Crystal structure of the NKX2-1 homeodomain bound to a palindromic DNA recognition sequence

NKX2-1 (thyroid transcription factor 1, TTF-1) is a homeodomain transcription factor that plays critical roles in the development and function of the thyroid, lung and forebrain. Here, we report the crystal structure of the NKX2-1 homeodomain bound to a 19 bp DNA duplex containing two palindromically arranged NK2-recognition motifs, refined to 3.26 Å resolution. The structure reveals two homeodomains bound to a single DNA duplex and demonstrates that the overall fold and DNA-binding interactions are highly conserved relative to those of NKX2-5. Comparison with NKX2-5 further shows that the amino-acid residues that differ between the two homeodomains are located away from the protein-DNA interface, suggesting that functional differences between these transcription factors are unlikely to arise from distinct DNA-recognition mechanisms. These findings provide a structural framework for understanding DNA recognition by NKX2-1 and for interpreting the effects of pathogenic variants within its homeodomain.