Published online 10 August 2004
Nucleic Acids Research, Vol. 32 No. 14 © Oxford University Press 2004; all rights reserved
Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA
Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
* To whom correspondence should be addressed. Tel: +31 20 5121959; Fax: +31 20 5121954; Email: t.sixma{at}nki.nl
Present address: Gertie van Pouderoyen, Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
Received June 22, 2004; Revised and Accepted July 27, 2004
The bipartite DNA-binding domain of Tc3 transposase, Tc3A, was crystallized in complex with its transposon 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 linker 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 backbone contacts, as well as shape-recognition of the distortions in the DNA. Charged interactions are primarily 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 contrast to the Tn5 synaptic complex, the two Tc3A DNA-binding domains bind to a single Tc3 transposon end.
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