The global structure of the VS ribozyme

Daniel A. Lafontaine, David G. Norman, David M. J. Lilley

    Research output: Contribution to journalArticlepeer-review

    74 Citations (Scopus)

    Abstract

    The VS ribozyme comprises five helical segments (II–VI) in a formal H shape, organized by two three-way junctions. It interacts with its stem–loop substrate (I) by tertiary interactions. We have determined the global shape of the 3–4–5 junction (relating helices III–V) by electrophoresis and FRET. Estimation of the dihedral angle between helices II and V electrophoretically has allowed us to build a model for the global structure of the complete ribozyme. We propose that the substrate is docked into a cleft between helices II and VI, with its loop making a tertiary interaction with that of helix V. This is consistent with the dependence of activity on the length of helix III. The scissile phosphate is well placed to interact with the probable active site of the ribozyme, the loop containing A730
    Original languageEnglish
    Pages (from-to)2461-2471
    Number of pages11
    JournalEMBO Journal
    Volume21
    Issue number10
    DOIs
    Publication statusPublished - 2002

    Keywords

    • FRET
    • Metal ions
    • RNA catalysis
    • RNA folding

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