Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases.

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dc.contributor.author Carter, Charles W en
dc.contributor.author Wills, Peter en
dc.date.accessioned 2019-03-10T21:06:08Z en
dc.date.issued 2018-10 en
dc.identifier.citation Nucleic acids research 46(18):9667-9683 Oct 2018 en
dc.identifier.issn 1362-4962 en
dc.identifier.uri http://hdl.handle.net/2292/45878 en
dc.description.abstract Class I and II aaRS recognition of opposite grooves was likely among the earliest determinants fixed in the tRNA acceptor stem bases. A new regression model identifies those determinants in bacterial tRNAs. Integral coefficients relate digital dependent to independent variables with perfect agreement between observed and calculated grooves for all twenty isoaccepting tRNAs. Recognition is mediated by the Discriminator base 73, the first base pair, and base 2 of the acceptor stem. Subsets of these coefficients also identically compute grooves recognized by smaller numbers of aaRS. Thus, the model is hierarchical, suggesting that new rules were added to pre-existing ones as new amino acids joined the coding alphabet. A thermodynamic rationale for the simplest model implies that Class-dependent aaRS secondary structures exploited differential tendencies of the acceptor stem to form the hairpin observed in Class I aaRS•tRNA complexes, enabling the earliest groove discrimination. Curiously, groove recognition also depends explicitly on the identity of base 2 in a manner consistent with the middle bases of the codon table, confirming a hidden ancestry of codon-anticodon pairing in the acceptor stem. That, and the lack of correlation with anticodon bases support prior productive coding interaction of tRNA minihelices with proto-mRNA. en
dc.format.medium Print en
dc.language eng en
dc.relation.ispartofseries Nucleic acids research en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.rights.uri https://creativecommons.org/licenses/by-nc/4.0/ en
dc.subject Amino Acyl-tRNA Synthetases en
dc.subject Amino Acids en
dc.subject Codon en
dc.subject RNA, Transfer en
dc.subject Anticodon en
dc.subject Crystallography, X-Ray en
dc.subject Binding Sites en
dc.subject Base Sequence en
dc.subject Nucleic Acid Conformation en
dc.subject Protein Binding en
dc.subject Substrate Specificity en
dc.subject Genetic Code en
dc.subject Models, Molecular en
dc.title Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases. en
dc.type Journal Article en
dc.identifier.doi 10.1093/nar/gky600 en
pubs.issue 18 en
pubs.begin-page 9667 en
pubs.volume 46 en
dc.rights.holder Copyright: The authors en
pubs.end-page 9683 en
pubs.publication-status Published en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Research Support, Non-U.S. Gov't en
pubs.subtype research-article en
pubs.subtype Journal Article en
pubs.subtype Research Support, N.I.H., Extramural en
pubs.elements-id 753052 en
pubs.org-id Science en
pubs.org-id Physics en
dc.identifier.eissn 1362-4962 en
pubs.record-created-at-source-date 2018-07-18 en
pubs.dimensions-id 30016476 en

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