SPECIFIC PURINE N-7-NITROGENS ARE CRITICAL FOR HIGH-AFFINITY BINDING BY THE TRP REPRESSOR

We have analysed the interaction of the frp repressor with the trpEDCB A operator using a series of modified trp operator sequences incorpora ting two isosteric purine analogues that lack N-7-nitrogens. Our resul ts suggest that as well as the direct contact between Arg69 and G(-9r) three additional purine N-7-nitrogens, implicated in specific, water- mediated contacts to the repressor, are critical for formation of the high-affinity repressor-operator complex. We conclude that the crystal structure obtained by Otwinowski et al. reflects high-affinity sequen ce-specific binding of the trp repressor to the trp operator, and that in some cases proteins can use water molecules to extend amino acid s ide chains in order to derive favorable binding energy in complex form ation.