As mentioned previously, homeodomain proteins generally recognize the sequence aTtA (tAaT) where the lowercase indicates the bases where known exceptions to the conserved sequence exist. Just as the sequences of the proteins and the sequences recognized by the proteins are conserved, so are the protein-DNA contacts, for the most part.
Generally conserved are the contacts made by the amino acids R3, R5, I47, Q50, N51, and M54. While the arginine residues make contacts in the minor groove of the DNA duplex, the others make specific contacts in the major groove.
It is interesting that MAT alpha2, which has different residues in the N-terminal residues that contact DNA and at one of the key recognition helix positions (N47 instead of I47) and correspondingly recognizes the sequence GTAA instead of the consensus ATTA.
Information in this project comes primarily from these references.
This page has been developed Donovan C. Haines as part of a VSNS-PPS course assignment. Email comments or problems to DCHaines@wsuhub.uc.twsu.edu.