On the conformation of the anticodon loops of initiator and elongator methionine tRNAs

Journal of Molecular Biology

Volumn 267, Issue 3, 1997, Pages 505-519

  Schweisguth, David C ^a   Moore, Peter B ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Initiator; Methionine; NMR; Structure; tRNA

Indexed keywords

METHIONINE TRANSFER RNA;

ANTICODON; ARTICLE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; RNA CONFORMATION; RNA SEQUENCE; TRANSCRIPTION INITIATION;

EID: 0031552368     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0903     Document Type: Article

References (55)

1. Altona C. Conformational analysis of nucleic acids: determination of backbone geometry of single-helical RNA and DNA in aqueous solution. J. Royal Neth. Chem. Soc. 101 (12):1982;413-433.
2. Basavappa R., Sigler P. B. The 3 Å crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination. EMBO J. 10 (10):1991;3105-3111.
3. Beckett D., Uhlenbeck O. C. Enzymatic synthesis of oligoribonucleotides. Oligonucleotide Synthesis: A Practical Approach. 1984;IRL Press, Oxford.
4. Brünger A. T. X-PLOR Version 3.1: A System For X-Ray Crystallography and NMR. 1992;Yale University Press, New Haven.
5. 1H-N.M.R. study. Biochem. J. 221 (3):1984;737-751.
6. Dirheimer G., Keith G., Dumas P., Westhof E. Primary, secondary and tertiary structures of tRNAs. Söll D., RajBhandary U. tRNA: Structure, Biosynthesis and Function. 1995;American Society of Microbiology, Washington, DC.
7. Dube S. K., Rudland P. S., Clark B. F. C., Marcker K. A. A structural requirement for codon-anticodon interaction on the ribosome. C.S.H. Symp. Quant. Biol. 34:1969;161-166.
8. Fountain M. A., Serra M. J., Krugh T. R., Turner D. H. Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA. Biochem. 35 (21):1996;6539-6548.
9. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA. 83:1986;9373-9377.
10. Gorenstein D., Goldfield E. High-resolution phosphorus nuclear magnetic resonance spectroscopy of transfer ribonucleic acids: multiple conformations in the anticodon loop. Biochemistry. 21 (23):1982;5839-5849.
11. Gorenstein D. G. Phosphorus-31 chemical shifts: principles and empirical observations. Gorenstein D. G. Phosphorus-31 NMR: Principles and Applications. 1984;Academic Press, Orlando, FL.
12. Pheanticodon is dependent on RNA-like modifications of the bases of the stem. Biochemistry. 31 (45):1992;11004-11011.
13. Hartz D., Binkley J., Hollingsworth T., Gold L. Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3. Genes Dev. 4 (10):1990;1790-1800.
14. 1H nuclear magnetic resonance assignment procedure for RNA duplexes. J. Am. Chem. Soc. 113:1991;4360-4361.
15. Phe. J. Mol. Biol. 124:1978;523.
16. Holbrook S. R., Sussman J. L., Warrant R. W., Kim S.-H. Crystal structure of yeast phenylalanine tRNA. II. Structural features and functional implications. J. Mol. Biol. 123:1978;631.
17. Huang S. G., Wang Y. X., Draper D. E. Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs. J. Mol. Biol. 258 (2):1996;308-321.
18. Jack A., Ladner J. E., Klug A. Crystallographic refinement of yeast phenylalanine tRNA at 2.5 Å resolution. J. Mol. Biol. 108:1976;619-649.
19. Kellogg G. W. Proton-detected hetero-TOCSY experiments with application in nucleic acids. J. Magn. Reson. 98:1992;176-182.
20. 1H resonances in RNA. J. Am. Chem. Soc. 114:1992;2727-2728.
21. Kim Y., Prestegard J. H. Measurement of vicinal couplings from cross peaks in COSY spectra. J. Magn. Reson. 84:1989;9-13.
22. Kuchino Y., Ihara M., Yabusaki Y., Nishimura S. Initiator tRNAs from archaebacteria show common unique sequence characteristics. Nature. 298 (5874):1982;684-685.
23. Labuda D., Porschke D. Magnesium ion inner sphere complex in the anticodon loop of phenylalanine transfer ribonucleic acid. Biochemistry. 21:1982;49-53.
24. Mandal N., Mangroo D., Dalluge J. J., McCloskey J. A., RajBhandary U. L. Role of the three consecutive G-C base pairs conserved in the anticodon stem of initiator tRNAs in initiation of protein synthesis in Escherichia coli. RNA. 2(5):1996;473-482.
