Structure of a DNA-bound Ultrabithorax–Extradenticle homeodomain complex

Abstract

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 pathways along the anterior-posterior axis. Hox proteins, such as Drosophila Ultrabithorax, have low DNA-binding specificity by themselves but gain affinity and specificity when they bind together with the homeoprotein Extradenticle (or Pbxl in mammals). To understand the structural basis of Hox-Extradenticle pairing, we determine here the crystal structure of an Ultrabithorax-Extradenticle-DNA complex at 2.4 A resolution, using the minimal polypeptides that form a cooperative heterodimer. The Ultrabithorax and Extradenticle homeodomains bind opposite faces of the DNA, with their DNA-recognition helices almost touching each other. However, most of the cooperative interactions arise from the YPWM amino-acid motif of Ultrabithorax-located amino-terminally to its homeodomain-which forms a reverse turn and inserts into a hydrophobic pocket on the Extradenticle homeodomain surface. 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 animals.

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

“…In all four structures the trajectory of the DNA backbone deviates from B-form DNA at the core GA base step within the Exd/Pbx1 binding site. This base step is critical for Exd/Pbx1 binding as observed in the crystal structure (32)(33)(34)(35) as well as our own comprehensive CSI microarray studies (46).…”

“…Most of this cooperative interaction is the result of a conserved N-terminal YPWM tetrapeptide on the Hox protein binding into a pocket on the Exd/Pbx1 homeodomain ( Figure 1, panel a). In addition to this direct interface between Hox and Exd/Pbx1, crystal structures of four Hox-Exd/Pbx1-DNA complexes reveal a discernible perturbation of DNA geometry in the ternary complex (32)(33)(34)(35). Importantly, there is compelling evidence that Hox-Exd-DNA complex may not require interaction between the Hox N-terminal docking peptide and Exd (28,36).…”

The Role ofHoxGenes in Female Reproductive Tract Development, Adult Function, and Fertility

“…Structural analyses have shown that the HD can self-fold, and form a structural motif called a "helix-turn-helix motif." Through this motif, the HD, a DNA binding domain, recognizes a typical core DNA sequence, typically TAATor TTAT, and regulates the expression of target genes, many of which play a role in axial development (Gehring et al 1994;Krumlauf 1994;Gruschus et al 1999;Passner et al 1999).…”

Downstream of Homeotic Genes: In the Heart of Hox function

“…Significantly, it has been possible to uncouple the two processes by using an AbdA variant mutated in the hexapeptide (Monier B, Merabet S, Perrin L, Sémériva M, unpublished data), a peptide motif required for Hox binding to their cofactor Exd. 72,73 Mutation of this domain does not affect cell lineage choice at stages 8-10, or activation of wg expression in Svp-cells at stage 16. However, the integrity of the motif is required for activation of Ih in Tin-cells at stage 16.…”