title: Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site.
abstract: The cleavage site of the Neurospora VS RNA ribozyme is located in a separate hairpin domain containing a hexanucleotide internal loop with an A-C mismatch and two adjacent G-A mismatches. The solution structure of the internal loop and helix la of the ribozyme substrate hairpin has been determined by nuclear magnetic resonance (NMR) spectroscopy. The 2 nt in the internal loop, flanking the cleavage site, a guanine and adenine, are involved in two sheared G.A base pairs similar to the magnesium ion-binding site of the hammerhead ribozyme. Adjacent to the tandem G.A base pairs, the adenine and cytidine, which are important for cleavage, form a noncanonical wobble A+-C base pair. The dynamic properties of the internal loop and details of the high-resolution structure support the view that the hairpin structure represents a ground state, which has to undergo a conformational change prior to cleavage. Results of chemical modification and mutagenesis data of the Neurospora VS RNA ribozyme can be explained in context with the present three-dimensional structure.
authors.affiliation: NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, The Netherlands.
authors.forename: P J
authors.initials: PJ
authors.lastname: Michiels
authors.forename: C H
authors.initials: CH
authors.lastname: Schouten
authors.forename: C W
authors.initials: CW
authors.lastname: Hilbers
authors.forename: H A
authors.initials: HA
authors.lastname: Heus
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D006868:Hydrolysis; D008274:Magnesium / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009492:Neurospora crassa / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry*; D012331:RNA, Fungal / Q000737:chemistry*; D019244:RNA, Satellite / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D016337:RNA, Catalytic; D012331:RNA, Fungal; D019244:RNA, Satellite; D008274:Magnesium