NMR structure of the peptidyl transferase RNA inhibitor antibiotic amicetin

Christos Shammas, James A. Donarski, Vasudevan Ramesh

    Research output: Contribution to journalArticlepeer-review

    Abstract

    In this communication, we report the solution state NMR structure determination of the peptidyl transferase RNA inhibitor antibiotic amicetin. We have successfully characterised the NMR spectrum of amicetin using a range of homo- and heteronuclear NMR techniques. Using experimental ROE-based distance and 1H-1H scalar coupling derived dihedral angle geometrical constraints as input into the three-dimensional structure determination protocol, we have generated an energy-minimised average structure of the antibiotic. Amicetin adopts a stable well-folded conformation in solution, mediated by a network of hydrogen bonds caused by proton donor and acceptor groups at either end of the molecule. The NMR structure of amicetin shows that the cytosine moiety occupies the critical turn position within the fold, which may be structurally significant for interaction with peptidyl transferase ribosomal RNA. The structure is distinctly different from the published X-ray crystal structure of amicetin in which it adopts a linear, extended chain-like conformation with a number of intermolecular hydrogen bonds. In addition to structure, we have probed the dynamics of amicetin in solution and have observed retarded exchange of the amide proton involved in folding. We have also characterised the ionisation properties of amicetin by carrying out NMR pH titration and measuring the pKa of the primary and tertiary amino groups, 7.27 and 7.52, respectively, which are in agreement with the reported values in literature. Solving the NMR structure of amicetin provides a valuable opportunity to determine the structure of its complex with RNA in solution state. Copyright © 2006 John Wiley & Sons, Ltd.
    Original languageEnglish
    Pages (from-to)133-141
    Number of pages8
    JournalMagnetic Resonance in Chemistry
    Volume45
    Issue number2
    DOIs
    Publication statusPublished - Feb 2007

    Keywords

    • 23S ribosomal RNA
    • 13C
    • 15N
    • 1H
    • Amicetin antibiotic
    • Antibiotic resistance
    • NMR
    • Peptidyl transferase centre
    • RNA

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