Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex

During the development of multicellular organisms, gene expression must be tightly regulated, both spatially and temporally, One set of transcription factors that are important in animal development is encoded by the homeotic (Hox) genes, which govern the choice between alternative developmental pat hways along the anterior-posterior axis(1,2). Hox proteins, such as Drosoph ila Ultrabithorax, have low DNA-binding specificity by themselves but gain affinity and specificity when they bind together with the homeoprotein Extr adenticle (or Pbx1 in mammals)(3,4). To understand the structural basis of Hox-Extradenticle pairing, we determine here the crystal structure of an Ul trabithorax-Extradenticle-DNA complex at 2.4 Angstrom resolution, using the minimal polypeptides that form a cooperative heterodimer. The Ultrabithora x and Extradenticle homeodomains bind opposite faces of the DNA, with their DNA-recognition helices almost touching each other. However, most of the c ooperative interactions arise from the YPWM amino-acid motif of Ultrabithor ax-located amino-terminally to its homeodomain-which forms a reverse turn a nd inserts into a hydrophobic pocket on the Extradenticle homeodomain surfa ce. Together, these protein-DNA and protein-protein interactions define the general principles by which homeotic proteins interact with Extradenticle (or Pbx1) to affect development along the anterior-posterior axis of animal s.