id: Pfam:PF04411
pfam_id: PF04411
name: PD-(D/E)XK nuclease superfamily
short_name: PDDEXK_7
seed_status: EX_DUF
characterization_status: UNSCORED
curation_status: SEEDED
source_url: https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04411
counters:
  proteins: 970
  matches: 972
  proteomes: 917
  taxa: 1891
  structures: 0
  alphafold_models: 623
  domain_architectures: 8
provenance:
  snapshot_id: interpro-pfam-duf-2026-10-10
  path: data/worklists/interpro-pfam-duf-2026-10-10.json
  sha256: 17fb625876c9326ed284263a47bcd84e0d7844a31c040dc06cd2260c36f1c383
  generated_at: '2026-10-10T07:44:21.614711Z'
  source_url: https://www.ebi.ac.uk/interpro/api/entry/pfam/
interpro_id: InterPro:IPR007505
description: 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]].