The DNA-binding domain of the MotA transcription factor from bacteriophage T4 shows structural similarity to the TATA-binding protein.

The bacteriophage T4 middle-mode transcription factor MotA consists of two domains of approximately equal size. The C-terminal domain has been shown to contain the DNA-binding elements of the molecule, and the N-terminal domain appears to interact with RNA polymerase. A 12.5-kDa fragment of the C-terminal domain (MotCF), comprising residues 105-211 of MotA, was found to be suitable for structural studies by NMR. The 1H and 15N assignments have been made for MotCF by using two-dimensional homonuclear and heteronuclear experiments. A secondary structure has been determined which consists of a six-stranded antiparallel beta-pleated sheet with three alpha-helical segments. The secondary structure of MotCF has a clear similarity to one half of the eukaryotic TATA-binding protein (TBP), which is an intramolecular dimer. Therefore, MotCF may be related to a monomeric ancestral protein of TBP. TBP binds its target DNA in the minor groove by specific interactions with hydrophobic and aromatic residues on the exposed sheet surface of the protein. Similar residues are also present on the beta-sheet surface of MotCF, suggesting that it too binds DNA in the minor groove.