title: Structure and dynamics of the deoxyguanosine-sensing riboswitch studied by NMR-spectroscopy.
abstract: The mfl-riboswitch regulates expression of ribonucleotide reductase subunit in Mesoplasma florum by binding to 2'-deoxyguanosine and thereby promoting transcription termination. We characterized the structure of the ligand-bound aptamer domain by NMR spectroscopy and compared the mfl-aptamer to the aptamer domain of the closely related purine-sensing riboswitches. We show that the mfl-aptamer accommodates the extra 2'-deoxyribose unit of the ligand by forming a more relaxed binding pocket than these found in the purine-sensing riboswitches. Tertiary structures of the xpt-aptamer bound to guanine and of the mfl-aptamer bound to 2'-deoxyguanosine exhibit very similar features, although the sequence of the mfl-aptamer contains several alterations compared to the purine-aptamer consensus sequence. These alterations include the truncation of a hairpin loop which is crucial for complex formation in all purine-sensing riboswitches characterized to date. We further defined structural features and ligand binding requirements of the free mfl-aptamer and found that the presence of Mg(2+) is not essential for complex formation, but facilitates ligand binding by promoting pre-organization of key structural motifs in the free aptamer.
authors.affiliation: Institute for Organic Chemistry and Chemical Biology, Max von Laue-Strasse 7, Frankfurt am Main, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Wacker
authors.forename: Janina
authors.initials: J
authors.lastname: Buck
authors.forename: Daniel
authors.initials: D
authors.lastname: Mathieu
authors.forename: Christian
authors.initials: C
authors.lastname: Richter
authors.forename: Jens
authors.initials: J
authors.lastname: Wöhnert
authors.forename: Harald
authors.initials: H
authors.lastname: Schwalbe
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D003849:Deoxyguanosine / Q000737:chemistry*; D045622:Entomoplasmataceae / Q000235:genetics; D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011522:Protons; D058928:Riboswitch; D013696:Temperature
chemical_list: D008024:Ligands; D011522:Protons; D058928:Riboswitch; D003849:Deoxyguanosine; D008274:Magnesium