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. 1991 Oct 15;88(20):9272–9276. doi: 10.1073/pnas.88.20.9272

Four sites in the acceptor helix and one site in the variable pocket of tRNA(Ala) determine the molecule's acceptor identity.

W H McClain 1, K Foss 1, R A Jenkins 1, J Schneider 1
PMCID: PMC52696  PMID: 1924390

Abstract

The structural features that determine tRNA(Ala) acceptor identity have been studied with amber-suppressor tRNAs in Escherichia coli cells. Previous work established that a wobble pair composed of guanosine at position 3 and uridine at position 70 (G3-U70) in the acceptor helix of tRNA(Ala) is a determinant of the molecule's acceptor identity. We show that additional determinants are located at three other sites in the acceptor helix and at one site in the variable pocket of tRNA(Ala). These latter determinants are less important than G3.U70 since their individual alterations in mutants of tRNA(Ala) have smaller degrading effects on the functions of the molecules, and subsets of the determinants, when combined with G3.U70, are sufficient to switch the identities of several other tRNAs to that of tRNA(Ala). Other workers are using fragments of the tRNA(Ala) acceptor helix to study the molecule's acceptor identity. Our demonstration that the variable pocket contributes to tRNA(Ala) acceptor identity means that such fragments do not faithfully replicate the structure-function relationship of the cellular process.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Francklyn C., Schimmel P. Aminoacylation of RNA minihelices with alanine. Nature. 1989 Feb 2;337(6206):478–481. doi: 10.1038/337478a0. [DOI] [PubMed] [Google Scholar]
  2. Hou Y. M., Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature. 1988 May 12;333(6169):140–145. doi: 10.1038/333140a0. [DOI] [PubMed] [Google Scholar]
  3. Hou Y. M., Schimmel P. Modeling with in vitro kinetic parameters for the elaboration of transfer RNA identity in vivo. Biochemistry. 1989 Jun 13;28(12):4942–4947. doi: 10.1021/bi00438a005. [DOI] [PubMed] [Google Scholar]
  4. Knowlton R. G., Soll L., Yarus M. Dual specificity of su+ 7 tRNA. Evidence for translational discrimination. J Mol Biol. 1980 Jun 5;139(4):705–720. doi: 10.1016/0022-2836(80)90056-x. [DOI] [PubMed] [Google Scholar]
  5. Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414–4418. doi: 10.1073/pnas.72.11.4414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. McClain W. H., Chen Y. M., Foss K., Schneider J. Association of transfer RNA acceptor identity with a helical irregularity. Science. 1988 Dec 23;242(4886):1681–1684. doi: 10.1126/science.2462282. [DOI] [PubMed] [Google Scholar]
  7. McClain W. H., Foss K. Changing the acceptor identity of a transfer RNA by altering nucleotides in a "variable pocket". Science. 1988 Sep 30;241(4874):1804–1807. doi: 10.1126/science.2459773. [DOI] [PubMed] [Google Scholar]
  8. McClain W. H., Foss K. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end. Science. 1988 May 6;240(4853):793–796. doi: 10.1126/science.2452483. [DOI] [PubMed] [Google Scholar]
  9. McClain W. H., Foss K., Jenkins R. A., Schneider J. Nucleotides that determine Escherichia coli tRNA(Arg) and tRNA(Lys) acceptor identities revealed by analyses of mutant opal and amber suppressor tRNAs. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9260–9264. doi: 10.1073/pnas.87.23.9260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. McClain W. H., Foss K., Jenkins R. A., Schneider J. Rapid determination of nucleotides that define tRNA(Gly) acceptor identity. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6147–6151. doi: 10.1073/pnas.88.14.6147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. McClain W. H., Foss K. Nucleotides that contribute to the identity of Escherichia coli tRNA(Phe). J Mol Biol. 1988 Aug 20;202(4):697–709. doi: 10.1016/0022-2836(88)90551-7. [DOI] [PubMed] [Google Scholar]
