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

NMR spectroscopy has revealed pH‐dependent structural changes in the highly conserved catalytic domain 5 of a bacterial group II intron. Two adenines with p K 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 p K a  value controls the conformational change between the two steps of splicing.