Metal Ion Stabilization of the U-Turn of the A37 N 6-Dimethylallyl-Modified Anticodon Stem-Loop of Escherichia coli tRNAPhe

Biochemistry

Volumn 43, Issue 1, 2004, Pages 55-66

  Cabello Villegas, Javier ^a,b   Tworowska, Izabela ^a   Nikonowicz, Edward P ^a  

^a RICE UNIVERSITY   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POSITIVE IONS; PROTONS; RNA; SOLUTIONS;

METAL ION STABILIZATION; NUCLEOSIDES;

ESCHERICHIA COLI;

ALLYL COMPOUND; CATION; COBALT; MANGANESE; METAL ION; METHYL GROUP; NITROGEN 15; PROTON; RIBOSOME RNA; TRANSFER RNA;

ANTICODON; ARTICLE; BINDING AFFINITY; BINDING SITE; ESCHERICHIA COLI; MOLECULAR MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE;

ESCHERICHIA COLI;

EID: 0347988156     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0353676     Document Type: Article

References (57)

1. Kim, S. H., Suddath, F. L., Quigley, G. J., McPherson, A., Sussman, J. L., Wang, A. H., Seeman, N. C., and Rich, A. (1974) Three-dimensional tertiary structure of yeast phenylalanine tranfer RNA, Science 185, 435-440.
2. Robertus, J. D., Ladner, J. E., Finch, J. T., Rhodes, D., Brown, R. S., Clark, B. F. C., and Klug, A. (1974) Structure of yeast phenylalanine tRNA at 3 Å resolution, Nature 250, 546-551.
3. Jucker, F. M., Heus, H. A., Yip, P. F., Moors, E. H., and Pardi, A. (1996) A network of heterogeneous hydrogen bonds in GNRA tetraloops, J. Mol. Biol. 264, 968-980.
4. Butcher, S. E., Dieckmann, T., and Feigon, J. (1997) Solution structure of a GAAA tetraloop receptor RNA, EMBO J. 16, 7490-7499.
5. Puglisi, E. V., and Puglisi, J. D. (1998) HIV-1 A-rich RNA loop mimics the tRNA anticodon structure, Nat. Struct. Biol. 5, 1033-1036.
6. Pley, H. W., Flaherty, K. M., and McKay, D. B. (1994) Three-dimensional structure of a hammerhead ribozyme, Nature 372, 68-74.
7. Fountain, M. A., Serra, M. J., Krugh, T. R., and Turner, D. H. (1996) Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA, Biochemistry 35, 6539-6548.
8. Huang, S., Wang, Y. X., and Draper, D. E. (1996) Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs, J. Mol. Biol. 258, 308-321.
9. Schweisguth, D. C., and Moore, P. B. (1997) On the conformation of the anticodon loops of initiator and elongator methionine tRNAs, J. Mol. Biol. 267, 505-519.
10. Lys,3 by an A+C base-pair and by pseudouridine, J. Mol. Biol. 285, 115-131.
11. 6-dimethylallyl modified anticodon stem-loops of Escherichia coli tRNA(Phe), J. Mol. Biol. 319, 1015-1034.
12. Phe, Nucleic Acids Res. 4, 2811-2820.
13. Quigley, G. J., Teeter, M. M., and Rich, A. (1978) Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA, Proc. Natl. Acad. Sci. U.S.A. 75, 64-68.
14. Shi, H., and Moore, P. (2000) The crystal structure of yeast phenylalanine tRNA at 1.93Å resolution: A classic structure revisited, RNA 6, 1091-1105.
15. Guéron, M., and Leroy, J. L. (1982) Significance and mechanism of divalent-ion binding to transfer RNA, Biophys. J. 38, 231-236.
16. 2+ in RNA structure and function, Progr. Nucleic Acid Res. 53, 79-129.
17. 6A, Biochemistry 39, 13396-13404.
18. Lys stabilize a canonical U-turn structure, Biochemistry 39, 12575-12584.
19. Val: an imino proton NMR investigation, Biochemistry 33, 8905-8911.
20. Leung, H. C., Chen, Y., and Winkler, M. E. (1997) Regulation of substrate recognition by the MiaA tRNA prenyltransferase modification enzyme of Escherichia coli K-12, J. Biol. Chem. 272, 13073-13083.
21. Davanloo, P., Rosenberg, A. H., Dunn, J. J., and Sturdier, F. W. (1984) Cloning and expression of the gene for bacteriophage T7 RNA polymerase, Proc. Natl. Acad. Sci. U.S.A. 81, 2035-2039.
22. 15N Labeled RNAs for Heteronuclear Multi-Dimensional NMR Studies, Nucleic Acids Res. 20, 4507-4513.
23. 13C alpha carbons, J. Am. Chem. Soc. 116, 8266-8278.
24. 2)-isopentenyl]-adenine by the quantum chemical PCILO calculations, Int. J. Quantum Chem. 34, 133-142.
25. Allain, F. H.-T., and Varani, G. (1995) Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns, Nucleic Acids Res. 23, 341-350.
26. Gonzalez, R. L., and Tinoco, I. J. (2001) Identification and characterization of metal ion binding sites in RNA, Methods Enzymol. 338, 521-443.
27. Allain, F. H., and Varani, G. (1995) Structure of the P1 helix from group I self-splicing introns, J. Mol. Biol. 250, 333-353.
28. Kieft, J. S., and Tinoco, I. J. (1997) Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine, Structure 5, 713-721.
