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
Dill, K.A. Dominant forces in protein folding. Biochemistry 29, 7133–7155 (1990).
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).
Loria, A. & Pan, T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2, 551–563 (1996).
Pyle, A.M. Ribozymes: a distinct class of metalloenzymes. Science 261, 709–714 (1993).
Cole, P.E., Yang, S.K. & Crothers, D.M. Conformational changes of transfer ribonnucleic acid: Equilibrium phase diagrams Biochemistry 11, 4358–4368 (1972).
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).
Zarrinkar, P.P. & Williamson, J.R. Kinetic intermediates in RNA folding. Science 265, 918–924 (1994).
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).
Pley, H.W., Flaherty, K.M. & McKay, D.B. Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68–74 (1994).
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).
Celander, D.W. & Cech, T.R. Visualizing the higher order folding of a catalytic RNA molecule. Science 251, 401–407 (1991).
Doherty, E.A. & Doudna, J.A. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry 363, 159–3169 (1997).
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).
Murphy, F.L. & Cech, T.R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32, 5291–5300 (1993).
Cate, J.H. et al. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273, 1678–1685 (1996).
Cate, J.H. & Doudna, J.A. Metal binding sites in the major groove of a large ribozyme domain. Structure 4, 1221–1229 (1996).
Cate, J.H. et al. RNA tertiary structure mediation by adenosine platforms. Science 273, 1696–1699 (1996).
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).
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).
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).
Gish, G. & Eckstein, F. DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240, 1520–1522 (1988).
Frey, P.A. & Sammons, R.D. Bond order and charge localization in nucleoside phosphorothioates. Science 228, 541–545 (1985).
Hinrichs, W., Steifa, M., Saenger, W. & Eckstein, F. Absolute configuration of Rp-uridine 3′,5′-cyclic phosphorothioate. Nucleic Acids Res. 15, 4945–4955 (1987).
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).
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).
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).
Hendsch, Z.S. & Tidor, B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Prot. Sci. 3, 211–226 (1994).
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).
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).
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).
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).
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).
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).
Laggerbauer, B., Murphy, F.L. & Cech, T.R. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 13, 2669–2676 (1994).
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).
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).
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).
Coleman, J.E. Zinc proteins: enzymes, storage proteins, transcription factors and replication proteins. Annu. Rev. Biochem. 61, 897–946 (1992).
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).
Brünger, A. X-PLOR Manual, Version 3.1: A System for X-ray Crystallography and NMR (Yale University Press, New Haven, Connecticut; 1993).
Collaborative Computing Project, N.4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr.. D 50, 760–763 (1994).
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).
Carson, M. Ribbons 2.0. J. Appl. Crystallogr. 24, 958–961 (1991).
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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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DOI: https://doi.org/10.1038/nsb0797-553
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