Homeodomains are conserved DNA-binding domains found in the transcription factors of a wide variety of organisms. There are also known to play an important role in embryogenesis. Homeodomains all bind to DNA at a TAAT core motif. Msx-1 is a homeodomain encoded by a subfamily of homeobox genes. In a developing embryo, these genes are expressed in craniofacial structures, the neural tube, and in the limbs. Msx-1 specifically interacts with DNA at the sequence (C/G)TAATTG. Biologically, Msx-1 acts as a transcriptional repressor.
Homeodomains are about 60 amino acid residues long, and they consist of three alpha-helices (red) and one flexible N-terminal arm (green). Msx-1 is exactly 60 residues long. Helices 2 and 3 adopt a helix-turn-helix motif. The structure of the Msx-1 homeodomain has been determined using homology modeling.