25. Maniatis T., Fritsch E. F., Sambrook J. Molecular Cloning: A Laboratory Manual. 1982;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. Metin their aminoacylation by Escherichia coli methionyl-transfer RNA synthetase. J. Mol. Biol. 229 (1):1993;26-36.
27. Milligan J. F., Groebe D., Witherell G., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15 (21):1987;8783-8798.
28. Mirmira S. R., Tinoco I. NMR structure of a bacteriophage T4 RNA hairpin involved in translational repression. Biochemistry. 35 (24):1996a;7664-7674.
29. Mirmira S. R., Tinoco I. A quadruple mutant T4 RNA hairpin with the same structure as the wild-type translational repressor. Biochemistry. 35 (24):1996b;7675-7683.
30. Moore P. B. Determination of RNA conformation by nuclear magnetic resonance. Accts. Chem. Res. 28 (6):1995;251-256.
31. Parkinson G., Voitechovsky J., Clowney L., Brünger A. T., Berman H. New parameters for the refinement of nucleic acid-containing structures. Acta Crystallog. sect D. 52:1996;57-64.
32. Perona J. J., Rould M. A., Steitz T. A., Risler J.-L., Zelwer C., Brunie S. Structural similarities in glutaminyl- and methionyl-tRNA synthetases suggest a common overall orientation of tRNA binding. Proc. Natl Acad. Sci. USA. 88:1991;2903-2907.
33. Pley H. W., Flaherty K. M., Mckay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 372 (6501):1994;68-74.
34. Glnand ATP at 2.8Å resolution. Science. 246 (4934):1989;1135-1142.
35. Saenger W. Principles of Nucleic Acid Structure. 1983;Springer-Verlag, New York.
36. 31P NMR. Eur. J. Biochem. 115:1981;635-641.
37. Schevitz R. W., Podjarny A. D., Krishnamachari N., Hughes J. J., Sigler P. B. Crystal structure of a eukaryotic initiator tRNA. Nature. 278:1979;188-190.
38. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81 (7):1995;991-1002.
39. Seong B., RajBhandary U. Escherichia coli formylmethionine tRNA: mutations of GGG:CCC sequence conserved in anticodon stem of initiator tRNAs affect initiation of protein synthesis and conformation of anticodon loop. Proc. Natl Acad. Sci. USA. 84 (2):1987;334-338.
40. 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy. FEBS Letters. 208 (1):1986;94-98.
41. Sprinzl M., Steegborn C., Hubel G., Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids Res. 24 (1):1996;68-72.
42. Phe. J. Biomolec. Struct. Dynam. 7 (2):1989;235-256.
43. Szewczak A. A., White S. A., Gewirth D. T., Moore P. B. On the use of T7 RNA polymerase transcripts for physical investigation. Nucl. Acids Res. 18 (14):1990;4139-4142.
44. 1H correlation spectroscopy with spin-echo and gradient pulses. FEBS Letters. 327(3):1993a;261-264.
45. Szewczak A. A., Moore P. B., Chan Y. L., Wool I. G. The Conformation of the Sarcin/Ricin Loop from 28S Ribosomal RNA. Proc. Natl Acad. Sci. USA. 90 (20):1993b;9581-9585.
46. van den Hoogen, F. 1988, NMR studies concerning base-base interactions in oligonucleotides, Ph.D. thesis, Leiden.
47. Varani G., Tinoco I. RNA structure and NMR spectroscopy. Quart. Rev. Biophys. 24 (4):1991;479-532.
48. Wakao H., Romby P., Westhof E., Laalami S., Grunberg-Manago M., Ebel J.-P., Ehresmann C., Ehresmann B. The solution structure of the Escherichia coli initiator tRNA and its interactions with initiation factor 2 and the ribosomal 30S subunit. J. Biol. Chem. 264 (34):1989;20363-20371.
49. Westhof E., Sundaralingam M. Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA: temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles. Biochemistry. 25 (17):1986;4868-4878.
50. Westhof E., Dumas P., Moras D. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallog. sect. A. 44:1988;112.
51. f. Nature. 286:1980;346-351.
52. f. Nucl. Acids Res. 7 (6):1979;1457-1467.
53. Wrede P., Woo N. H., Rich A. Initiator tRNAs have a unique anticodon loop conformation. Proc. Natl Acad. Sci. USA. 76 (7):1979;3289-3293.
54. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;Wiley-Interscience, New York.
55. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244 (4900):1989;48-52.