The bacteriophage λ integrase protein (λ Int) belongs to a family of tyrosine recombinases that catalyze DNA rearrangements. We have determined a crystal structure of λ Int complexed with a cleaved DNA substrate through a covalent phosphotyrosine bond. In comparison to an earlier unliganded structure, we observe a drastic conformational change in DNA-bound λ Int that brings Tyr342 into the active site for cleavage of the DNA in cis. A flexible linker connects the central and the catalytic domains, allowing the protein to encircle the DNA. Binding specificity is achieved through direct interactions with the DNA and indirect readout of the flexibility of the att site. The conformational switch that activates λ Int for DNA cleavage exposes the C-terminal 8 residues for interactions with a neighboring Int molecule. The protein interactions mediated by λ Int's C-terminal tail offer a mechanism for the allosteric control of cleavage activity in higher order λ Int complexes.