title: Ribozyme catalysis from the major groove of group II intron domain 5.
abstract: The most highly conserved nucleotides in D5, an essential active site component of group II introns, consist of an AGC triad, of which the G is invariant. To understand how this G participates in catalysis, the mechanistic contribution of its functional groups was examined. We observed that the exocyclic amine of G participates in ground state interactions that stabilize D5 binding from the minor groove. In contrast, each major groove heteroatom of the critical G (specifically N7 or O6) is essential for chemistry. Thus, major groove atoms in an RNA helix can participate in catalysis, despite their presumed inaccessibility. N7 or O6 of the critical G could engage in critical tertiary interactions with the rest of the intron or they could, together with phosphate oxygens, serve as a binding site for catalytic metal ions.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, College of Physicians and Surgeons, New York, New York 10032, USA.
authors.forename: B B
authors.initials: BB
authors.lastname: Konforti
authors.forename: D L
authors.initials: DL
authors.lastname: Abramovitz
authors.forename: C M
authors.initials: CM
authors.lastname: Duarte
authors.forename: A
authors.initials: A
authors.lastname: Karpeisky
authors.forename: L
authors.initials: L
authors.lastname: Beigelman
authors.forename: A M
authors.initials: AM
authors.lastname: Pyle
mesh_terms: D001665:Binding Sites / Q000502:physiology; D007438:Introns / Q000502:physiology*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D017434:Protein Structure, Tertiary; D012326:RNA Splicing / Q000235:genetics*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D009711:Nucleotides; D016337:RNA, Catalytic