Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping.
An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.
Campbell
Dean O
DO
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.
Legault
Pascale
P
D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D002247:Carbon Isotopes / Q000737:chemistry; D002413:Cations, Divalent / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D004722:Endoribonucleases / Q000737:chemistry* / Q000378:metabolism*; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism*; D008969:Molecular Sequence Data; D009491:Neurospora / Q000201:enzymology; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D012331:RNA, Fungal / Q000737:chemistry*; D000077278:RNA, Mitochondrial; D013379:Substrate Specificity; D013816:Thermodynamics
D002247:Carbon Isotopes; D002413:Cations, Divalent; D016337:RNA, Catalytic; D012331:RNA, Fungal; D000077278:RNA, Mitochondrial; D012313:RNA; D004722:Endoribonucleases; C438195:varkud satellite ribozyme; D008274:Magnesium