Structural principles of RNA catalysis in a 2'-5' lariat-forming ribozyme.

Teresa Carlomagno, Irene Amata, Luca Codutti, Melanie Falb, Jörg Fohrer, Pawel Masiewicz, Bernd Simon

Structural and Computational Biology Unit, EMBL, Meyerhofstraße 1, D-69117 Heidelberg, Germany. teresa.carlomagno@embl.de

Journal of the American Chemical Society 2013 Mar 20

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RNA-catalyzed lariat formation is present in both eukaryotes and prokaryotes. To date we lack structural insights into the catalytic mechanism of lariat-forming ribozymes. Here, we study an artificial 2'-5' AG1 lariat-forming ribozyme that shares the sequence specificity of lariat formation with the pre-mRNA splicing reaction. Using NMR, we solve the structure of the inactive state of the ribozyme in the absence of magnesium. The reaction center 5'-guanosine appears to be part of a helix with an exceptionally widened major groove, while the lariat-forming A48 is looped out at the apex of a pseudoknot. The model of the active state built by mutational analysis, molecular modeling, and small-angle X-ray scattering suggests that A48 is recognized by a conserved adenosine, juxtaposed to the 5'-guanosine in one base-pair step distance, while the G1-N7 coordinates a magnesium ion essential for the activation of the nucleophile. Our findings offer implications for lariat formation in RNA enzymes including the mechanism of the recognition of the branch-site adenosine.

Citation

Teresa Carlomagno, Irene Amata, Luca Codutti, Melanie Falb, Jörg Fohrer, Pawel Masiewicz, Bernd Simon. Structural principles of RNA catalysis in a 2'-5' lariat-forming ribozyme. Journal of the American Chemical Society. 2013 Mar 20;135(11):4403-11