Quasi-equivalence in site-specific recombinase structure and function: Crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction

The crystal structure of a novel Cre-Lox synapse was solved using phases fr om multiple isomorphous replacement and anomalous scattering, and refined t o 2.05 Angstrom resolution. In this complex, a symmetric protein trimer is bound to a Y-shaped three-way DNA junction, a marked departure from the pse udo-4-fold symmetrical tetramer associated with Cre-mediated LoxP recombina tion. The three-way DNA junction was accommodated by a simple kink without significant distortion of the adjoining DNA duplexes. Although the mean ang le between DNA arms in the Y and X structures was similar, adjacent Cre tri mer subunits rotated 29 degrees relative to those in the tetramers. This ro tation was accommodated at the protein-protein and DNA-DNA interfaces by in teractions that are "quasi-equivalent" to those in the tetramer, analogous to packing differences of chemically identical viral subunits at non-equiva lent positions in icosahedral capsids. This structural quasi-equivalence ex tends to function as Cre can bind to, cleave and perform strand transfer wi th a three-way Lox substrate. The structure explains the dual recognition o f three and four-way junctions by site-specific recombinases as being due t o shared structural features between the differently branched substrates an d plasticity of the protein-protein interfaces. To our knowledge, this is t he first direct demonstration of quasi-equivalence in both the assembly and function of an oligomeric enzyme. (C) 2001 Academic Press.