title: Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch.
abstract: The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of N10-formyl-tetrahydrofolate, a key component of one-carbon metabolism. Here, we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the base, ribose sugar, and phosphate moieties of the ligand. Unique to nucleobase recognition by RNAs, the Z base is inner-sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over chemically similar compounds such as ATP/AMP.
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA.
authors.forename: Jeremiah J
authors.initials: JJ
authors.lastname: Trausch
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA.
authors.forename: Joan G
authors.initials: JG
authors.lastname: Marcano-Velázquez
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA.
authors.forename: Michal M
authors.initials: MM
authors.lastname: Matyjasik
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA. Electronic address: robert.batey@colorado.edu.
authors.forename: Robert T
authors.initials: RT
authors.lastname: Batey
mesh_terms: D000620:Aminoimidazole Carboxamide / Q000737:chemistry; D052157:Aptamers, Nucleotide / Q000737:chemistry; D001483:Base Sequence; D018360:Crystallography, X-Ray; D008274:Magnesium; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry*; D012265:Ribonucleotides / Q000737:chemistry; D058928:Riboswitch; D013763:Tetrahydrofolates
chemical_list: D052157:Aptamers, Nucleotide; D012329:RNA, Bacterial; D012265:Ribonucleotides; D058928:Riboswitch; D013763:Tetrahydrofolates; D000620:Aminoimidazole Carboxamide; C030371:5,6,7,8-tetrahydrofolic acid; C098395:5-aminoimidazole-4-carboxamide-1-ribofuranosyl triphosphate; D008274:Magnesium