THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves

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Abstract
THAP family proteins bind DNA and are involved in diverse DNA processes. The structure of the DNA-bound Drosophila P element transposase THAP domain now shows that the conserved β-sheet docks into the major groove, while a C-terminal basic loop binds the minor groove, a mode that is likely conserved and indicates the basis of bipartite sequence recognition. THAP-family C2CH zinc-coordinating DNA-binding proteins function in diverse eukaryotic cellular processes, such as transposition, transcriptional repression, stem-cell pluripotency, angiogenesis and neurological function. To determine the molecular basis for sequence-specific DNA recognition by THAP proteins, we solved the crystal structure of the Drosophila melanogaster P element transposase THAP domain (DmTHAP) in complex with a natural 10-base-pair site. In contrast to C2H2 zinc fingers, DmTHAP docks a conserved β-sheet into the major groove and a basic C-terminal loop into the adjacent minor groove. We confirmed specific protein-DNA interactions by mutagenesis and DNA-binding assays. Sequence analysis of natural and in vitro–selected binding sites suggests that several THAPs (DmTHAP and human THAP1 and THAP9) recognize a bipartite TXXGGGX(A/T) consensus motif; homology suggests THAP proteins bind DNA through a bipartite interaction. These findings reveal the conserved mechanisms by which THAP-family proteins engage specific chromosomal target elements.