1ow9

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NMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site

Overview

Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme, involves a structural change in the stem-loop I substrate from an inactive, to an active conformation. We have determined the NMR solution structure, of a mutant stem-loop I that mimics the active conformation of the, cleavage site internal loop. This structure shares many similarities, but, also significant differences, with the previously determined structures of, the inactive internal loop. The active internal loop displays different, base-pairing interactions and forms a novel RNA fold composed exclusively, of sheared G-A base pairs. From chemical-shift mapping we identified two, Mg2+ binding sites in the active internal loop. One of the Mg2+ binding, sites forms in the active but not the inactive conformation of the, internal loop and is likely important for catalysis. Using the structure, comparison program mc-search, we identified the active internal loop fold, in other RNA structures. In Thermus thermophilus 16S rRNA, this RNA fold, is directly involved in a long-range tertiary interaction. An analogous, tertiary interaction may form between the active internal loop of the, substrate and the catalytic domain of the VS ribozyme. The combination of, NMR and bioinformatic approaches presented here has identified a novel RNA, fold and provides insights into the structural basis of catalytic function, in the Neurospora VS ribozyme.

About this Structure

1OW9 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site., Hoffmann B, Mitchell GT, Gendron P, Major F, Andersen AA, Collins RA, Legault P, Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7003-8. Epub 2003 Jun 2. PMID:12782785

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