DSSR-PyMOL cartoon-block schematics: PDB entry 2m58

PDB-id

2m58; DSSR-derived features in text and JSON formats

Class

RNA

Method

NMR

Summary

Structure of 2'-5' ag1 lariat forming ribozyme in its inactive state

Reference

Carlomagno T, Amata I, Codutti L, Falb M, Fohrer J, Masiewicz P, Simon B (2013): "Structural principles of RNA catalysis in a 2'-5' lariat-forming ribozyme." J.Am.Chem.Soc., 135, 4403-4411. doi: 10.1021/ja311868t.

Abstract

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.