Molecuar model of the DNA interaction site for the cyclic AMP receptor protein.

Abstract

A topological model of the DNA binding site for cAMP receptor protein (CRP) is presented. A consensus sequence drawn from the known CRP binding sites has several symmetrical subregions that are spatially resolved onto different faces of the DNA helix. Consideration of available biochemical and genetic data suggests one particular choice among the possible symmetrical arangements. In this case, the sequence in its helical form presents nearly the same pattern of exposed base pairs on 2 faces of the helix. These 2 faces are separated by a helix angle of 72.degree.; the similar sequences that are exposed in the grooves occur in opposite orientations on the 2 faces. This inverted symmetry arrangement may provide each of the identical subunits of the CRP with a similar recognition region within the overall site. In the bacterial gal and ara operons, the site appears to accommodate a single molecule of the CRP; in the lac operon, the site repeats the symmetrical arrangement and should accommodate 2 molecules of the CRP.