THE COMPLEX BETWEEN PHAGE-434 REPRESSOR DNA-BINDING DOMAIN AND OPERATOR SITE O(R)3 - STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NONCONSENSUS HALF-SITES

Background: The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (O(R)1, O(R)2, O(R)3, O(L)1, O(L)2 and O(L)3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. O(R)3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind. Results: We have determined the structure at 2.5 Angstrom resolution of a complex of R1-69 with DNA containing the O(R)3 Site and compared it with previously studied complexes of R1-69 bound to O(R)1 and O(R)2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of O(R)3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer. Conclusions: Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G.C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.