title: Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron.
abstract: NMR spectroscopy has revealed pH-dependent structural changes in the highly conserved catalytic domain 5 of a bacterial group II intron. Two adenines with pK(a) values close to neutral pH were identified in the catalytic triad and the bulge. Protonation of the adenine opposite to the catalytic triad is stabilized within a G(syn)-AH(+) (anti) base pair. The pH-dependent anti-to-syn flipping of this G in the catalytic triad modulates the known interaction with the linker region between domains 2 and 3 (J23) and simultaneously the binding of the catalytic Mg(2+) ion to its backbone. Hence, this here identified shifted pK(a) value controls the conformational change between the two steps of splicing.
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna.
authors.forename: Maria
authors.initials: M
authors.lastname: Pechlaner
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna.
authors.forename: Daniela
authors.initials: D
authors.lastname: Donghi
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna.
authors.forename: Veronika
authors.initials: V
authors.lastname: Zelenay
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna. roland.sigel@chem.uzh.ch.
authors.forename: Roland K O
authors.initials: RK
authors.lastname: Sigel
mesh_terms: D000225:Adenine / Q000737:chemistry; D016948:Azotobacter vinelandii / Q000737:chemistry* / Q000201:enzymology*; D001483:Base Sequence; D020134:Catalytic Domain; D006863:Hydrogen-Ion Concentration; D007438:Introns; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011522:Protons; D012326:RNA Splicing; D016337:RNA, Catalytic / Q000737:chemistry*
chemical_list: D011522:Protons; D016337:RNA, Catalytic; D000225:Adenine
keywords: NMR spectroscopy; RNA; group II introns; ribozymes; structure-function relationships