PI-Scel is a bifunctional yeast protein that propagates its mobile gen
e by catalyzing protein splicing and site specific DNA double-strand c
leavage. Here, we report the 2.4 Angstrom crystal structure of the PI-
Scel protein. The structure is composed of two separate domains (I and
II) with novel folds and different functions. Domain I, which is elon
gated and formed largely from seven beta sheets, harbors the N and C t
ermini residues and two His residues that are implicated in protein sp
licing. Domain II, which is compact and is primarily composed of two s
imilar alpha/beta motifs related by local twofold symmetry, contains t
he putative nuclease active site with a cluster of two acidic residues
and one basic residue commonly found in restriction endonucleases. Th
is report presents prototypic structures of domains with single endonu
clease and protein splicing active sites.