Sandbox Reserved 402: Difference between revisions

Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria.  These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.

Within the bacterium, Bacillus subtilus, the guanine riboswitch is found.  The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs.  When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism.  <ref>PMID: 17175531 </ref>