Fig. 1.

Structure of the lariat-3′ exon (pre-2s) intermediate. a Pathway for group II intron splicing. The bulged adenosine residue attacks the 5′ splice site in the first step of splicing to form the lariat-3′ exon intermediate. The 3′-OH of the 5′ exon then attacks the 3′ splice site in the second step that results in exon ligation. The dashed rectangle indicates the state which is captured in the pre-2s structure discussed in the present study. b Secondary structure of the P.li.LSUI2 group II intron. Six domains emanate from a central wheel and are numbered I through VI. Different colors correspond to each of the domains. c The overall structure of the lariat-3′ exon intermediate. Domains are colored and numbered as shown in the secondary structure in Fig. 1b. Inset image shows the intact 3′ splice site positioned in close proximity to the catalytic two-metal-ion center (orange spheres) and the 3′-OH nucleophile of 5′ exon. This state directly precedes the second step of splicing with the 3′-OH poised to engage in nucleophilic attack upon the 3′ splice site. Domain VI (purple) and the IBS3-EBS3 interaction serve to properly position the 3′ splice site in the active site. These interactions result in the 3′ splice site backbone being distorted to present the scissile phosphate to the nucleophile in the second step of splicing