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Transition-state stabilization in Escherichia coli ribonuclease P RNA-mediated cleavage of model substrates
Department of Cell and Molecular Biology, Uppsala University.
Department of Cell and Molecular Biology, Uppsala University.
Department of Cell and Molecular Biology, Uppsala University.
Department of Cell and Molecular Biology, Uppsala University.ORCID iD: 0000-0002-0468-9664
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2014 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 1, 631-642 p.Article in journal (Refereed) Published
Abstract [en]

We have used model substrates carrying modified nucleotides at the site immediately 5' of the canonical RNase P cleavage site, the -1 position, to study Escherichia coli RNase P RNA-mediated cleavage. We show that the nucleobase at -1 is not essential but its presence and identity contribute to efficiency, fidelity of cleavage and stabilization of the transition state. When U or C is present at -1, the carbonyl oxygen at C2 on the nucleobase contributes to transition-state stabilization, and thus acts as a positive determinant. For substrates with purines at -1, an exocyclic amine at C2 on the nucleobase promotes cleavage at an alternative site and it has a negative impact on cleavage at the canonical site. We also provide new insights into the interaction between E. coli RNase P RNA and the -1 residue in the substrate. Our findings will be discussed using a model where bacterial RNase P cleavage proceeds through a conformational-assisted mechanism that positions the metal(II)-activated H2O for an in-line attack on the phosphorous atom that leads to breakage of the phosphodiester bond.

Place, publisher, year, edition, pages
2014. Vol. 42, no 1, 631-642 p.
National Category
Theoretical Chemistry
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URN: urn:nbn:se:hkr:diva-12005DOI: 10.1093/nar/gkt853ISI: 000331136000056PubMedID: 24097434OAI: oai:DiVA.org:hkr-12005DiVA: diva2:719825
Funder
Swedish Research Council
Available from: 2014-05-27 Created: 2014-05-27 Last updated: 2017-12-05Bibliographically approved

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Trobro, Stefan

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