The -1 residue and transition-state stabilization in RNase P RNA-mediated cleavage
(English)Manuscript (preprint) (Other academic)
We have used model substrates carrying modified nucleotides at the site immediately 5' of the scissile bond, the -1 position, to get a detailed understanding of RNase P RNA mediated cleavage. We show that the base at -1 is not essential but its presence and identity contributes to efficiency, correctness of cleavage and stabilization of the transitions state by 5.1 kcal. When U or C is present at -1, the carbonyl oxygen at position 2 contributes by 2.6 kcal of the 5.1 kcal and thus acts as a positive factor. For substrates with purines at -1, an exocyclic amine at position 2 has as a negative impact on cleavage at the canonical site. We will discuss our findings in view of a model where RNase P cleavage proceeds through a conformational-assisted mechanism that positions the metal-activated H2O for an in-line attack on the phosphorous atom that leads to breakage of the phosphodiester bond.
RNase P RNA, -1 residue
Biochemistry and Molecular Biology
Research subject Biology with specialization in Molecular Biology
IdentifiersURN: urn:nbn:se:uu:diva-159310OAI: oai:DiVA.org:uu-159310DiVA: diva2:444081