Crystal structure of the archaeal Holliday Junction resolvase Hjc and implications for DNA recognition

Background: Homologous recombination is a crucial mechanism in determining genetic diversity and repairing damaged chromosomes. Holliday junction is t he universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. Hjc is an archaeal endonuclea se, which specifically resolves the junction DNA to produce two separate re combinant DNA duplexes. The atomic structure of Hjc should clarify the mech anisms of the specific recognition with Holliday junction and the catalytic reaction. Results: The crystal structure of Hjc from the hyperthermophilic archaeon P yrococcus furiosus has been determined at 2.0 Angstrom resolution. The acti ve Hjc molecule forms a homodimer, where an extensive hydrophobic interface tightly assembles two subunits of a single compact domain. The folding of the Hjc subunit is clearly different from any other Holliday junction resol vases thus far known. Instead, it resembles those of type II restriction en donucleases, including the configurations of the active site residues, whic h constitute the canonical catalytic motifs. The dimeric Hjc molecule displ ays an extensive basic surface on one side, which contains many conserved a mino acids, including those in the active site. Conclusions: The architectural similarity of Hjc to restriction endonucleas es allowed us to construct a putative model of the complex with Holliday ju nction. This model accounts for how Hjc recognizes and resolves the junctio n DNA in a specific manner. Mutational and biochemical analyses highlight t he importance of some loops and the amino terminal region in interaction wi th DNA.