{"metadata":{"accession":"PF04720","entry_id":null,"type":"family","go_terms":null,"source_database":"pfam","member_databases":null,"integrated":"IPR006502","hierarchy":null,"name":{"name":"PDDEXK-like family of unknown function","short":"PDDEXK_6"},"description":[{"text":"<p>PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix [[cite:PUB00044133]]. The family is not in general fused with any other domains, so its function cannot be predicted [[cite:PUB00075365]].</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"},"PUB00075365":{"PMID":22936940,"ISBN":null,"volume":"3","issue":null,"year":2012,"title":"Conserved Peptide Upstream Open Reading Frames are Associated with Regulatory Genes in Angiosperms.","URL":null,"raw_pages":"191","medline_journal":"Front Plant Sci","ISO_journal":"Front Plant Sci","authors":["Jorgensen RA","Dorantes-Acosta AE."],"DOI_URL":"http://dx.doi.org/10.3389/fpls.2012.00191"}},"set_info":null,"overlaps_with":null,"counters":{"subfamilies":0,"domain_architectures":86,"interactions":0,"matches":6430,"pathways":0,"proteins":6363,"proteomes":428,"sets":0,"structural_models":{"alphafold":5140},"structures":0,"taxa":1179},"entry_annotations":{"hmm":0,"logo":0,"alignment:seed":82,"alignment:full":4155},"cross_references":{},"is_llm":false,"is_reviewed_llm":false,"is_updated_llm":false,"representative_structure":null}}