2903-2908 (1997).
18. Pyle, A.M., Murphy, F.L. & Cech, T.R. RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme. Nature 358, 123-128 (1992).
19. Gaur, R.K. & Krupp, G. Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme. Nucleic Acids Res. 21, 21-26 (1993).
20. Conrad, F., Hanne, A., Gaur, R.K. & Krupp, G. Enzymatic synthesis of 2prime;-modified nucleic acids: identification of important phosphate and ribose moieties in RNase P substrates. Nucleic Acids Res. 23, 1845-1853 (1995).
21. Eckstein, F. Nucleoside phosphorothioates. Ann. Rev. Biochem. 54, 367-402 (1985).
22. Arabshahi, A. & Frey, P.A. A simplified procedure for synthesizing nucleoside 1-thiotriphosphates: dATPαS, dGTPαS, UTPαS, and dTTPαS. Biochem. Biophys. Res. Com. 204, 150-155 (1994).
23. Beaudry, A.A. & Joyce, G.F. Directed evolution of an RNA enzyme. Science 257, 635-641 (1992).
24. Sousa, R. & Padilla, R. A mutant T7 RNA polymerase asa DNA polymerase. EMBO J. 14, 4609-4621 (1995).
25. Mei, R. & Herschlag, D. Mechanistic investigations of a ribozyme derived from the Tetrahymena group I intron. Insights into catalysis and the second step of self-splicing. Biochemistry 35, 5796-5809 (1996).
26. Gish, G. & Eckstein, F. DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240, 1520-1522 (1988).
27. 2 in solution from NMR and restrained moleuclar dynamics. Biochemistry 32, 12612-12623 (1993).
28. Damberger, S.H. & Gutell, R.R. A comparative database of group I intron structures. Nucleic Acids Res. 22, 3508-3510 (1994).
29. Allain, F.H.T. & Varani, G. Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol. 250, 333-353 (1995).
30. Pyle, A.M. et al. Replacement of the Conserved G-U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity. Biochemistry 33, 13856-13863 (1994).
31. Knitt, D.S., Narlikar, G.J. & Herschlag, D. Dissection of the role of the conserved G-U pair in group I RNA self-splicing. Biochemistry 33, 13864-13879 (1994).
32. Doudna, J.A., Ccrmack, B.P. & Szostak, J.W. RNA structure, not sequence, determines the 5 splice-site specificity of a group I intron. Proc. Natl. Acad. Sci. USA 86, 7402-7406 (1989).
33. Gautheret, D., Konings, D. & Gutell, R.R. A major family of motifs involving G-A mismatches in ribosomal RNA. J. Mol. Biol. 242, 1-8 (1994).
34. SantaLucia, J., Kierzek, R. & Turner, D.H. Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry 29, 8813-8819 (1990).
35. Gautheret, D., Konings, D. & Gutell, R.R. G-U base pairing motifs in ribosomal RNA. RNA 1, 807-814 (1995).
36. Murphy, F.L & Cech, T.R. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J. Mol. Biol. 236, 49-63 (1994).
37. Pley, H.W., Flaherty, K.M. & McKay, D.B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372, 111-113 (1994).
38. lle of the purple bacterium Azoarcus. RNA 2, 74-83 (1996).
39. Costa, M. & Michel, F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14, 1276-1285 (1995).
40. Christian, E.L. & Yarus, M. Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena. Biochemistry 32, 4475-4480 (1993).
41. Carson, M. RIBBONS 2.0 Manual (University of Alabama at Birmingham, Alabama, USA; 1991).
42. Nicholls, A., GRASP: graphical respresentation and analysis of surface properties (Columbia University, New York, USA; 1993).