This domain can be found in uncharacterised proteins in viruses, archaea and bacteria, most notably it is found in YhcG proteins found in E.coli. This entry represents the C-terminal PDDEXK domain belonging to the PD-(D/E)XK superfamily of nucleases involved in DNA recombination and repair [1]. Profile HMM analysis identified a relationship between this C-terminal domain of YhcG and Pfam:PF01939 , a family of NucS endonucleases [2]. YHcG was identified in association with DNA processing enzymes, including the restriction complexes HsdMRS and McrABC, the integrases IntF and IntS, and the recombinase PinE [1].

1: Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A; PLoS Biol. 2009;7:e96. PMID:19402753

2: The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. Kosinski J, Feder M, Bujnicki JM; BMC Bioinformatics. 2005;6:172. PMID:16011798