Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch

Aiming Ren, Kanagalaghatta R. Rajashankar and Dinshaw J. Patel ()
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Aiming Ren: Structural Biology Program, Memorial Sloan-Kettering Center
Kanagalaghatta R. Rajashankar: NE-CAT, Advanced Photon Source, Argonne National Laboratory, Chicago, Illinois 60439, USA
Dinshaw J. Patel: Structural Biology Program, Memorial Sloan-Kettering Center

Nature, 2012, vol. 486, issue 7401, 85-89

Abstract: Abstract Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure–function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson–Crick and Hoogsteen A•U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg2+ ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.

Date: 2012
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DOI: 10.1038/nature11152

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