title: The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis.
abstract: The genome of the human hepatitis delta virus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal structure shows the dangling nucleotides 5' of the cleavage site projecting away from the catalytic core. This 5'-sequence contains a clinically conserved U-1 that we find to be essential for fast cleavage, as the order of activity follows U-1 > C-1 > A-1 > G-1, with a >25-fold activity loss from U-1 to G-1. Terbium(III) footprinting detects conformations for the P1.1 stem, the cleavage site wobble pair and the A-minor motif of the catalytic trefoil turn that depend on the identity of the N-1 base. The most tightly folded catalytic core, resembling that of the reaction product, is found in the U-1 wild-type precursor. Molecular dynamics simulations demonstrate that a U-1 forms the most robust kink around the scissile phosphate, exposing it to the catalytic C75 in a previously unnoticed U-turn motif found also, for example, in the hammerhead ribozyme and tRNAs. Strikingly, we find that the common structural U-turn motif serves distinct functions in the HDV and hammerhead ribozymes.
authors.affiliation: Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109-1055, USA.
authors.forename: Jana
authors.initials: J
authors.lastname: Sefcikova
authors.forename: Maryna V
authors.initials: MV
authors.lastname: Krasovska
authors.forename: Jirí
authors.initials: J
authors.lastname: Sponer
authors.forename: Nils G
authors.initials: NG
authors.lastname: Walter
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D016679:Genome, Viral; D003698:Hepatitis Delta Virus / Q000201:enzymology* / Q000235:genetics; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D016337:RNA, Catalytic / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry*; D013725:Terbium / Q000737:chemistry; D014498:Uracil / Q000737:chemistry
chemical_list: D011687:Purines; D011743:Pyrimidines; D016337:RNA, Catalytic; D012367:RNA, Viral; D013725:Terbium; D014498:Uracil; D008274:Magnesium