A guanine nucleobase important for catalysis by the VS ribozyme

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    Abstract

    A guanine (G638) within the substrate loop of the VS ribozyme plays a critical role in the cleavage reaction. Replacement by any other nucleotide results in severe impairment of cleavage, yet folding of the substrate is not perturbed, and the variant substrates bind the ribozyme with similar affinity, acting as competitive inhibitors. Functional group substitution shows that the imino proton on the N1 is critical, suggesting a possible role in general acid-base catalysis, and this in accord with the pH dependence of the reaction rate for the natural and modified substrates. We propose a chemical mechanism for the ribozyme that involves general acid-base catalysis by the combination of the nucleobases of guanine 638 and adenine 756. This is closely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for the two ribozymes appear topologically equivalent. This has probably arisen by convergent evolution.
    Original languageEnglish
    Pages (from-to)2489-2500
    Number of pages12
    JournalEMBO Journal
    Volume26
    Issue number10
    DOIs
    Publication statusPublished - 16 May 2007

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    Keywords

    • Base Pairing
    • Binding Sites
    • Catalysis
    • Endoribonucleases
    • Guanine
    • Hydrogen-Ion Concentration
    • Kinetics
    • Models, Chemical
    • Molecular Sequence Data
    • Nucleic Acid Conformation
    • RNA, Catalytic
    • Substrate Specificity

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