title: The Novel Chemical Mechanism of the Twister Ribozyme.
abstract: We describe the multifactorial origins of catalysis by the twister ribozyme. We provide evidence that the adenine immediately 3' to the scissile phosphate (A1) acts as a general acid. Substitution of ring nitrogen atoms indicates that very unusually the N3 of A1 is the proton donor to the oxyanion leaving group. A1 is accommodated in a specific binding pocket that raises its pKa toward neutrality, juxtaposes its N3 with the O5' to be protonated, and helps create the in-line trajectory required for nucleophilic attack. A1 performs general acid catalysis while G33 acts as a general base. A 100-fold stereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stabilization of the transition state by the ribozyme, and functional group substitution at G33 indicates that its exocyclic N2 interacts directly with the scissile phosphate. A model of the ribozyme active site is proposed that accommodates these catalytic strategies.
authors.affiliation: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee , Dow Street, Dundee DD1 5EH, U.K.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Wilson
authors.affiliation: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee , Dow Street, Dundee DD1 5EH, U.K.
authors.forename: Yijin
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
authors.forename: Christof
authors.initials: C
authors.lastname: Domnick
authors.affiliation: Life and Medical Sciences Institute, University of Bonn , Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kath-Schorr
authors.affiliation: Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee , Dow Street, Dundee DD1 5EH, U.K.
authors.forename: David M J
authors.initials: DM
authors.lastname: Lilley
mesh_terms: D000225:Adenine / Q000737:chemistry; D002384:Catalysis; D020134:Catalytic Domain; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry*; D013237:Stereoisomerism
chemical_list: D016337:RNA, Catalytic; D000225:Adenine