Fig. 7.

Model for the second step of group II intron splicing. This model illustrates events occurring after the first step with the exit of the 2′–5′ lariat phosphodiester bond from the active site. a The catalytic triplex prepares for the second step with J2/3 residue A422 disengaging from A551. b U549 replaces the position previously occupied by A422. c EBS3-IBS3 then forms to anchor the 3′ end of the intron (not shown) and causes A586 of J5/6 to displace U549 at the base of DV to activate the catalytic triplex for the second step. This creates a binding pocket for A420 (γ), which enters its active conformation by stacking under A573 and allows subsequent pairing with the 3′ splice site. d The formation of γ–γ′ draws the 3′ splice site near the catalytic metal ions and promotes exon ligation. e The 3′-OH of the 5′ exon engages in nucleophilic attack at the 3′ splice site. f Intron is in the post-catalytic state with ligated exons bound in the active site before subsequent release