Group II intron splicing cycle. Upon transcription, group II introns fold into an active structure, which catalyzes the first splicing step by hydrolysis (A1) or transesterification (branching, A2). Successively, the intron rearranges its active site conformation (B) to recruit the 3′-splice junction into the active site. The 3′-splice junction is then subject to nucleophilic attack by the free 5′-exon (second splicing step, C) to form ligated exons and a ligand-free intron (D). The latter is still a highly active ribozyme. In vitro it tends to rehydrolyze ligated exons by SER, following a reaction mechanism that shares the same stereochemistry as the first step of reverse splicing, by which the intron retrotransposes into DNA or RNA targets (E). In the top right corner of each panel is a schematic of the reaction (5′-exon in blue, intron in green, 3′-exon in brown, nucleophilic water molecules in cyan spheres, branch site nucleophile in red spheres, nucleophilic attacks as black arrows). In the middle of each panel are snapshots of the active sites from representative structures or models (same color code, ions M1-M2 as yellow and K1-K2 as violet spheres, conformational changes as grey dotted arrows). At the bottom of each panel are the Protein Data Bank identifiers of all structures corresponding to each stage of the cycle, or the phrase ‘This is a model’ for those states that were not obtained crystallographically but by modeling. SER: spliced-exon reopening.