Structure of the P22 att site. Conservation and divergence in the lambda motif of recombinogenic complexes

We have defined the bacterial and viral DNA targets (att sites) of P22 site-specific recombination and characterized their interaction with integrase (Int) protein. The bacterial DNA target, attB, is approximately 27 base pairs and consists of two core type Int binding sites as inverted repeats. The top and bottom Int cleavage sites fall within the core type Int binding sites and are separated by a 7-base pair overlap region. A similar core region is found in the viral DNA target, attP, which is approximately 260 base pairs long and contains two IHF binding sites and five arm type binding sites for Int. The results suggest that P22 Int, like lambda Int, is a heterobivalent DNA-binding protein that is capable of forming complex higher order structures with recombinogenic function. Although P22 and lambda recombination involve very similar multiprotein interactions and core region structures, there are significant differences in the arrangements of distal protein binding sites. These differences are discussed in terms of the possible flexibility of the Int protein and the specificity with which the higher order complexes assemble and/or function.