Variation of the acceptor-anticodon interstem angles among mitochondrial and non-mitochondrial tRNAs

Journal of Molecular Biology

Volumn 343, Issue 2, 2004, Pages 313-325

  Frazer Abel, Ashley A ^a   Hagerman, Paul J ^b  

^a Ctr Cancer Causation Prev AMC C   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

birefringence; evolution; phylogeny; RNA structure; translation

Indexed keywords

TRANSFER RNA;

AMINO ACID SEQUENCE; ANTICODON; ARTICLE; BIREFRINGENCE; CONTROLLED STUDY; CRYSTALLOGRAPHY; MITOCHONDRION; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; STRUCTURE ANALYSIS;

METAZOA;

EID: 4644235825     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.07.087     Document Type: Article

References (52)

1. B. Hingerty, R.S. Brown, and A. Jack Further refinement of the structure of yeast tRNAPhe J. Mol. Biol. 124 1978 523 534
2. S.R. Holbrook, J.L. Sussman, R.W. Warrant, and S.H. Kim Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications J. Mol. Biol. 123 1978 631 660
3. J.L. Sussman, S.R. Holbrook, R.W. Warrant, G.M. Church, and S.H. Kim Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement J. Mol. Biol. 123 1978 607 630
4. Asp Nature 288 1980 669 674
5. fMet Nature 286 1980 346 351
6. M.A. Rould, J.J. Perona, D. Soll, and T.A. Steitz Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution Science 246 1989 1135 1142
7. R. Basavappa, and P.B. Sigler The 3 Å crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination EMBO J. 10 1991 3105 3111
8. M. Ruff, S. Krishnaswamy, M. Boeglin, A. Poterszman, A. Mitschler, and A. Podjarny Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp) Science 252 1991 1682 1689
9. S. Price, S. Cusack, F. Borel, C. Berthet-Colominas, and R. Leberman Crystallization of the seryl-tRNA synthetase:tRNAS(Ser) complex of Escherichia coli FEBS Letters 324 1993 167 170
10. V. Biou, A. Yaremchuk, M. Tukalo, and S. Cusack The 2.9 Å crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser) Science 263 1994 1404 1410
11. G. Eriani, and J. Gangloff Yeast aspartyl-tRNA synthetase residues interacting with tRNA(Asp) identity bases connectively contribute to tRNA(Asp) binding in the ground and transition-state complex and discriminate against non-cognate tRNAs J. Mol. Biol. 291 1999 761 773
12. H. Shi, and P.B. Moore The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited RNA 6 2000 1091 1105
13. A. Yaremchuk, S. Cusack, and M. Tukalo Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG) EMBO J. 19 2000 4745 4758
14. S. Sekine, O. Nureki, D.Y. Dubois, S. Bernier, R. Chenevert, and J. Lapointe ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding EMBO J. 22 2003 676 688
15. A.A. Frazer-Abel, and P.J. Hagerman Determination of the angle between the acceptor and anticodon stems of a truncated mitochondrial tRNA J. Mol. Biol. 285 1999 581 593
16. M. Sprinzl, C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg Compilation of tRNA sequences and sequences of tRNA genes Nucl. Acids Res. 26 1998 148 153
17. S. Anderson, M.H. de Bruijn, A.R. Coulson, I.C. Eperon, F. Sanger, and I.G. Young Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome J. Mol. Biol. 156 1982 683 717
18. R. Okimoto, J.L. Macfarlane, D.O. Clary, and D.R. Wolstenholme The mitochondrial genomes of two nematodes. Caenorhabditis elegans and Ascaris suum Genetics 130 1992 471 498
19. S. Steinberg, and R. Cedergren Structural compensation in atypical mitochondrial tRNAs Nature Struct. Biol. 1 1994 507 510
20. J.P. Cooper, and P.J. Hagerman Geometry of a branched DNA structure in solution Proc. Natl Acad. Sci. USA 86 1989 7336 7340
21. K.M. Amiri, and P.J. Hagerman Global conformation of a self-cleaving hammerhead RNA Biochemistry 33 1994 13172 13177
22. M. Zacharias, and P.J. Hagerman Bulge-induced bends in RNA: quantification by transient electric birefringence J. Mol. Biol. 247 1995 486 500
23. M.W. Friederich, F.U. Gast, E. Vacano, and P.J. Hagerman Determination of the angle between the anticodon and aminoacyl acceptor stems of yeast phenylalanyl tRNA in solution Proc. Natl Acad. Sci. USA 92 1995 4803 4807
24. Phe as a model system Proc. Natl Acad. Sci. USA 95 1998 3572 3577
