An engineered class I transfer RNA with a class II tertiary fold

RNA

Volumn 5, Issue 3, 1999, Pages 434-445

  Nissan, T Amar ^a   Oliphant, Bryant ^a   Perona, John J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Aminoacyl tRNA synthetases; Extra arm; RNA engineering; RNA structure; tRNA identity

Indexed keywords

GLUTAMINE TRANSFER RNA LIGASE; TRANSFER RNA;

ARTICLE; ENZYME PURIFICATION; ESCHERICHIA COLI; GENETIC ENGINEERING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; RNA ANALYSIS; STRUCTURE ANALYSIS; THERMUS THERMOPHILUS;

ACYLATION; BASE SEQUENCE; ESCHERICHIA COLI; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; RNA, BACTERIAL; RNA, TRANSFER, GLN; RNA, TRANSFER, SER; SEQUENCE ALIGNMENT; TEMPERATURE; THERMUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA; THERMUS THERMOPHILUS;

EID: 0033015536     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299981827     Document Type: Article

References (56)

1. Ser: Sequence elements necessary for serylation and maturation of a tRNA with a long extra arm. EMBO J 12:3333-3338.
2. Gln complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure. Biochemistry 32:7560-7567.
3. Ser by its characteristic tertiary structure. J Mol Biol 236:738-748.
4. Basavappa R, Sigler PB. 1991. The 3 Å crystal structure of yeast initiator tRNA: Functional implications in initiator/elongator discrimination. EMBO J 10:3105-3111.
5. Ser. Science 263:1404-1410.
6. Cole PE, Yang SK, Crothers DM. 1972. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry 11:4358-4368.
7. Crothers DM, Cole PE, Hilbers CW, Shulman RG. 1974. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol 87:63-88.
8. Pro anticodon recognition by Thermus thermophilus prolyl-tRNA synthetase. Structure 6:101-108.
9. Ser (yeast). Eur J Biochem 70:25-31.
10. Frugier M, Söll D, Giege R, Florentz C. 1994. Identity switches between tRNAs aminoacylated by class I glutaminyl-and class II aspartyl-tRNA synthetases. Biochemistry 33:9912-9921.
11. Giege R, Puglisi JD, Florentz C. 1993. tRNA structure and aminoacylation efficiency. Prog Nucleic Acids Res Mol Biol 45:129-206.
12. Phe. Structure 5:59-68.
13. Grodberg J, Dunn JJ. 1988. OmpT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. J Bacteriol 170:1245-1258.
14. Gln by glutaminyl-tRNA synthetase: A complete identity set. EMBO J 11:4159-4165.
15. Hoben P, Royal N, Cheung A, Yamao F, Biemann K, Söll D. 1982. Escherichia coli glutaminyl-tRNA synthetase. J Biol Chem 257:11644-11650.
16. Hoben P, Söll D. 1985. Glutaminyl-tRNA synthetase of Escherichia coli. Methods Enzymol 113:55-59.
17. Hong K-W, Ibba M, Weygand-Durasevic I, Rogers MJ, Thomann H-U, Söll D. 1996. Transfer RNA-dependent cognate amino acid recognition by an aminoacyl-tRNA synthetase. EMBO J 15:1983-1991.
18. Hou Y-M, Westhof E, Giege R. 1993. An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA. Proc Natl Acad Sci USA 90:6776-6780.
19. Ibba M, Hong K-W, Sherman JM, Sever S, Söll D. 1996. Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc Natl Acad Sci USA 93:6953-6958.
20. Inokuchi H, Hoben P, Yamao F, Ozeki H, Söll D. 1984. Transfer RNA mischarging mediated by a mutant Escherichia coli glutaminyl-tRNA synthetase. Proc Natl Acad Sci USA 81:5076-5080.
21. Ioudovitch A, Steinberg SV. 1998. Modeling the tertiary interactions in the eukaryotic selenocysteine tRNA. RNA 4:365-373.
22. Gln are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature 352:258-260.
23. Kim SH, Suddath FL, Quigley GJ, McPherson A, Sussman JL, Wang AHJ, Seeman NC, Rich A. 1974. Three dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185:435-440.
24. Kitabatake M, Ibba M, Hong K-W, Soll D, Inokuchi H. 1996. Genetic analysis of functional connectivity between substrate recognition domains of Escherichia coli glutaminyl-tRNA synthetase. Mol Gen Genet 252:717-722.
