Classification of multi-helical DNA-binding domains and application to predict the DBD structures of sigma factor, LysR, OmpR/PhoB, CENP-B, Rapl, and Xy1S/Ada/AraC.

We have systematically compared structures of multi-helical DNA-binding domains (DBDs) which have been determined by crystallography or NMR spectroscopy. All the known multi-helical DBDs are very similar. The core of these structures consists of two alpha-helices in the helix-turn-helix combination, associated with one or two other helices. The structures can be classified according to either additional structural compositions or the configuration of the helices. Many DBDs, whose structures are currently unknown, have sequences which resemble those of known structures, permitting outlines of the new structures to be predicted.