Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair - PubMed (original) (raw)
Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair
Penny J Beuning et al. RNA. 2002 May.
Abstract
Specific aminoacylation by aminoacyl-tRNA synthetases requires accurate recognition of cognate tRNA substrates. In the case of alanyl-tRNA synthetase (AlaRS), RNA duplexes that mimic the acceptor stem of the tRNA are efficient substrates for aminoacylation in vitro. It was previously shown that recognition by AlaRS is severely affected by a simple base pair transversion of the G2:C71 pair at the second position in the RNA helix. In this study, we determined the aminoacylation efficiencies of 50 variants of the tRNA(Ala) acceptor stem containing substitutions at the 2:71 position. We find that there is not a single functional group of the wild-type G2:C71 base pair that is critical for positive recognition. Rather, we observed that base-pair orientation plays an important role in recognition. In particular, pyrimidine2:purine71 combinations generally resulted in decreased aminoacylation efficiency compared to the corresponding purine:pyrimidine pair. Moreover, the activity of a pyrimidine:purine variant could be partially restored by the presence of a major groove amino group at position 71. In an attempt to understand this result further, dielectric continuum electrostatic calculations were carried out, in some cases with additional inclusion of van der Waals interaction energies, to determine interaction potentials of the wild-type duplexAla and seven 2:71 variants. This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency.
Similar articles
- Functional evidence for indirect recognition of G.U in tRNA(Ala) by alanyl-tRNA synthetase.
Gabriel K, Schneider J, McClain WH. Gabriel K, et al. Science. 1996 Jan 12;271(5246):195-7. doi: 10.1126/science.271.5246.195. Science. 1996. PMID: 8539617 - Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants.
Nagan MC, Beuning P, Musier-Forsyth K, Cramer CJ. Nagan MC, et al. Nucleic Acids Res. 2000 Jul 1;28(13):2527-34. doi: 10.1093/nar/28.13.2527. Nucleic Acids Res. 2000. PMID: 10871402 Free PMC article. - Evidence for class-specific discrimination of a semiconserved base pair by tRNA synthetases.
Liu H, Kessler J, Peterson R, Musier-Forsyth K. Liu H, et al. Biochemistry. 1995 Aug 1;34(30):9795-800. doi: 10.1021/bi00030a017. Biochemistry. 1995. PMID: 7542924 - The uniqueness of AlaRS and its human disease connections.
Zhang H, Yang XL, Sun L. Zhang H, et al. RNA Biol. 2021 Nov;18(11):1501-1511. doi: 10.1080/15476286.2020.1861803. Epub 2020 Dec 23. RNA Biol. 2021. PMID: 33317386 Free PMC article. Review. - A metal-binding motif implicated in RNA recognition by an aminoacyl-tRNA synthetase and by a retroviral gene product.
Miller WT, Schimmel P. Miller WT, et al. Mol Microbiol. 1992 May;6(10):1259-62. doi: 10.1111/j.1365-2958.1992.tb00846.x. Mol Microbiol. 1992. PMID: 1379318 Review.
Cited by
- The tRNA identity landscape for aminoacylation and beyond.
Giegé R, Eriani G. Giegé R, et al. Nucleic Acids Res. 2023 Feb 28;51(4):1528-1570. doi: 10.1093/nar/gkad007. Nucleic Acids Res. 2023. PMID: 36744444 Free PMC article. Review. - Principles of tRNAAla Selection by Alanyl-tRNA Synthetase Based on the Critical G3·U70 Base Pair.
Kumar A, Åqvist J, Satpati P. Kumar A, et al. ACS Omega. 2019 Sep 11;4(13):15539-15548. doi: 10.1021/acsomega.9b01827. eCollection 2019 Sep 24. ACS Omega. 2019. PMID: 31572855 Free PMC article. - The selective tRNA aminoacylation mechanism based on a single G•U pair.
Naganuma M, Sekine S, Chong YE, Guo M, Yang XL, Gamper H, Hou YM, Schimmel P, Yokoyama S. Naganuma M, et al. Nature. 2014 Jun 26;510(7506):507-11. doi: 10.1038/nature13440. Epub 2014 Jun 11. Nature. 2014. PMID: 24919148 Free PMC article.
References
- Nat Struct Biol. 1999 Nov;6(11):1055-61 - PubMed
- Proc Natl Acad Sci U S A. 1997 Sep 16;94(19):10150-4 - PubMed
- Nucleic Acids Res. 1982 Jul 24;10(14):4383-95 - PubMed
- Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373-7 - PubMed
- Science. 1988 May 6;240(4853):793-6 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases