A POU‐A related region dictates DNA binding specificity of LFB1/HNF1 by orienting the two XL‐homeodomains in the dimer.

LFB1/HNF1 regulates the hepatocyte‐specific transcription of several genes, binding as a dimer to cis‐acting elements that match the inverted palindrome GTTAATNATTAAC. The DNA binding domain of LFB1/HNF1 is characterized by a unique tripartite structure that includes an unusually long homeodomain (domain C), a region related to the POU‐specific A‐box (domain B) and a short N‐terminal dimerization domain (domain A). We report that a recombinant peptide corresponding to the isolated homeodomain of LFB1/HNF1 binds as a monomer to a half‐palindrome binding site, but shows diminished sequence specificity. Domain B, in addition to the homeodomain, is required and sufficient for proper recognition of LFB1/HNF1‐responsive sites. A protein consisting of only these latter two domains is a monomer in solution, but forms dimers upon DNA binding. The protein‐protein contacts established within the bound dimer restrain the orientation of the two homeodomains with respect to one another, thus contributing in a critical fashion to the recognition of the dyad symmetry‐related LFB1/HNF1 sites. The DNA‐independent dimerization domain (domain A) is required to increase the affinity of DNA binding, but does not influence the dimer geometry.