Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine

Riboswitches are genetic regulatory elements found in the 5′ untranslated region of messenger RNA that act in the absence of protein cofactors 1 , 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 metabolism 3 . 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 transcription 3 , 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.