Locations of contacts between individual zinc fingers of Xenopus laevis transcription factor IIIA and the internal control region of a 5S RNA gene.

A set of mutants of transcription factor IIIA (TFIIIA) have been prepared in which successive zinc-finger domains have been deleted from the carboxyl terminus of the protein. These have been analyzed by hydroxyl radical footprinting to map the location of contacts to DNA by individual zinc-finger domains of TFIIIA. The results suggest that the nine zinc fingers of TFIIIA are organized into three DNA-binding domains of three fingers each. The spatial relationship between zinc-finger contacts to 5S DNA suggests that the two domains which interact with either end of the DNA-binding site of TFIIIA (fingers 1-3 and 7-9) have a compact conformation, similar to that exemplified by the zif268 cocrystal structure [Pavletich, N.P., & Pabo, C.O. (1991) Science 252, 809-817]. However, the central domain (fingers 4-6) has a much more extended conformation, following a path nearly parallel to the helix axis and contacting over 20 base pairs of DNA in the center of the binding site of TFIIIA. These results strongly support two recently proposed and radically new models for the TFIIIA/5S DNA complex [Hayes, J.J., & Tullius, T.D. (1992) J. Mol. Biol. 227, 407-417; Clemens, K.R., Liao, X., Wolf, V., Wright, P.E., & Gottesfeld, J.M. (1992) Proc. Natl. Acad. Sci. U.S.A. (in press)].