Structure, flexibility, and mechanism of the Bacillus stearothermophilus RecU holliday junction resolvase

Here we report a high resolution structure of RecU‐Holliday junction resolvase from Bacillus stearothermophilus. The functional unit of RecU is a homodimer that contains a “mushroom” like structure with a rigid cap and two highly flexible loops extending outwards. These loops appear to be highly flexible/dynamic, and presumably are directly involved in DNA binding and holding it for catalysis. Structural modifications of both the protein and DNA upon their interaction are essential for catalysis. An Mg 2+ ion is present in each of the two active sites in this homodimeric enzyme, and two water molecules are coordinated with each Mg 2+ ion. Our data are consistent with one of these water molecules acting as a nucleophile and the other as a general acid. The identities of the general base and general acid involved in catalysis and the Lewis acid that stabilizes the pentacovalent transition state phosphate ion are proposed. A model for the RecU‐Holliday junction DNA complex is also proposed and discussed in thecontext of DNA binding and cleavage. Proteins 2007. © 2007 Wiley‐Liss, Inc.