Structural parsimony in endonuclease active sites:: should the number of homing endonuclease families be redefined?

Homing endonucleases are classified into four families based on active site sequence motifs, Through structural comparisons we have found structural similarities between the endonuclease domain of colicin E9, an H-N-H motif-containing enzyme, acid both the non-specific nuclease from Serratia and I-PpoI, a His-Cys box-containing homing endonuclease. Our comparison identifies conservation at the heart of all three enzyme active sites and so argues for a re-classification of H-NH and His-Cys box homing endonucleases as a single family. We suggest the 'beta beta alpha-Me family' of homing enzymes to reflect the three elements of secondary structure and the metal ion that define the motif. (C) 1999 Federation of European Biochemical Societies.