  12. McClain W. H., Guerrier-Takada C., Altman S. Model substrates for an RNA enzyme. Science. 1987 Oct 23;238(4826):527–530. doi: 10.1126/science.2443980. [DOI] [PubMed] [Google Scholar]
  13. Musier-Forsyth K., Scaringe S., Usman N., Schimmel P. Enzymatic aminoacylation of single-stranded RNA with an RNA cofactor. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):209–213. doi: 10.1073/pnas.88.1.209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nicholas H. B., Chen Y. M., McClain W. H. Comparison of tRNA sequences. Comput Appl Biosci. 1987 Mar;3(1):53–53. doi: 10.1093/bioinformatics/3.1.53. [DOI] [PubMed] [Google Scholar]
  15. Normanly J., Kleina L. G., Masson J. M., Abelson J., Miller J. H. Construction of Escherichia coli amber suppressor tRNA genes. III. Determination of tRNA specificity. J Mol Biol. 1990 Jun 20;213(4):719–726. doi: 10.1016/S0022-2836(05)80258-X. [DOI] [PubMed] [Google Scholar]
  16. Normanly J., Ogden R. C., Horvath S. J., Abelson J. Changing the identity of a transfer RNA. Nature. 1986 May 15;321(6067):213–219. doi: 10.1038/321213a0. [DOI] [PubMed] [Google Scholar]
  17. Rich A., Schimmel P. R. Structural organization of complexes of transfer RNAs with aminoacyl transfer RNA synthetases. Nucleic Acids Res. 1977;4(5):1649–1665. doi: 10.1093/nar/4.5.1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rould M. A., Perona J. J., Söll D., Steitz T. A. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science. 1989 Dec 1;246(4934):1135–1142. doi: 10.1126/science.2479982. [DOI] [PubMed] [Google Scholar]
  19. Ruff M., Krishnaswamy S., Boeglin M., Poterszman A., Mitschler A., Podjarny A., Rees B., Thierry J. C., Moras D. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science. 1991 Jun 21;252(5013):1682–1689. doi: 10.1126/science.2047877. [DOI] [PubMed] [Google Scholar]
  20. Sampson J. R., Uhlenbeck O. C. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci U S A. 1988 Feb;85(4):1033–1037. doi: 10.1073/pnas.85.4.1033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Schulman L. H., Pelka H. The anticodon contains a major element of the identity of arginine transfer RNAs. Science. 1989 Dec 22;246(4937):1595–1597. doi: 10.1126/science.2688091. [DOI] [PubMed] [Google Scholar]
  22. Shi J. P., Francklyn C., Hill K., Schimmel P. A nucleotide that enhances the charging of RNA minihelix sequence variants with alanine. Biochemistry. 1990 Apr 17;29(15):3621–3626. doi: 10.1021/bi00467a005. [DOI] [PubMed] [Google Scholar]
  23. Shi J. P., Schimmel P. Aminoacylation of alanine minihelices. "Discriminator" base modulates transition state of single turnover reaction. J Biol Chem. 1991 Feb 15;266(5):2705–2708. [PubMed] [Google Scholar]
  24. Sprinzl M., Hartmann T., Weber J., Blank J., Zeidler R. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1989;17 (Suppl):r1–172. doi: 10.1093/nar/17.suppl.r1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Swanson R., Hoben P., Sumner-Smith M., Uemura H., Watson L., Söll D. Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science. 1988 Dec 16;242(4885):1548–1551. doi: 10.1126/science.3144042. [DOI] [PubMed] [Google Scholar]
  26. Yaniv M., Folk W. R., Berg P., Soll L. A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J Mol Biol. 1974 Jun 25;86(2):245–260. doi: 10.1016/0022-2836(74)90016-3. [DOI] [PubMed] [Google Scholar]
  27. Yarus M. Intrinsic precision of aminoacyl-tRNA synthesis enhanced through parallel systems of ligands. Nat New Biol. 1972 Sep 27;239(91):106–108. doi: 10.1038/newbio239106a0. [DOI] [PubMed] [Google Scholar]

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