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

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.

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Figure 1: Sequence, binding affinity and structure of the sensing domain of the T. petrophila fluoride riboswitch in the ligand-bound state.
Figure 2: Details of long-range interactions within the structure of the T. petrophila fluoride riboswitch in the ligand-bound state.
Figure 3: Details of the fluoride ion binding site in the T. petrophila fluoride riboswitch in the ligand-bound state.

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Protein Data Bank

Data deposits

Atomic coordinates of the structure of the fluoride riboswitch in the bound state have been deposited in the RCSB Protein Data Bank under the accession code 4ENC for the native structure and 4ENB for the Ir(NH3)63+-containing structure of the fluoride-bound riboswitch, as well as 3VRS, 4ENA and 4EN5 for crystals of the complex soaked in Mn2+-, Cs+- and Tl+-containing solutions.

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Acknowledgements

We thank J. Goldberg and C. Lima for discussion and insights, Y. Liu for recording imino proton NMR spectra, and the personnel of the synchrotron beamlines 24-ID-C/E at the Advanced Photon Source, Argonne National Laboratory for their assistance. This research was funded by NIH grant GM34504 to D.J.P.

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A.R. generated and purified RNA constructs, grew diffraction quality crystals, collected synchrotron data sets and solved the structure of the fluoride riboswitch in the bound state under the supervision of D.J.P.; K.R.R. assisted in crystallographic aspects of the structure determination, including finding unique solutions to the positioning of the Mg and fluoride ions. D.J.P. wrote the manuscript with the assistance of the other authors, all of whom discussed the results and commented on the manuscript.

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Correspondence to Dinshaw J. Patel.

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The authors declare no competing financial interests.

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Ren, A., Rajashankar, K. & Patel, D. Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature 486, 85–89 (2012). https://doi.org/10.1038/nature11152

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