25. McClain WH, Foss K. 1988a. Changing the acceptor identity of a transfer RNA by altering nucleotides in a "variable pocket". Science 241:1804-1807.
26. Phe. J Mol Biol 202:697-709.
27. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 21:8783-8798.
28. Asp. Nature 288:669-674.
29. Normanly J, Ollick T, Abelson J. 1992. Eight base changes are sufficient to convert a leucine-inserting tRNA into a serine-inserting tRNA. Proc Natl Acad Sci USA 89:5680-5684.
30. Nureki O, Niimi T, Muramatsu T, Kanno H, Kohno T, Florentz C, Giege R, Yokoyama S. 1994. Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli. J Mol Biol 236:710-724.
31. Gln complex. J Mol Biol 202:121-126.
32. Perret V, Florentz C, Puglisi JD, Giege R. 1992. Effect of conformational features on the aminoacylation of tRNAs and consequences on the permutation of tRNA specificities. J Mol Biol 226:323-333.
33. Phe variants from a randomized library using two proteins. EMBO J 12:2959-2967.
34. Peterson ET, Uhlenbeck OC. 1992. Determination of recognition nucleotides for Escherichia coli phenylalanyl-tRNA synthetase. Biochemistry 31:10380-10389.
35. Pleiss JA, Derrick ML, Uhlenbeck OC. 1998. T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates. RNA 4:1313-1317.
36. Privalov PL, Filimonov VV. 1978. Thermodynamic analysis of transfer RNA unfolding. J Mol Biol 122:447-464.
37. Puglisi JD, Putz J, Florentz C, Giege R. 1993. Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase. Nucleic Acids Res 21:41-49.
38. Robertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BFC, Klug A. 1974. Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature 250:546-551.
39. Rogers KC, Söll D. 1993. Discrimination among tRNAs intermediate in glutamate and glutamine acceptor identity. Biochemistry 32: 14210-14219.
40. Rogers MJ, Adachi T, Inokuchi H, Soll D. 1994. Functional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase. Proc Natl Acad Sci USA 91:291-295.
41. Rogers MJ, Söll D. 1988. Discrimination between glutaminyl-tRNA synthetase and seryl-tRNA synthetase involves nucleotides in the acceptor helix of tRNA. Proc Natl Acad Sci USA 85:6627-6631.
42. Gln and ATP at 2.8 Å resolution. Science 246:1135-1142.
43. Rould MA, Perona JJ, Steitz TA. 1991. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature 352:213-218.
44. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
45. Phe required for the specific recognition by its cognate synthetase. Science 243:1363-1366.
46. Sampson JR, Uhlenbeck OC. 1988. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci USA 85:1033-1037.
47. Glu from Escherichia coli. J Mol Biol 256:685-700.
48. Sherman JM, Söll D. 1996. Aminoacyl-tRNA synthetases optimize both cognate tRNA recognition and discrimination against noncognate tRNAs. Biochemistry 35:601-607.
49. Sherman JM, Thomann H-U, Söll D. 1996. Functional connectivity between tRNA binding domains in glutaminyl-tRNA synthetase. J Mol Biol 256:818-828.
50. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26:148-153.
51. Steinberg S, Leclerc F, Cedergren R. 1997. Structural rules and conformational compensations in the tRNA L-form. J Mol Biol 266:269-282.
52. Swanson R, Hoben P, Sumner-Smith M, Uemura H, Watson L, Söll D. 1988. Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science 242:1548-1551.
53. Weygand-Durasevic I, Schwob E, Söll D. 1993. Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA. Proc Natl Acad Sci USA 90:2010-2014.
54. fMet. Nature 286:346-351.
55. Ser function as major identity elements for serylation in an orientation-dependent, but not sequence specific manner. Nucleic Acids Res 21:5589-5594.
56. Yang SK, Crothers DM. 1972. Conformational changes of transfer ribonucleic acid. Comparison of the early melting transition of two tyrosine-specific transfer ribonucleic acids. Biochemistry 11:4375-4381.