{"metadata":{"accession":"PF04411","entry_id":null,"type":"domain","go_terms":null,"source_database":"pfam","member_databases":null,"integrated":"IPR007505","hierarchy":null,"name":{"name":"PD-(D/E)XK nuclease superfamily","short":"PDDEXK_7"},"description":[{"text":"<p>This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches [[cite:PUB00044133]].  The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix.  It has been speculated that it could function as s methylation-dependent restriction [[cite:PUB00044133]]. The domain has two additional beta-strands inserted into the core fold after the first core alpha-helix. The PD-(D/E)XK signature is clearly conserved corresponding to an invariant PD (motif II) and DAK (motif III) motifs. There is also a conserved glutamic acid in motif I that is most likely to be involved in metal ion binding. The second core alpha-helix contains an invariant MHXYRD motif. It has been speculated that it could function as s methylation-dependent restriction enzyme [[cite:PUB00044133]].</p>","llm":false,"checked":false,"updated":false}],"wikipedia":null,"literature":{"PUB00044133":{"PMID":17584917,"ISBN":null,"volume":"7","issue":null,"year":2007,"title":"Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.","URL":null,"raw_pages":"40","medline_journal":"BMC Struct Biol","ISO_journal":"BMC Struct. Biol.","authors":["Knizewski L","Kinch LN","Grishin NV","Rychlewski L","Ginalski K."],"DOI_URL":"http://dx.doi.org/10.1186/1472-6807-7-40"}},"set_info":{"accession":"CL0236","name":"PDDEXK"},"overlaps_with":null,"counters":{"subfamilies":0,"domain_architectures":8,"interactions":0,"matches":972,"pathways":0,"proteins":970,"proteomes":917,"sets":1,"structural_models":{"alphafold":623},"structures":0,"taxa":1891},"entry_annotations":{"hmm":0,"logo":0,"alignment:seed":12,"alignment:full":470},"cross_references":{},"is_llm":false,"is_reviewed_llm":false,"is_updated_llm":false,"representative_structure":null}}