Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed

Using algorithms for protein sequence analysis we predict that some of the canonical type II and type IIS restriction enzymes have an active site with a substantially different architecture a nd fold from the typical PD-(D/E)xK superfamily, These results suggest that they are related to nucleases from the HNH and GIY-YIG superfamilies.