{"metadata":{"accession":"PF01345","entry_id":null,"type":"domain","go_terms":null,"source_database":"pfam","member_databases":null,"integrated":"IPR001434","hierarchy":null,"name":{"name":"CLIPPER domain","short":"CLIPPER"},"description":[{"text":"<p>This entry, previously known as DUF11, represents the CLIPPER domain, (Cross-Linked IsoPeptide Protein in the Extracellular Region) which is usually found in multiple copies in a number of archaebacterial proteins. CLIPPER domain adopts an Ig-like fold and contains a conserved N-terminal lysine and a C-terminal asparagine with central aspartate/glutamate residues that form an intramolecular isopeptide bond [[cite:PUB00163642]]. The positions of the residues predicted to form isopeptide bonds are not universally conserved suggesting that some domains appear to lack the intramolecular isopeptide bonds. CLIPPER domains are found in proteins from Gram-positive and Gram-negative bacteria. Some have also been identified in multiple cell-surface proteins from archaea. In Methanothermobacter sp. CaT2, this domain plays a key role as a membrane-bound adhesion protein in the aggregation of CaT2 [[cite:PUB00097782]].</p>","llm":false,"checked":false,"updated":false}],"wikipedia":null,"literature":{"PUB00163642":{"PMID":41236442,"ISBN":null,"volume":"34","issue":"12","year":2025,"title":"A global survey of intramolecular isopeptide bonds.","URL":null,"raw_pages":"e70342","medline_journal":"Protein Sci","ISO_journal":"Protein Sci","authors":["Costa F","Riziotis I","Andreeva A","Kalwan D","de Jong J","Hinchliffe P","Parmeggiani F","Race PR","Burston SG","Bateman A","Barringer R."],"DOI_URL":"https://doi.org/10.1002/pro.70342"},"PUB00097782":{"PMID":31189768,"ISBN":null,"volume":"34","issue":"3","year":2019,"title":"An Aggregation-defective Mutant of Methanothermobacter sp. CaT2 Reveals Unique Protein-dependent Aggregation.","URL":null,"raw_pages":"244-251","medline_journal":"Microbes Environ","ISO_journal":"Microbes Environ","authors":["Sumikawa K","Kosaka T","Mayahara N","Matsutani M","Udo K","Yamada M."],"DOI_URL":null}},"set_info":{"accession":"CL0159","name":"E-set"},"overlaps_with":null,"counters":{"subfamilies":0,"domain_architectures":3336,"interactions":0,"matches":33340,"pathways":0,"proteins":12543,"proteomes":5220,"sets":1,"structural_models":{"alphafold":5072},"structures":1,"taxa":8073},"entry_annotations":{"hmm":0,"logo":0,"alignment:seed":106,"alignment:full":17249},"cross_references":{},"is_llm":false,"is_reviewed_llm":false,"is_updated_llm":false,"representative_structure":{"accession":"9ifr","name":"CLIPPER domain from the Gram-negative fibrillar adhesin \"B9T28_05395"}}}