Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA

The bipartite DNA-binding domain of Tc3 transpo-sase, Tc3A, was crystallized in complex with its trans-poson recognition sequence. In the structure the two DNA-binding domains form structurally related helix– turn–helix (HTH) motifs. They both bind to the major groove on a single DNA oligomer, separated by a lin-ker that interacts closely with the minor groove. The structure resembles that of the transcription factor Pax6 DNA-binding domain, but the relative orientation of the HTH-domain is different. The DNA conformation is distorted, characterized by local narrowing of the minor groove and bends at both ends. The protein– DNA recognition takes place through base and back-bone contacts, as well as shape-recognition of the distortions in the DNA. Charged interactions are pri-marily found in the N-terminal domain and the linker indicating that these may form the initial contact area. Two independent dimer interfaces could be relevant for bringing together transposon ends and for binding to a direct repeat site in the transposon end. In con-trast to the Tn5 synaptic complex, the two Tc3A DNA-binding domains bind to a single Tc3 transposon end