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A magnesium ion core at the heart of a ribozyme domain

Abstract

Large ribozymes require divalent metal ions to fold. We show here that the tertiary structure of the Tetrahymena group I intron P4-P6 domain nucleates around a magnesium ion core. In the domain crystal structure, five magnesium ions bind in a three-helix junction at the centre of the molecule. Single atom changes in any one of four magnesium sites in this three-helix junction destroy folding of the entire 160-nucleotide P4-P6 domain. The magnesium ion core may be the RNA counterpart to the protein hydrophobic core, burying parts of the RNA molecule in the native structure.

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References

  1. Dill, K.A. Dominant forces in protein folding. Biochemistry 29, 7133–7155 (1990).

    CAS  PubMed  Google Scholar 

  2. 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).

    CAS  PubMed  Google Scholar 

  3. Loria, A. & Pan, T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2, 551–563 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Pyle, A.M. Ribozymes: a distinct class of metalloenzymes. Science 261, 709–714 (1993).

    CAS  PubMed  Google Scholar 

  5. Cole, P.E., Yang, S.K. & Crothers, D.M. Conformational changes of transfer ribonnucleic acid: Equilibrium phase diagrams Biochemistry 11, 4358–4368 (1972).

    CAS  PubMed  Google Scholar 

  6. Banerjee, A.R., Jaeger, J.A. & Turner, D.H. Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry 32, 153–163 (1993).

    CAS  PubMed  Google Scholar 

  7. Zarrinkar, P.P. & Williamson, J.R. Kinetic intermediates in RNA folding. Science 265, 918–924 (1994).

    CAS  PubMed  Google Scholar 

  8. Robillard, G.T., Tarr, C.E., Vosman, F. & Reid, B.R. A nuclear magnetic resonance study of secondary and tertiary structure in yeast tRNA Phe. Biochemistry 16, 5261–5273 (1977).

    CAS  PubMed  Google Scholar 

  9. Pley, H.W., Flaherty, K.M. & McKay, D.B. Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68–74 (1994).

    CAS  PubMed  Google Scholar 

  10. Scott, W.G., Murray, J.B., Arnold, J.R.P., Stoddard, B.L. & Klug, A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274, 2065–2069 (1996).

    CAS  PubMed  Google Scholar 

  11. Celander, D.W. & Cech, T.R. Visualizing the higher order folding of a catalytic RNA molecule. Science 251, 401–407 (1991).

    CAS  PubMed  Google Scholar 

  12. Doherty, E.A. & Doudna, J.A. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry 363, 159–3169 (1997).

    Google Scholar 

  13. Downs, W.D. & Cech, T.R. Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks. RNA 2, 718–732 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Murphy, F.L. & Cech, T.R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32, 5291–5300 (1993).

    CAS  PubMed  Google Scholar 

  15. Cate, J.H. et al. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273, 1678–1685 (1996).

    CAS  PubMed  Google Scholar 

  16. Cate, J.H. & Doudna, J.A. Metal binding sites in the major groove of a large ribozyme domain. Structure 4, 1221–1229 (1996).

    CAS  PubMed  Google Scholar 

  17. Cate, J.H. et al. RNA tertiary structure mediation by adenosine platforms. Science 273, 1696–1699 (1996).

    CAS  PubMed  Google Scholar 

  18. Christian, E.L. & Yarus, M. Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena. J Mol. Biol. 228, 743–758 (1992).

    CAS  PubMed  Google Scholar 

  19. Pecoraro, V.L., Hermes, J.D. & Cleland, W.W. Stability constants of Mg2+ and Cd2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of Mg–ATP and Mg–ADP. Biochemistry 23, 5262–5271 (1984).

    CAS  PubMed  Google Scholar 

  20. 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).

    CAS  PubMed  Google Scholar 

  21. Gish, G. & Eckstein, F. DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240, 1520–1522 (1988).

    CAS  PubMed  Google Scholar 

  22. Frey, P.A. & Sammons, R.D. Bond order and charge localization in nucleoside phosphorothioates. Science 228, 541–545 (1985).

