The HOX/HOM superfamily of homeodomain proteins controls cell fate and segmental
embryonic patterning by a mechanism that is conserved in all metazoans. The
linear arrangement of the Hox genes on the chromosome correlates with the
spatial distribution of HOX protein expression along the anterior-posterior axis
of the embryo. Most HOX proteins bind DNA cooperatively with members of the PBC
family of TALE-type homeodomain proteins, which includes human Pbx1. Cooperative
DNA binding between HOX and PBC proteins requires a residue N-terminal to the
HOX homeodomain termed the hexapeptide, which differs significantly in sequence
between anterior- and posterior-regulating HOX proteins. We report here the
1.9-A-resolution structure of a posterior HOX protein, HoxA9, complexed with
Pbx1 and DNA, which reveals that the posterior Hox hexapeptide adopts an altered
conformation as compared with that seen in previously determined anterior
HOX/PBC structures. The additional nonspecific interactions and altered DNA
conformation in this structure account for the stronger DNA-binding affinity and
altered specificity observed for posterior HOX proteins when compared with
anterior HOX proteins. DNA-binding studies of wild-type and mutant HoxA9 and
HoxB1 show residues in the N-terminal arm of the homeodomains are critical for
proper DNA sequence recognition despite lack of direct contact by these residues
to the DNA bases. These results help shed light on the mechanism of
transcriptional regulation by HOX proteins and show how DNA-binding proteins may
use indirect contacts to determine sequence specificity.
