A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor

Nature Structural Biology

Volumn 5, Issue 11, 1998, Pages 986-992

  Basu, Soumitra ^a   Rambo, Robert P ^a   Strauss Soukup, Juliane ^a   Cate, Jamie H ^a,b   Ferré D'Amaré, Adrian R ^a   Strobel, Scott A ^a   Doudna, Jennifer A ^a  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METAL ION; POTASSIUM ION; RIBOZYME; RNA;

ARTICLE; CRYSTALLOGRAPHY; INTRON; METAL BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; RNA BINDING; RNA STRUCTURE; TETRAHYMENA;

ADENINE; ANIMALS; BINDING SITES; CATIONS, MONOVALENT; CESIUM; CRYSTALLOGRAPHY, X-RAY; GUANOSINE; NUCLEIC ACID CONFORMATION; POTASSIUM; RNA SPLICING; RNA, CATALYTIC; RNA, PROTOZOAN; TETRAHYMENA; THALLIUM; THIONUCLEOSIDES;

AZOARCUS; TETRAHYMENA;

EID: 0031790171     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/2960     Document Type: Article

References (44)

1. Pyle, A.M. Ribozymes: a distinct class of metalloenzymes. Science 261, 709-714 (1993).
2. Pyle, A.M. Catalytic reaction mechanisms and structural features of group II intron ribozymes, in Catalytic RNA, Vol. 10 (eds Eckstein, F. & Lilley, D.M.J.) 75-107 (Springer, New York; 1996).
3. Nolan, J.M. & Pace, N.R. Structural analysis of the bacterial ribonuclease P RNA. in Catalytic RNA, Vol. 10 (eds. Eckstein, F. & Lilley, D.M.J.) 109-128 (Springer, New York; 1996).
4. Miskin, R., Zamir, A. & Elson, D. Inactivation and reactivation of ribosomal subunits: the peptidyl transferase activity of the 50S subunit of Escherichia coli. J. Mol. Biol. 54, 355-378 (1970).
5. Zamir, A., Miskin, R. & Elson, D. Inactivation and reactivation of ribosomal subunits: amino acyl-transfer RNA binding activity of the 30S subunit of Escherichia coli. J. Mol. Biol. 60, 347-364 (1971).
6. Manning, G.S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quart. Rev. Biophys. 2, 179-246 (1978).
7. Costa, M. & Michel, F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14, 1276-1285 (1995).
8. Cate, J.H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678-1685 (1996).
9. Cate, J.H. et al. RNA tertiary structure mediation by adenosine platforms. Science 273, 1696-1699 (1996).
10. 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).
11. Cate, J.H., Hanna, R.L. & Doudna, J.A. A magnesium ion core at the heart of a ribozyme domain. Nature Struct. Biol. 4, 553-558 (1997).
12. Cate, J.H. & Doudna, J.A. Metal-binding sites in the major groove of a large ribozyme domain. Structure 4, 1221-1229 (1996).
13. Pauling, L. The Nature of the Chemical Bond, (Cornell University Press, Ithaca, NY, 1960).
14. 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).
15. 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).
16. Pearson, R.G. Acids and Bases. Science 151, 172-177 (1966).
17. Heitner, H.I., Lippard, S.J. & Sunshine, H.R. Metal binding by thionucleosides. J. Amer. Chem. Soc. 94, 8936-8937 (1972).
18. Gish, G. & Eckstein, F. DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240, 1520-1522 (1988).
19. Boeyens, J.C.A. & Herbstein, F.H. Ionic complexes of thiourea. II. Chemical and crystallographic survey and determination of the crystal structures of some representative complexes. Inorg. Chem. 6, 1408-1425 (1967).
20. Ortoleva-Donnelly, L., Szewczak, A.A., Gutell, R.R. & Strobel, S.A. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4, 498-519 (1998),
21. Reinhold-Hurek, B. & Shub, D.A. Self-splicing introns in tRNA genes of widely divergent bacteria. Nature 357, 173-176 (1992).
22. lle of the purple bacterium Azoarcus. RNA 2, 74-83 (1996).
23. Beaudry, A.A. & Joyce, G.F. Directed evolution of an RNA enzyme. Science 257, 635-641 (1992).
24. Michel, F., Hanna, M., Green, R., Bartel, D.P. & Szostak, J.W. The guanosine binding site of the Tetrahymena ribozyme. Nature 342, 391-395 (1989).
25. Michel, F., Ellington, A.D., Couture, S. & Szostak, J.W. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature 347, 578-580 (1990).
26. 2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP. Biochemistry 23, 5262-5271 (1984).
27. Villeret, V., Huang, S., Fromm, H.J. & Lipscomb, W.N. Crystallographic evidence for the action of potassium, thallium, and lithium on fructose-1,6-bisphosphatase. Proc. Natl. Acad. Sci. USA 92, 8916-8920 (1995).
28. Wilbanks, S.M. & McKay, D.B. How potassium affects the activity of the molecular chaperone Hsc70. II. Potassium binds specifically in the ATPase active site. J. Mol. Biol. 270, 2251-2257 (1995).
29. Doyle, D.A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69-77 (1998).
30. Rosenberg, J.M. et al. Double helix at atomic resolution. Nature 243, 150-154 (1973).
31. Williamson, J.R., Raghuraman, M.K. & Cech, T.R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59, 871-880 (1989).
32. Cheong, C. & Moore, P.B. Solution structure of an unusually stable RNA tetraplex containing G-and U-quartet structures. Biochemistry 31, 8406-8414 (1992).
33. Laughlan, G. et al. The high resolution crystal structure of a parallel-stranded guanine tetraplex. Nature 265, 520-524 (1994).
34. Sundquist, W.I. & Heaphy, S. Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA. Proc. Natl. Acad. Sci. USA 90, 3393-3397 (1993).
35. Wang, Y.-W., Lu, M. & Draper, D.E. Specific ammonium ion requirement for functional ribosomal RNA tertiary structure. Biochemistry 32, 12279-12282 (1993).
36. Cox, B.G. & Schneider, H. Coordination and Transport Properties of Macrocyclic Compounds in Solution (Elsevier Science Publishers, New York; 1992).
37. Brown, I.B. What factors determine cation coordination numbers? Acta Crystallogr. B 44, 545-553 (1988).
38. Hinton, J.F., Turner, G. & Millett, F.S. Thallous ion interaction with gramicidin incorporated in micelles studied by thallium-205 NMR. Biochemistry 21, 651-654 (1982).
39. Hinton, J.F., Whaley, W.L., Shungu, D., Koeppe, R.E. & Millett, F.S. Equilibrium binding constants for the group I metal cations with gramicidin-A determined by competition studies and Tl+-205 nuclear magnetic resonance spectroscopy. Biophys. J. 50, 539-544 (1986).
40. Doudna, J.A., Grosshans, C., Gooding, A. & Kundrot, C.E. Crystallization of ribozymes and small RNA motifs by a sparce matrix approach. Proc. Natl. Acad. Sci. USA 90, 7829 (1993).
41. 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).
42. Fox, J.J., Wempen, I., Hampton, A. & Doerr, I.L. Thiation of nucleosides. I. Synthesis of 2-amino-6-mercapto-9-β-D-ribofuranosylpurine ("thioguanosine") and related purine nucleosides. J. Org. Chem. 80, 1669-1675 (1957).
43. Lingner, J. & Keller, W. 3′-end labeling of RNA with recombinant yeast poly(A) polymerase. Nucleic Acids Res. 21, 2917-2920 (1993).
44. Carson, M. RIBBONS 2.0 J. Appl. Crystallogr. 47, 110 (1991).