    CAS  PubMed  Google Scholar 

  23. Hinrichs, W., Steifa, M., Saenger, W. & Eckstein, F. Absolute configuration of Rp-uridine 3′,5′-cyclic phosphorothioate. Nucleic Acids Res. 15, 4945–4955 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Jack, A., Ladner, J.E., Rhodes, D., Brown, R.S. & Klug, A. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J. Mol. Biol. 111, 315–328 (1977).

    CAS  PubMed  Google Scholar 

  25. Holbrook, S.R., Sussman, J.L., Warrant, R.W., Church, G.M. & Kim, S.-H. RNA-ligand interactions: (I) magnesium binding sites in yeast tRNAPhe. Nucleic Acids Res. 4, 2811–2820 (1977).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Waldburger, C.D., Schildbach, J.F. & Sauer, R.T. Are buried salt bridges important for protein stability and conformational specificity? Nature Struct. Biol. 2, 122–128 (1995).

    CAS  PubMed  Google Scholar 

  27. Hendsch, Z.S. & Tidor, B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Prot. Sci. 3, 211–226 (1994).

    CAS  Google Scholar 

  28. Hendsch, Z.S., Jonsson, T., Sauer, R.T. & Tidor, B. Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests. Biochemistry 35, 7621–7625 (1996).

    CAS  PubMed  Google Scholar 

  29. Jaeger, J.A., Zuker, M. & Turner, D.H. Melting and chemical modification of a cyclized self-splicing group I intron: similarity of structures in 1 M Na+, in 10 mM Mg2+, and in the presence of substrate. Biochemistry 29, 10147–10158 (1990).

    CAS  PubMed  Google Scholar 

  30. Wang, J.-F. & Cech, T.R. Metal ion dependence of active-site structure of the Tetrahymena ribozyme revealed by site-specific photo-cross-linking. J. Am. Chem. Soc. 116, 4178 (1994).

    CAS  Google Scholar 

  31. 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).

    CAS  PubMed  Google Scholar 

  32. 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. U.S.A. 94, 2903 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Joyce, G.F., van der Horst, G. & Inoue, T. Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucleic Acids Res 17, 7879–7889 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Laggerbauer, B., Murphy, F.L. & Cech, T.R. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 13, 2669–2676 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. van der Horst, G., Christian, A. & Inoue, T. Reconstitution of a group I intron self-splicing reaction with an activator RNA. Proc. Natl. Acad. Sci. USA 88, 184–188 (1991).

    CAS  PubMed  Google Scholar 

  36. Lehnert, V., Jaeger, L., Michel, F. & Westhof, E. New loop-loop tertiary interactions in self-splicing introns of subgroup 1C and ID - A complete 3D model of the Tetrahymena thermophila ribozyme. Chem. & Biol. 3, 993–1009 (1996).

    CAS  Google Scholar 

  37. Zarrinkar, P.P. & Williamson, J.R. The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme. Nucleic Acids Res. 24, 854 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Coleman, J.E. Zinc proteins: enzymes, storage proteins, transcription factors and replication proteins. Annu. Rev. Biochem. 61, 897–946 (1992).

    CAS  PubMed  Google Scholar 

  39. Wu, L.C., Schulman, B.A., Peng, Z. & Kim, P.S. Disulfide determinants of calcium-induced packing in alpha-lactalbumin. Biochemistry 35, 859–863 (1996).

    CAS  PubMed  Google Scholar 

  40. Brünger, A. X-PLOR Manual, Version 3.1: A System for X-ray Crystallography and NMR (Yale University Press, New Haven, Connecticut; 1993).

    Google Scholar 

  41. Collaborative Computing Project, N.4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr.. D 50, 760–763 (1994).

    Google Scholar 

  42. Doudna, J.A., Grosshans, C., Gooding, A. & Kundrot, C.E. Crystallization of ribozymes and small RNA motifs by a sparse matrix approach. Proc Natal. Acad Sci USA 90, 7829–7833 (1993).

    CAS  Google Scholar 

  43. Carson, M. Ribbons 2.0. J. Appl. Crystallogr. 24, 958–961 (1991).

    Google Scholar 

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Cate, J., Hanna, R. & Doudna, J. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Mol Biol 4, 553–558 (1997). https://doi.org/10.1038/nsb0797-553

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