A mini-twister variant and impact of residues/cations on the phosphodiester cleavage of this ribozyme class
| Autor: | Sara Flür, Marija Košutić, Ronald Micura, Christoph Kreutz, Jan Seikowski, Claudia Höbartner, Dinshaw J. Patel, Kathrin Breuker, Nikola Vušurović, Aiming Ren, Christoph H. Wunderlich, Elisabeth Mairhofer, Sandro Neuner |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Models
Molecular Stereochemistry Cleavage (embryo) 01 natural sciences Catalysis Article 03 medical and health sciences Cations RNA Catalytic Binding site 030304 developmental biology Manganese 0303 health sciences biology GIR1 branching ribozyme Chemistry 010405 organic chemistry Adenine Ribozyme General Chemistry Nuclear magnetic resonance spectroscopy General Medicine Organophosphates 0104 chemical sciences Phosphodiester bond biology.protein Biocatalysis Hairpin ribozyme VS ribozyme Cadmium |
| Zdroj: | Angewandte Chemie International Edition |
| Popis: | Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pKa value of 5.1 was determined for a (13) C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg(2+) ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn(2+) or Cd(2+) accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X-ray structure of a 2'-OCH3 -U5 modified twister ribozyme. |
| Databáze: | OpenAIRE |
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