29. James, T. L., James, J. L., and Lapidot, A. (1981) Structural and dynamic information about double-stranded DNA from nitrogen-15 NMR spectroscopy, J. Am. Chem. Soc. 103, 6748-6750.
30. Nixon, P. L., Rangan, A., Kim, Y. G., Rich, A., Hoffman, D. W., Hennig, M., and Giedroc, D. P. (2002) Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot, J. Mol. Biol. 322, 621-633.
31. Majumdar, A., Kettani, A., Skripkin, E., and Patel, D. J. (2001) Pulse sequences for detection of NH2⋯N hydrogen bonds in sheared G-A mismatches via remote, nonexchangeable protons, J. Biomol. NMR 19, 103-113.
32. Poppe, L., and van Halbeek, H. (1994) NMR spectroscopy of hydroxyl protons in supercooled carbohydrates, Nat. Struct. Biol. 1, 215-216.
33. 2 determined by NMR, Nucleic Acids Res. 24, 3693-3699.
34. Gyi, J. I., Lane, A. N., Conn, G. L., and Brown, T. (1998) The orientation and dynamics of the C2′-OH and hydration of RNA and DNA-RNA hybrids. Nucleic Acids Res. 26, 3104-3110.
35. 2: hybrid junctions flanked by DNA duplexes, Nucleic Acids Res. 28, 1322-1331.
36. Cys-EF-Tu-GDPNP reveals general and specific features in the ternary complex in tRNA, Structure 7, 143-156.
37. Rüdisser, S., and Tinoco, I., Jr. (2000) Solution structure of cobalt-(III)hexammine complexed to the GAAA tetraloop, and metalion binding to G-A Mismatches, J. Mol. Biol. 295, 1211-1223.
38. Butcher, S. E., Allain, F. H.-T., and Feigon, J. (2000) Determination of metal ion binding sites within the hairpin ribozyme domains by NMR, Biochemistry 39, 2174-2182.
39. 3+. X-ray evidence for hydrogen bonding to pairs of guanine bases in the major groove, Biochim. Biophys. Acta 697, 78-82.
40. Phe. J. Biomol. Struct. Dyn. 7, 235-255.
41. 2+ binding to tRNA revisited: the nonlinear Poisson-Boltzmann model, J. Mol. Biol. 299, 813-825.
42. Misra, V. K., and Draper, D. E. (1999) On the role of magnesium ions in RNA stability, Biopolymers 48, 113-135.
43. Gonzalez, R. L., and Tinoco, I. J. (1999) Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot, J. Mol. Biol. 289, 1267-1282.
44. Xu, Q., Jampani, S. R. B., and Braunlin, W. H. (1993) Rotational dynamics of hexaamminecobalt(III) bound to oligomeric DNA: correlation with cation-induced structural transitions, Biochemistry 32, 11754-11760.
45. Robinson, H., and Wang, A. H.-J. (1996) Neomycin, spermine and hexaamminecobalt(III) share common structural motifs in converting B- to A-DNA. Nucleic Acids Res. 24, 676-682.
46. 2+ and a conformational transition at the anticodon stem-loop of yeast phenylalanyne tRNA, Biochemistry 32, 10249-10253.
47. 2+-dependent tRNA folding. Nucleic Acids Res. 30, 4751-4760.
48. Hall, K. B., Sampson, J. R., Uhlenbeck, O. C., and Redfield, A. G. (1989) Structure of an Unmodified tRNA molecule, Biochemistry 28, 5794-5801.
49. Ogle, J. M., Brodersen, D. E., Clemons, W. M. J., Tarry, M. J., Carter, A. P., and Ramakrishan, V. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897-902.
50. Dix, D. B., Wittenberg, W. L., Uhlenbeck, O. C., and Thompson, R. C. (1986) Effect of replacing uridine 33 in yeast tRNAPhe on the reaction with ribosomes, J. Biol. Chem. 261, 10112-10118.
51. Ashraf, S. S., Ansari, G., Guenther, R., Sochacka. E., Malkiewicz, A., and Agris, P. F. (1999) The uridine in "U-turn": contributions to tRNA-ribosomal binding, RNA 5, 503-511.
52. Phe from hist mutants: a structural role for pseudouridine, Biochemistry 30, 4223-4231.
53. Houssier, C., and Grosjean, H. (1985) Temperature jump relaxation studies on the interactions between transfer RNAs with complementary anticodons. The effect of modified bases adjacent to the anticodon triplet, J. Biomol. Struct. Dyn. 3, 387-408.
54. Tumbough, C. L., Jr., Neill, R. J., Landsberg, R., and Ames, B. N. (1979) Pseudouridylation of tRNAs and its role in regulation in Salmonella typhimurium, J. Biol. Chem. 254, 5111-5119.
55. Raychaudhuri, S., Niu, L., Conrad, J., Lane, B. G., and Ofengand, J. (1999) Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA, J. Biol. Chem. 274, 18880-18886.
56. Esberg, B., Leung, H. C., Tsui, H. C., Bjork, G. R., and Winkler, M. E. (1999) Identification of the miaB gene, involved in methylthiolation of isopentenylated A37 derivatives in the tRNA of Salmonella typhimurium and Escherichia coli, J. Bacteriol. 181, 7256-7265.
57. Newby, M. I., and Greenbaum, N. L. (2002) Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine, Nat. Struct. Biol. 9, 958-965.