This entry represents a domain found in retropepsin-like bacterial proteases such as RimB from Pseudomonas fluorescens and the related retropepsin-like osmotic stress tolerance peptidases (Rlo) from Pseudomonas aeruginosa [[cite:PUB00161732],[cite:PUB00161733]]. RimB is involved in rhizosphere colonisation and plant infection. It is a bifunctional retropepsin-like aspartic endopeptidase that uniquely recognises and removes glutamate residues from polyglutamated RpsF and stimulates poly-alpha-L-glutamate synthesis by RimK. While Rlo proteases are homologous to RimB, they contain N-terminal signal peptides and perform distinct biological functions. Mutants lacking all three secreted Rlo peptidases show defects in antibiotic resistance, biofilm formation, and cell morphology. Rlo peptidases have been structurally characterised, showing structural features characteristic of retroviral pepsins (PDB:9G59, PDB:9G58) [[cite:PUB00161733]]. Similar to RimB, RloA proteins cleave substrates that become polyglutamated post-translationally.
","llm":false,"checked":false,"updated":false}],"wikipedia":[{"title":"Domain_of_unknown_function","extract":"A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
","thumbnail":null}],"literature":{"PUB00161732":{"PMID":39978677,"ISBN":null,"volume":"301","issue":"3","year":2025,"title":"A retropepsin-like bacterial protease regulates ribosome modification and polypeptide production.","URL":null,"raw_pages":"108329","medline_journal":"J Biol Chem","ISO_journal":"J Biol Chem","authors":["Little RH","Chandra G","Saalbach G","Martins C","Thompson CMA","Malone JG."],"DOI_URL":"https://doi.org/10.1016/j.jbc.2025.108329"},"PUB00161733":{"PMID":40166241,"ISBN":null,"volume":null,"issue":null,"year":2025,"title":"Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation in <i>Pseudomonas aeruginosa</i>.","URL":null,"raw_pages":"2025.03.18.643919","medline_journal":"bioRxiv","ISO_journal":"bioRxiv","authors":["Lormand JD","Savelle CH","Teschler JK","Lopez E","Little RH","Malone JG","Yildiz FH","Garcia-Garcia MJ","Sondermann H."],"DOI_URL":"https://doi.org/10.1101/2025.03.18.643919"}},"set_info":{"accession":"CL0129","name":"Peptidase_AA"},"overlaps_with":null,"counters":{"subfamilies":0,"domain_architectures":9,"interactions":0,"matches":7218,"pathways":0,"proteins":7079,"proteomes":4665,"sets":1,"structural_models":{"alphafold":4590},"structures":3,"taxa":6703},"entry_annotations":{"hmm":0,"logo":0,"alignment:seed":10,"alignment:full":2926},"cross_references":{},"is_llm":false,"is_reviewed_llm":false,"is_updated_llm":false,"representative_structure":{"accession":"2pma","name":"Structural Genomics, the crystal structure of a protein Lpg0085 with unknown function (DUF785) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1."}}}