The transposase of IS911, a member of the IS3 family of bacterial insertion sequences, is composed of a catalytic domain located at its C-terminal end and a DNA binding domain located at its N-terminal end. Analysis of the transposases of over 60 members of the IS3 family revealed the presence of a helix-turn-helix (HTH) motif within the N-terminal region. Alignment of these potential secondary structures further revealed a completely conserved tryptophan residue similar to that found in the HTH motifs of certain homeodomain proteins. The analysis also uncovered a similarity between the IS3 family HTH and that of members of the LysR family of bacterial transcription factors. This information was used to design site-directed mutations permitting an assessment of its role in transposase function. A series of in vivo and in vitro tests demonstrated that the HTH domain is important in directing the transposase to bind the terminal inverted repeats of IS911.