HOW CRO AND LAMBDA-REPRESSOR DISTINGUISH BETWEEN OPERATORS - THE STRUCTURAL BASIS UNDERLYING A GENETIC SWITCH

Knowledge of the three-dimensional structures of the lambda-Cro and la mbda-repressor proteins in complex with DNA has made it possible to ev aluate how these proteins discriminate between different operators in phage lambda. As anticipated in previous studies, the helix-turn-helix units of the respective proteins bind in very different alignments, I n Cro the recognition helices are 29 Angstrom apart and are tilted by 55 degrees with respect to each other, but bind parallel to the major groove of the DNA. In lambda-repressor [Beamer, L. J. & Pabo, C. O. (1 992) J. Mol. Biol. 227, 177-196] the helices are 34 Angstrom apart and are essentially parallel to each other, but are inclined to the major grooves, The DNA is much more bent when bound by Cro than in the case with lambda-repressor, The first two amino acids of the recognition h elices of the two proteins, Gln-27 and Ser-28 in Cro, and Gln-44 and S er-45 in lambda-repressor, make very similar interactions with the inv ariant bps 2 and 4. There are also analogous contacts between the thym ine of bp 5 and, respectively, the backbone of Ala-29 of Cro and the b ackbone of Gly-46 of lambda-repressor. Otherwise, however, unrelated p arts of the two proteins are used in sequence-specific recognition, It appears that similar contacts to the invariant or almost invariant bp s (especially 2 and 4) are used by both Cro and lambda-repressor to di fferentiate the operator sites as a group from other sites on the DNA, The discrimination of Cro and lambda-repressor between their differen t operators is more subtle and seems to be achieved primarily through differences in van der Waals contacts at bp 3', together with weaker, less direct effects at bps 5' and 8', all in the nonconsensus half of the operators, The results provide further support fur the idea that t here is no simple code for DNA-protein recognition.