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Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Publication date 2015
Author Pechlaner Maria, Donghi Daniela, Zelenay Veronika, Sigel Roland K. O.,
Project Metal Ion-Guided Assembly and Structures of the Catalytic Core of Ribozymes
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Original article (peer-reviewed)

Journal Angewandte Chemie
Volume (Issue) 127(33)
Page(s) 9823 - 9826
Title of proceedings Angewandte Chemie
DOI 10.1002/ange.v127.33


NMR spectroscopy has revealed pH-dependent structural changes in the highly conserved catalytic domain 5 of a bacterial group II intron. Two adenines with pKa 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 Mg2+ ion to its backbone. Hence, this here identified shifted pKa value controls the conformational change between the two steps of splicing.