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The active centre of the spliceosome consists of an intricate network formed by U5,
U2 and U6 snRNAs, and a pre-mRNA substrate. Prp8, a component of the U5 snRNP, crosslinks
extensively with this RNA catalytic core. We present the crystal structure of yeast
Prp8 (residues 885-2413) in complex with the U5 snRNP assembly factor Aar2. The structure
reveals new tightly associated domains of Prp8 resembling a bacterial group II intron
reverse transcriptase and a type II restriction endonuclease. Suppressors of splice
site mutations and an intron branchpoint crosslink map to a large cavity formed by
the reverse transcriptase thumb, endonuclease-like and the RNaseH-like domains. This
cavity is large enough to accommodate the catalytic core of group II intron RNA. The
structure provides crucial insights into the architecture of the spliceosome’s active
site and reinforces the notion that nuclear pre-mRNA splicing and group II intron
splicing have a common origin.