An RNA conformational change between the two chemical steps of group II self-splicing

As for nuclear pre-mRNA introns, the splicing pathway of group II self-splicing introns proceeds by two successive transesterifications involving substrates with different chemical configurations. These two reactions have been proposed to be catalysed by two active sites, or alternatively by a single active site rearranging its components to accommodate the successive substrates. Here we show that the structural elements specific for the second splicing step are clustered in peripheral structures of domains II and VI. We show that these structures are not required for catalysis of the second chemical step but, instead, take part in a conformational change that occurs between the two catalytic steps. This rearrangement involves the formation of a tertiary contact between part of domain II and a GNRA tetraloop at the tip of domain VI. The fact that domain VI, which carries the branched structure, is involved in this structural rearrangement and the fact that modifications affecting the structures involved have almost no effect when splicing proceeds without branch formation, suggest that the conformational change results in the displacement of the first-step product out of the active site. These observations give further support to the existence of a single active site in group II introns.