Abstract
Riboswitches are genetic regulatory elements found in the 5′ untranslated region of messenger RNA that act in the absence of protein cofactors1,2. They are broadly distributed across bacteria and account for the regulation of more than 2% of all genes in Bacillus subtilis, underscoring their importance in the control of cellular metabolism3. The 5′ untranslated region of many mRNAs of genes involved in purine metabolism and transport contain a guanine-responsive riboswitch that directly binds guanine, hypoxanthine or xanthine to terminate transcription3,4. Here we report the crystal structure at 1.95 Å resolution of the purine-binding domain of the guanine riboswitch from the xpt–pbuX operon of B. subtilis bound to hypoxanthine, a prevalent metabolite in the bacterial purine salvage pathway. This structure reveals a complex RNA fold involving several phylogenetically conserved nucleotides that create a binding pocket that almost completely envelops the ligand. Hypoxanthine functions to stabilize this structure and to promote the formation of a downstream transcriptional terminator element, thereby providing a mechanism for directly repressing gene expression in response to an increase in intracellular concentrations of metabolite.
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Acknowledgements
We thank S. Edwards for maintaining and managing the Biochemistry Division X-ray Crystallography facility; and T. Cech, A. Pardi, D. Wuttke, J. Kieft and R. Rambo for discussions and comments on the manuscript. This work was funded in part from a grant from the Research Corporation and the University of Colorado Butcher Biotechnology Initiative. S.D.G. was supported in part by a NIH predoctoral training grant.
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Batey, R., Gilbert, S. & Montange, R. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411–415 (2004). https://doi.org/10.1038/nature03037
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DOI: https://doi.org/10.1038/nature03037
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