Interaction of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) with the group I intron P4-P6 domain. Thermodynamic analysis and the role of metal ions

Journal of Molecular Biology
M G CapraraA M Lambowitz

Abstract

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the catalytically active structure of the intron's catalytic core. Previous studies suggested a model in which the protein binds first to the intron's P4-P6 domain, and then makes additional contacts with the P3-P9 domain to stabilize the two domains in the correct relative orientation to form the intron's active site. Here, we analyzed the interaction of CYT-18 with a small RNA (P4-P6 RNA) corresponding to the isolated P4-P6 domain of the N. crassa mitochondrial large subunit ribosomal RNA intron. RNA footprinting and modification-interference experiments showed that CYT-18 binds to this small RNA around the junction of the P4-P6 stacked helices on the side opposite the active-site cleft, as it does to the P4-P6 domain in the intact intron. The binding is inhibited by chemical modifications that disrupt base-pairing in P4, P6, and P6a, indicating that a partially folded structure of the P4-P6 domain is required. The temperature-dependence of binding indicates that the interaction is driven by a favorable enthalpy change, but is accompanied by an unfavorable entropy change. The latter ...Continue Reading

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Citations

May 7, 2002·RNA·Amanda SolemMark G Caprara
Oct 20, 2007·Nature Protocols·Pilar TijerinaRick Russell
Jul 23, 2009·The Journal of Biological Chemistry·Michal T BonieckiSusan A Martinis
Apr 26, 2005·Nucleic Acids Research·Rupert GrossbergerRenée Schroeder
Feb 3, 2007·Nucleic Acids Research·Oliver MayerRenée Schroeder
Sep 5, 2002·Genes & Development·Christina WaldsichRenée Schroeder
Feb 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Christopher A MyersAlan M Lambowitz
Aug 16, 2019·Wiley Interdisciplinary Reviews. RNA·Ofri LeviYoav Arava
Jun 12, 2001·Journal of Molecular Biology·A E WebbK M Weeks

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