Transition-state stabilization in Escherichia coli ribonuclease P RNA-mediated cleavage of model substrates

Shiying Wu, Yu Chen, Guanzhong Mao, Stefan Trobro, Marek Kwiatkowski, Leif A. Kirsebom

Forskningsoutput: TidskriftsbidragArtikelPeer review

5 Citeringar (Scopus)

Sammanfattning

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.

OriginalspråkEngelska
Sidor (från-till)631-642
Antal sidor11
TidskriftNucleic Acids Research
Volym42
Utgåva1
DOI
StatusPublicerad - 2014
Externt publiceradJa

Nationell ämneskategori

  • Teoretisk kemi (10407)

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