Type I topoisomerases alter DNA topology by cleaving and rejoining one
strand of duplex DNA through a covalent protein-DNA intermediate. Her
e we show that vaccinia topoisomerase, a eukaryotic type IB enzyme, ca
talyzes site-specific endoribonucleolytic cleavage of an RNA-containin
g strand. The RNase reaction occurs via transesterification at the sci
ssile ribonucleotide to form a covalent RNA-3'-phosphoryl-enzyme inter
mediate, which is then attacked by the vicinal 2' OH of the ribose sug
ar to yield a free 2', 3' cyclic phosphate product. Introduction of a
single ribonucleoside at the scissile phosphate of an otherwise all-DN
A substrate suffices to convert the topoisomerase into an endonuclease
. Human topoisomerase I also has endoribonuclease activity. These find
ings suggest potential roles for topoisomerases in RNA processing.