Sequence similarity among type-II restriction endonucleases, related by their recognized 6-bp target and tetranucleotide-overhang cleavage.

The type-II restriction endonucleases (ENases) EcoRI (recognition sequence G decreases AATTC), RsrI (G decreases AATTC), XcyI (C decreases CCGGG), Cfr9I (C decreases CCGGG) and MunI (C decreases AATTG), all cleave hexanucleotide palindromic sequences, leaving tetranucleotide 5'-overhangs. Two regions of similarity that appear in the same order and relative position were identified among the amino-acid sequences of ENases. These regions map to the structural elements of EcoRI involved in the building of the catalytic site and in interactions with the central nucleotides of the recognized sequence. We propose that these ENases might all share a similar structural organization of the active site and structural motifs involved in interactions with specific DNA recognition sequences.