Restriction Enzymes
PD . . . D/EXK motif
PD-(D/E)XK superfamily of Mg2+-dependent nucleases
type II restriction enzymes (REases) (reviews: [1, 2]) and later found in diverse enzymes involved in DNA replication, repair, and recombination, including phage λ exonuclease [3], bacterial enzymes exerting ssDNA nicking in the context of methyl-directed and very-short-patch DNA repair: MutH [4] and Vsr [5], Tn7 transposase TnsA [6], archaeal Holliday junction resolvases (AHJRs) Hjc/Hje [7, 8, 9], phage T7 endonuclease I [10], the XPF/Rad1/Mus81 family of nucleases that cleaves branched structures generated during DNA repair, replication, and recombination [11], and RecB nuclease
PD and D/EXK, are not invariant, and can be separated (‘…’) by anywhere from 4 (BcnI) to 51 (SgrAI) amino acids. Compounding matters, in some enzymes, the D/E or K residues, are recruited from other parts of the protein (e.g. EcoRII (310); BspD6I (311)).