How Cro and λ-repressor distinguish between operators: The structural basis underlying a genetic switch

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Abstract
Knowledge of the three-dimensional structures of the λ-Cro and λ-repressor proteins in complex with DNA has made it possible to evaluate how these proteins discriminate between different operators in phage λ. As anticipated in previous studies, the helix–turn–helix units of the respective proteins bind in very different alignments. In Cro the recognition helices are 29 Å apart and are tilted by 55° with respect to each other, but bind parallel to the major groove of the DNA. In λ-repressor [Beamer, L. J. & Pabo, C. O. (1992) J. Mol. Biol. 227, 177–196] the helices are 34 Å 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 λ-repressor. The first two amino acids of the recognition helices of the two proteins, Gln-27 and Ser-28 in Cro, and Gln-44 and Ser-45 in λ-repressor, make very similar interactions with the invariant bps 2 and 4. There are also analogous contacts between the thymine of bp 5 and, respectively, the backbone of Ala-29 of Cro and the backbone of Gly-46 of λ-repressor. Otherwise, however, unrelated parts of the two proteins are used in sequence-specific recognition. It appears that similar contacts to the invariant or almost invariant bps (especially 2 and 4) are used by both Cro and λ-repressor to differentiate the operator sites as a group from other sites on the DNA. The discrimination of Cro and λ-repressor between their different 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 for the idea that there is no simple code for DNA-protein recognition.