Crystal structure of the NurA–dAMP–Mn complex

Generation of the 30 overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 50–30 nuclease, NurA, plays an important role in generating 30 singlestranded DNA during archaeal HR, together with Mre11–Rad50 and HerA. We have determined the crystal structures of apoand dAMP-Mn-bound NurA from Pyrococcus furiousus (Pf NurA) to provide the basis for its cleavage mechanism. Pf NurA forms a pyramid-shaped dimer containing a large central channel on one side, which becomes narrower towards the peak of the pyramid. The structure contains a PIWI domain with high similarity to argonaute, endoV nuclease and RNase H. The two active sites, each of which contains Mn ion(s) and dAMP, are at the corners of the elliptical channel near the flat face of the dimer. The 30 OH group of the ribose ring is directed toward the channel entrance, explaining the 50–30 nuclease activity of Pf NurA. We provide a DNA binding and cleavage model for Pf NurA.