Structural basis for the second step of group II intron splicing

Russell T Chan,Navtej Toor,Jessica K Peters,Aaron R Robart,Kanagalaghatta R Rajashankar,Timothy Wiryaman

doi:10.1038/s41467-018-06678-0

Abstract

The group II intron and the spliceosome share a common active site architecture and are thought to be evolutionarily related. Here we report the 3.7 Å crystal structure of a eukaryotic group II intron in the lariat-3′ exon form, immediately preceding the second step of splicing, analogous to the spliceosomal P complex. This structure reveals the location of the intact 3′ splice site within the catalytic core of the group II intron. The 3′-OH of the 5′ exon is positioned in close proximity to the 3′ splice site for nucleophilic attack and exon ligation. The active site undergoes conformational rearrangements with the catalytic triplex having different configurations before and after the second step of splicing. We describe a complete model for the second step of group II intron splicing that incorporates a dynamic catalytic triplex being responsible for creating the binding pocket for 3′ splice site capture.

Highlights

The group II intron and the spliceosome share a common active site architecture and are thought to be evolutionarily related
Structures of the spliceosome were determined at high-resolution using cryo-electron microscopy and revealed that its active site architecture is highly conserved with that of group II introns, with both utilizing a twoa
This crystal structure (Rfree = 25.3%; Rwork = 21.7%) represents the catalytic state of the group II intron immediately preceding the second step of splicing (Figure 1c and Table 1)

Summary

Introduction

The group II intron and the spliceosome share a common active site architecture and are thought to be evolutionarily related. The spliceosomal U2-U6 snRNA pairing is analogous to domain V in group II introns with these regions forming the active site that binds the catalytic metal ions. We report the 3.7 Å crystal structure of a eukaryotic group IIB intron from the brown algae Pylaiella littoralis (P.li.LSUI2) in the lariat-3′ exon form with an intact 3′ splice site docked into the catalytic core.

Results

Conclusion