25. M.W. Friederich, and P.J. Hagerman The angle between the anticodon and aminoacyl acceptor stems of yeast tRNA(Phe) is strongly modulated by magnesium ions Biochemistry 36 1997 6090 6099
26. M.A. Leehey, C.A. Squassoni, M.W. Friederich, J.B. Mills, and P.J. Hagerman A noncanonical tertiary conformation of a human mitochondrial transfer RNA Biochemistry 34 1995 16235 16239
27. E. Vacano, and P.J. Hagerman Analysis of birefringence decay profiles for nucleic acid helices possessing bends: the tau-ratio approach Biophys. J. 73 1997 306 317
28. P.J. Hagerman, and B.H. Zimm Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains Biopolymers 20 1981 1481 1502
29. 2+ changes with metabolic state in isolated heart mitochondria Biochemistry 29 1990 4121 4128
30. 2+ in isolated heart mitochondria using fluorescent probes Magnes. Trace Elem. 10 1991 151 164
31. 2+ in the matrix of heart mitochondria Arch. Biochem. Biophys. 332 1996 19 29
32. M. Valle, A. Zavialov, W. Li, S.M. Stagg, J. Sengupta, and R.C. Nielsen Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy Nature Struct. Biol. 10 2003 899 906 Oct 2019
33. Ile gene Hum. Mol. Genet. 7 1998 347 354
34. K.M. Harrington, I.A. Nazarenko, D.B. Dix, R.C. Thompson, and O.C. Uhlenbeck In vitro analysis of translational rate and accuracy with an unmodified tRNA Biochemistry 32 1993 7617 7622
35. I. Hayashi, T. Yokogawa, G. Kawai, T. Ueda, K. Nishikawa, and K. Watanabe Assignment of imino proton signals of G-C base pairs and magnesium ion binding: an NMR study of bovine mitochondrial tRNA(SerGCU) lacking the entire D arm J. Biochem. (Tokyo) 121 1997 1115 1122
36. J.A. Kowalak, J.J. Dalluge, J.A. McCloskey, and K.O. Stetter The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles Biochemistry 33 1994 7869 7876
37. M. Helm, H. Brule, F. Degoul, C. Cepanec, J.P. Leroux, R. Giege, and C. Florentz The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA Nucl. Acids Res. 26 1998 1636 1643
38. J.R. Sampson, and O.C. Uhlenbeck Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro Proc. Natl Acad. Sci. USA 85 1988 1033 1037
39. K.B. Hall, J.R. Sampson, O.C. Uhlenbeck, and A.G. Redfield Structure of an unmodified tRNA molecule Biochemistry 28 1989 5794 5801
40. V. Perret, A. Garcia, J. Puglisi, H. Grosjean, J.P. Ebel, C. Florentz, and R. Giege Conformation in solution of yeast tRNA(Asp) transcripts deprived of modified nucleotides Biochimie 72 1990 735 743
41. V. Dao, R. Guenther, A. Malkiewicz, B. Nawrot, E. Sochacka, and A. Kraszewski Ribosome binding of DNA analogs of tRNA requires base modifications and supports the "extended anticodon" Proc. Natl Acad. Sci. USA 91 1994 2125 2129
42. H. Grosjean, J. Edqvist, K.B. Straby, and R. Giege Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture J. Mol. Biol. 255 1996 67 85
43. Ser GCU derivatives in Escherichia coli Nucl. Acids Res. 25 1997 3503 3507
44. J.G. Arnez, and T.A. Steitz Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure Biochemistry 33 1994 7560 7567
45. Lys Biochemistry 38 1999 13338 13346
46. M.H. de Bruijn, P.H. Schreier, I.C. Eperon, B.G. Barrell, E.Y. Chen, and P.W. Armstrong A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem Nucl. Acids Res. 8 1980 5213 5222
47. P. Arcari, and G.G. Brownlee The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria Nucl. Acids Res. 8 1980 5207 5212
48. K.R. Hagerman, and P.J. Hagerman Helix rigidity of DNA: the meroduplex as an experimental paradigm J. Mol. Biol. 260 1996 207 223
49. S.M. Stagg, A.A. Frazer-Abel, P.J. Hagerman, and S.C. Harvey Structural studies of the tRNA domain of tmRNA J. Mol. Biol. 309 2001 727 735
50. S. Gutmann, P.W. Haebel, L. Metzinger, M. Sutter, B. Felden, and N. Ban Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB Nature 424 2003 699 703
51. Z. Shen, and P.J. Hagerman Conformation of the central, three-helix junction of the 5 S ribosomal RNA of Sulfolobus acidocaldarius J. Mol. Biol. 241 1994 415 430
52. W.H. Press, W.T. Vetterling, S.A. Teukolsky, and B.P. Flannery Numerical Recipes in Fortran: The Art of Scientific Computation 1992 Cambridge University Press Cambridge