Low specificity of metal ion binding in the metal ion core of a folded RNA

RNA

Volumn 13, Issue 8, 2007, Pages 1205-1213

  Travers, Kevin J ^a,b   Boyd, Nathan ^a   Herschlag, Daniel ^a  

^a STANFORD UNIVERSITY   (United States)

^b Thermo Fisher Scientific   (United States)

Author keywords

Hydroxyl radical footprinting; Metal ion specificity; P4 P6 domain; RNA folding; Tertiary structure formation

Indexed keywords

BARIUM; CALCIUM ION; MAGNESIUM ION; MANGANESE; METAL ION; MONOVALENT CATION; NICKEL; RIBOZYME; RNA; STRONTIUM; ZINC ION;

ARTICLE; BINDING AFFINITY; BINDING SITE; INTRON; METAL BINDING; NONHUMAN; PRIORITY JOURNAL; RNA BINDING; RNA STRUCTURE; STEREOSPECIFICITY; TETRAHYMENA THERMOPHILA; X RAY CRYSTALLOGRAPHY;

ANIMALS; BASE SEQUENCE; METALS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; TETRAHYMENA;

TETRAHYMENA;

EID: 34447521717     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.566007     Document Type: Article

References (35)

1. Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., and Strobel, S.A. 2004. Crystal structure of a self-splicing group I intron with both exons. Nature 430: 45-50.
2. Babu, C.S., Dudev, T., Casareno, R., Cowan, J.A., and Lim, C. 2003. A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: Application to E. coli ribonuclease H1. J. Am. Chem. Soc. 125: 9318-9328.
3. Basu, S., Rambo, R.P., Strauss-Soukup, J., Cate, J.H., Ferre-D'Amare, A.R., Strobel, S.A., and Doudna, J.A. 1998. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat. Struct. Biol. 5: 986-992.
4. Battle, D.J. and Doudna, J.A. 2002. Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. 99: 11676-11681.
5. Brannvall, M., Mikkelsen, N.E., and Kirsebom, L.A. 2001. Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions. Nucleic Acids Res. 29: 1426-1432.
6. Brantl, S. 2006. Bacterial gene regulation: Metal ion sensing by proteins or RNA. Trends Biotechnol. 24: 383-386.
7. Bukhman, Y.V. and Draper, D.E. 1997. Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure. J. Mol. Biol. 273: 1020-1031.
8. Cate, J.H. and Doudna, J.A. 1996. Metal-binding sites in the major groove of a large ribozyme domain. Structure 4: 1221-1229.
9. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., and Doudna, J.A. 1996. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273: 1678-1685.
10. Cate, J.H., Hanna, R.L., and Doudna, J.A. 1997. A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol. 4: 553-558.
11. Celander, D.W. and Cech, T.R. 1991. Visualizing the higher-order folding of a catalytic RNA molecule. Science 251: 401-407.
12. Chowrira, B.M., Berzal-Herranz, A., and Burke, J.M. 1993. Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme. Biochemistry 32: 1088-1095.
13. Creighton, T. 1993. Proteins: Structures and molecular properties. W.H. Freeman and Company, New York.
14. Dahm, S.C. and Uhlenbeck, O.C. 1991. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30: 9464-9469.
15. Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., and Altman, R.B. 2005a. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11: 344-354.
16. 2+ stoichiometry for folding an RNA metal ion core. J. Am. Chem. Soc. 127: 8272-8273.
17. Draper, D.E. 2004. A guide to ions and RNA structure. RNA 10: 335-343.
18. 2+. Biophys. J. 69: 2623-2641.
19. Ennifar, E., Walter, P., and Dumas, P. 2003. A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res. 31: 2671-2682.
20. Feig, A.L. and Uhlenbeck, O.C. 1999. The role of metal ions in RNA biochemistry. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
21. Grosshans, C.A. and Cech, T.R. 1989. Metal ion requirements for sequence-specific endoribonuclease activity of the Tetrahymena ribozyme. Biochemistry 28: 6888-6894.
22. Guerrier-Takada, C., Haydock, K., Allen, L., and Altman, S. 1986. Metal ion requirements and other aspects of the reaction catalyzed by M1 RNA, the RNA subunit of ribonuclease P from Escherichia coli. Biochemistry 25: 1509-1515.
23. Heilman-Miller, S.L., Thirumalai, D., and Woodson, S.A. 2001. Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations. J. Mol. Biol. 306: 1157-1166.
24. Irving, H. and Williams, R.J.P. 1948. Order of stability of metal complexes. Nature 162: 746-747.
25. Juneau, K., Podell, E., Harrington, D.J., and Cech, T.R. 2001. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure 9: 221-231.
26. 2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory. J. Mol. Biol. 294: 1135-1147.
27. Nakano, S., Cerrone, A.L., and Bevilacqua, P.C. 2003. Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry 42: 2982-2994.
28. Pearson, R.G. 1988. Absolute hardness: Application in inorganic chemistry. Inorg. Chem. 27: 734-740.
29. Pley, H.W., Flaherty, K.M., and McKay, D.B. 1994. Three-dimensional structure of a hammerhead ribozyme. Nature 372: 68-74.
30. 2+ binding in the group I intron core. J. Mol. Biol. 329: 229-238.
31. Rosenzweig, A.C. 2002. Metallochaperones: Bind and deliver. Chem. Biol. 9: 673-677.
32. Scott, W.G., Finch, J.T., and Klug, A. 1995. The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage. Cell 81: 991-1002.
33. Shannon, R.D. 1976. Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides. Acta Crystallogr. A 32: 751-767.
34. Shi, H. and Moore, P.B. 2000. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited. RNA 6: 1091-1105.
35. Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., and Chance, M.R. 2004. Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J. Mol. Biol. 343: 1195-1206.