The contribution of metal ions to the structural stability of the large ribosomal subunit

RNA

Volumn 10, Issue 9, 2004, Pages 1366-1379

  Klein, Daniel J ^a   Moore, Peter B ^a   Steitz, Thomas A ^a,b  

^a YALE UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Coordination; Magnesium; Metal ion; Monovalent cation; Ribosome structure; RNA structure

Indexed keywords

CATION; LARGE SUBUNIT RIBOSOMAL RNA; MAGNESIUM ION; METAL ION; OXYGEN; RIBOSOME RNA; RNA 23S;

ARTICLE; HALOARCULA MARISMORTUI; METAL BINDING; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; RIBOSOME; RNA BINDING; RNA STABILITY; RNA STRUCTURE;

BASE PAIRING; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; HALOARCULA MARISMORTUI; LIGANDS; MAGNESIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OXYGEN; PEPTIDYL TRANSFERASES; PHOSPHATES; RIBOSOMES; RNA, BACTERIAL; RNA, RIBOSOMAL, 23S; RUBIDIUM;

HALOARCULA; HALOARCULA MARISMORTUI;

EID: 4344569647     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.7390804     Document Type: Article

References (34)

1. Auffinger, P., Bielecki, L., and Westhof, E. 2004. Anion binding to nucleic acids. Structure 12: 379-388.
2. Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920.
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. Batey, R.T. and Doudna, J.A. 2002. Structural and energetic analysis of metal ions essential to SRP signal recognition domain assembly. Biochemistry 41: 11703-11710.
5. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
6. Cate, J.H. and Doudna, J.A. 1996. Metal-binding sites in the major groove of a large ribozyme domain. Structure 4: 1221-1229.
7. 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.
8. 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.
9. Chao, F.C. 1957. Dissociation of macromolecular ribonucleoprotein of yeast. Arch. Biochem. Biophys. 70: 426-431.
10. Chao, F.C. and Schachman, H.K. 1956. The isolation and characterization of a macro-molecular ribonucleoprotein from yeast. Arch. Biochem. Biophys. 61: 220-230.
11. + complex. J. Mol. Biol. 318: 963-973.
12. Gordon, J. and Lipmann, F. 1967. Role of divalent ions in poly U-directed phenylalanine polymerization. J. Mol. Biol. 23: 23-33.
13. Hurwitz, C. and Rosano, C.L. 1967. The intracellular concentration of bound and unbound magnesium ions in Escherichia coli. J. Biol. Chem. 242: 3719-3722.
14. Jones, T.A., Zou, J.Y., Cowan, S., and Kjeldgaard, M. 1991. Improved methods for building proteins models in electron density maps and the location of errors in these models. Acta Crystallogr. A46: 110-119.
15. 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.
16. Khawaja, J.A. and Raina, A. 1970. Effect of spermine and magnesium on the attachment of free ribosomes to endoplasmic reticulum membranes. Biochem. Biophys. Res. Commun. 41: 512-518.
17. Kieft, J.S. and Tinoco Jr., I. 1997. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine. Structure 5: 713-721.
18. Kimes, B.W. and Morris, D.R. 1973. Cations and ribosome structure. II. Effects on the 50S subunit of substituting polyamines for magnesium ion. Biochemistry 12: 442-449.
19. Lusk, J.E., Williams, R.J., and Kennedy, E.P. 1968. Magnesium and the growth of Escherichia coli. J. Biol. Chem. 243: 2618-2624.
20. McCarthy, B.J. 1962. Effects of magnesium starvation on ribosome content of Escherichia coli. Biochim. Biophys. Acta. 55: 880-888.
21. Misra, V.K. and Draper, D.E. 1999. On the role of magnesium ions in RNA stability. Biopolymers 48: 113-135.
22. Moore, P.B. 1966. Polynucleotide attachment to ribosomes. J. Mol. Biol. 18: 8-20.
23. Naslund, P.H. and Hultin, T. 1970. Effects of potassium deficiency on mammalian ribosomes. Biochim. Biophys. Acta. 204: 237-247.
24. -. 1971. Structural and functional defects in mammalian ribosomes after potassium deficiency. Biochim. Biophys. Acta. 254: 104-116.
25. Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. 2000. The structural basis of ribosome activity in peptide bond synthesis. Science 289: 920-930.
26. Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B., and Steitz, T.A. 2001. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl. Acad. Sci. 98: 4899-4903.
27. Otwinowski, Z. and Minor, W. 1987. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
28. Pyle, A.M. 2002. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7: 679-690.
29. Schmeing, T.M., Seila, A.C., Hansen, J.L., Freeborn, B., Soukup, J.K., Scaringe, S.A., Strobel, S.A., Moore, P.B., and Steitz, T.A. 2002. A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nat. Struct. Biol. 9: 225-230.
30. Shiman, R. and Draper, D.E. 2000. Stabilization of RNA tertiary structure by monovalent cations. J. Mol. Biol. 302: 79-91.
31. Tissieres, A., Watson, J.D., Schlessinger, D., and Hollingworth, B.R. 1959. Ribonucleoprotein particles from Escherichia coli. J. Mol. Biol. 1: 221-233.
32. Wacker, W.E. 1969. The biochemistry of magnesium. Ann. N. Y. Acad. Sci. 162: 717-726.
33. 2+ by inorganic cations. Biochemistry 12: 450-456.
34. Zitomer, R.S. and Flaks, J.G. 1972. Magnesium dependence and equilibrium of Escherichia coli ribosomal subunit association. J. Mol. Biol. 71: 263-279.