Solution structure of the POU-specific DNA-binding domain of Oct-1

Abstract

THE transcription factor Oct-1 belongs to a family containing a POU DNA-binding domain. This bipartite domain is composed of a POU-specific domain (POU_s) and a POU-homeodomain (POU_hd) connected by a flexible linker. The left half of the optimal POU binding site, the octamer ATGCAAAT, is recognized by POU_s and the right half by POU_hd. We have determined the solution structure of POU_s by nuclear magnetic resonance. It consists of four α-helices connected by short loops. Helices I and IV are in a parallel coiled-coil arrangement. The folding topology appears to be similar to that of the bacteriophage Λ-represser and 434 represser. For the well defined parts of the protein (residues 1–71), the average root-mean square deviation for the backbone atoms is 0.9 Å. Based on the observed selective exchange broadening in the (¹⁵N, ¹H)-HMQC (heteronuclear multiple quantum coherence) spectrum of the POU_s–DNA complex we conclude that DNA-binding is mediated by helix III. We propose a model for the POU–DNA complex in which both recognition helices from the two subdomains have adjacent positions in the major groove.