Presence of a characteristic D-D-E motif in IS1 transposase

Transposases encoded by various transposable DNA elements and retroviral integrases belong to a family of proteins with three conserved acidic amino acids, D, D, and E, constituting the D-D-E motif that represents the active center of the proteins. IS 1 , one of the smallest transposable elements in bacteria, encodes a transposase which has been thought not to belong to the family of proteins with the D-D-E motif. In this study, we found several IS 1 family elements that were widely distributed not only in eubacteria but also in archaebacteria. The alignment of the transposase amino acid sequences from these IS 1 family elements showed that out of 14 acidic amino acids present in IS 1 transposase, three (D, D, and E) were conserved in corresponding positions in the transposases encoded by all the elements. Comparison of the IS 1 transposase with other proteins with the D-D-E motif revealed that the polypeptide segments surrounding each of the three acidic amino acids were similar. Furthermore, the deduced secondary structures of the transposases encoded by IS 1 family elements were similar to one another and to those of proteins with the D-D-E motif. These results strongly suggest that IS 1 transposase has the D-D-E motif and thus belongs to the family of proteins with the D-D-E motif. In fact, mutant IS 1 transposases with an amino acid substitution for each of the three acidic amino acids possibly constituting the D-D-E motif were not able to promote transposition of IS 1 , supporting this hypothesis. The D-D-E motif identified in IS 1 transposase differs from those in the other proteins in that the polypeptide segment between the second D and third E in IS 1 transposase is the shortest, 24 amino acids in length. Because of this difference, the presence of the D-D-E motif in IS 1 transposase has not been discovered for some time.