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

NMR spectroscopy has revealed pH-dependent structural changes in the highly conserved catalytic domain5 of a bacterial groupII 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 domains2 and 3 (J23) and simultaneously the binding of the catalytic Mg2+ ion to its backbone. Hence, this here identified shifted pK(a)value controls the conformational change between the two steps of splicing.