Assignment of imino proton signals of G-C base pairs and magnesium ion binding: An NMR study of bovine mitochondrial tRNA(Ser)(GCU) lacking the entire D arm

Journal of Biochemistry

Volumn 121, Issue 6, 1997, Pages 1115-1122

  Hayashi, Ikuko ^a   Yokogawa, Takashi ^b,c   Kawai, Gota ^a   Ueda, Takuya ^a   Nishikawa, Kazuya ^b,c   Watanabe, Kimitsuna ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^c GIFU UNIVERSITY   (Japan)

Author keywords

15N labeling; 1H NMR; Assignment of imino proton signals; Magnesium effect; Mitochondrial tRNA

Indexed keywords

IMINO ACID; MAGNESIUM ION; MITOCHONDRIAL RNA; PROTON; RNA POLYMERASE; SERINE TRANSFER RNA;

ARTICLE; CATTLE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PROTON NUCLEAR MAGNETIC RESONANCE; RNA STRUCTURE;

BOS TAURUS; BOVINAE; MAMMALIA;

EID: 0030759652     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a021703     Document Type: Article

References (32)

1. Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J.H., Staden, R., and Young, I.G. (1982) Comparison of the Human and Bovine Mitochondrial Genomes. Mitochondrial Genes, pp. 5-43, Cold Spring Harbor Laboratory, New York
2. Roe, B.A., Wong, J.F.H., Chen, E.Y., Armstrong, P.W., Stankierwicz, A., Ma, D.P., and McDonough, J. (1982) Mammalian Mitochondrial tRNAs: A Modified Nucleotide 3′ to the Anticodon May Modulate Their Codon Response. Mitochondrial Genes, pp. 45-49, Cold Spring Harbor Laboratory, New York
3. Arcari, P. and Brownlee, G.G. (1980) The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria. Nucleic Acids Res. 8, 5207-5212
4. de Bruijn, M.H., Schreier, P.H., Eperon, I.C., Barrell, B.G., Chen, E.Y., Armstrong, P.W., Wong, J.F., and Roe, B.A. (1980) A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem. Nucleic Acids Res. 8, 5213-5222
5. Ueda, T., Ohta, T., and Watanabe, K. (1985) Large-scale isolation and some properties of AGY-specific serine tRNA from bovine heart mitochondria. J. Biochem. 98, 1275-1284
6. Ser to common three-dimensional constrains. J. Mol. Biol. 236, 982-989
7. SerUGA: chemical modification and computer modeling. Nucleic Acids Res. 22, 5328-5384
8. de Bruijn, M.H. and Klug, A. (1983) A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem. EMBO J. 2, 1309-1321
9. Wolstenholme, D.R. (1992) Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141, 173-216
10. Hare, D.R., Ribeiro, N.S., Wemmer, D.E., and Reid, B.R. (1985) Complete assignment of the imino protons of Escherichia coli valine transfer RNA: two-dimensional NMR studies in water. Biochemistry 24, 4300-4306
11. Asp. Nucleic Acids Res. 9, 7073-7083
12. Phe. I. Assignments of the iminoproton resonances of the acceptor and D stem by means of nuclear Overhauser effect experiments at 500 MHz. Nucleic Acids Res. 10, 6981-7000
13. Phe. II. Assignments of the iminoproton resonances of the anticodon and T stem by means of nuclear Overhauser effect experiments at 500 MHz. Nucleic Acids Res. 11, 4483-4499
14. Phe. III. Assignments of the iminoproton resonances of the tertiary structure by means of nuclear Overhauser effect experiments at 500 MHz. Nucleic Acids Res. 11, 4501-4520
15. Hall, K.B., Sampson, J.R., Uhlenbeck, O.C., and Redfield, A.G. (1989) Structure of an unmodified tRNA molecule. Biochemistry 28, 5794-5801
16. Ser(AGY) is a main recognition site for homologous seryl-tRNA synthetase. Nucleic Acids Res. 20, 2217-2222
17. Sampson, J.R. and Uhlenbeck, O.C. (1988) Biochemical and physical characterization of an unmodified yeast phenylalanine transfer tRNA transcribed in vitro. Proc. Natl. Acad. Sci. USA 85, 1033-1037
18. Plateau, P. and Gueron, M. (1982) Exchangeable proton NMR without base line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104, 7310-7311
19. 1H spin-spin coupling constants in proteins. Biochem. Biophys. Res. Commun. 113, 967-974
20. Macura, S. and Ernst, R.R. (1980) Elucidation of cross relaxation in liquids by two-dimensional NMR spectroscopy. Mol. Phys. 41, 95-117
21. Bax, A., Griffey, R.H., and Hawkins, B.L. (1983) Correlation of proton and nitrogen-15 chemical shifts by multiple quantum NMR. J. Magn. Reson. 55, 301-315
22. Shaka, A.J., Barker, P.B., and Freeman, R. (1985) Computer-optimized decoupling scheme for wideband applications and low-level operation. J. Magn. Reson. 64, 547-552
23. Kearns, D.R., Patel, D., Shulman, R.G., and Yamane, T. (1971) High resolution nuclear magnetic resonance study of base pairing in four purified transfer RNA molecules. J. Mol. Biol. 61, 265-270
24. Shen, L.X. and Tinoco, I. (1995) The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus. J. Mol. Biol. 247, 963-978
25. Lapham, J. and Crothers, D.M. (1996) RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA 2, 289-296
26. Asp1. J. Biochem. 117, 515-520
27. Hare, D.R. and Reid, B.R. (1982) Nuclear Overhauser assignment of the imino protons of the acceptor helix and the ribothymidine helix in the nuclear magnetic resonance spectrum of Escherichia coli isoleucine transfer ribonucleic acid: evidence for costacked helices in solution. Biochemistry 21, 5129-5135
28. Gly3. Eur. J Biochem. 155, 57-68
29. Val: An imino proton NMR investigation. Biochemistry 33, 8905-8911
30. Jack, A., Ladner, J.E., Rhodes, D., Brown, R.S., and Klug, A. (1977) A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J. Mol. Biol. 111, 315-328
31. Phe. Nucleic Acids Res. 4, 2811-2820
32. 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. USA 75, 64-68