NEW INSIGHTS ON DNA RECOGNITION BY ETS PROTEINS FROM THE CRYSTAL-STRUCTURE OF THE PU.1 ETS DOMAIN DNA COMPLEX

Transcription factors belonging to the ets family regulate gene expres sion and share a conserved ETS DNA-binding domain that binds to the co re sequence 5'-(C/ A)GGA(A/T)-3'. The domain is similar to alpha+beta (''winged'') helix-turn-helix DNA-binding proteins. The crystal struct ure of the PU.1 ETS domain complexed to a 16-base pair oligonucleotide revealed a pattern for DNA recognition from a novel loop-helix-loop a rchitecture (Kodandapani, R., Pio, F., Ni, C.-Z., Piccialli, G., Klems z, M., McKercher, S., Maki, R. A., and Ely, K. R. (1996) Nature 380, 4 56-460). Correlation of this model with mutational analyses and chemic al shift data on other ets proteins confirms this complex as a paradig m for ets DNA recognition. The second helix in the helix-turn-helix mo tif lies deep in the major groove with specific contacts with bases in both strands in the core sequence made by conserved residues in alpha 3. On either side of this helix, two loops contact the phosphate back bone. The DNA is bent (8 degrees) but uniformly curved without distinc t kinks. ETS domains bind DNA as a monomer yet make extensive DNA cont acts over 30 Angstrom. DNA bending likely results from phosphate neutr alization of the phosphate backbone in the minor groove by both loops in the loop-helix-loop motif. Contacts from these loops stabilize DNA bending and may mediate specific base interactions by inducing a bend toward the protein.