{"uniprot":"D6R9N7","gene":"USP17L18","name":"Ubiquitin carboxyl-terminal hydrolase 17-like protein 18","organism":"Homo sapiens (Human)","status":"dark","length":530,"sequence":"MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSCETRVDLCDDLAPVARQLAPREKLPLSSRRPAAVGAGLQNMGNTCYVNASLQCLTYTPPLANYMLSREHSQTCHRHKGCMLCTMQAHITRALHNPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGHKQVDHHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVQQALEQLVKPEELNGENAYHCGVCLQRAPASKTLTLHTSAKVLILVLKRFSDVTGNKIAKNVQYPECLDMQPYMSQTNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKAQEGQWYKMDDAEVTASSITSVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRRAKQGELKRDHPCLQAPELDEHLVERATQESTLDHWKFLQEQNKTKPEFNVRKVEGTLPPDVLVIHQSKYKCGMKNHHPEQQSSLLNLSSTTPTHQESMNTGTLASLRGRARRSKGKNKHSKRALLVCQ","function_summary":"A soluble human deubiquitinase that uses a papain-like catalytic core to hydrolyze ubiquitin from protein substrates, thereby editing ubiquitin signals that govern proteostasis and cell-fate pathways. It concentrates within nucleolar RNA-rich assemblies, where auxiliary RNA and hyaluronan-binding surfaces help recruit the enzyme to ribosome biogenesis hubs. By reversing ubiquitination, it modulates pathways that control ubiquitin-dependent protein turnover and can promote apoptotic programs in epithelial cells through selective stabilization and remodeling of signaling complexes.","plain_language":"USP17L18 has barely been studied. The model's best guess: A soluble human deubiquitinase that uses a papain-like catalytic core to hydrolyze ubiquitin from protein substrates, thereby editing ubiquitin signals that govern proteostasis and cell-fate pathways. It concentrates within nucleolar RNA-rich assemblies, where auxiliary RNA and hyaluronan-binding surfaces help recruit the enzyme to ribosome biogenesis hubs.","uniprot_summary":"Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate different cellular processes.","go_terms":{"molecular_function":[{"id":"GO:0004843","label":"cysteine-type deubiquitinase activity"},{"id":"GO:0019783","label":"ubiquitin-like protein peptidase activity"},{"id":"GO:0003723","label":"RNA binding"},{"id":"GO:0005540","label":"hyaluronic acid binding"}],"biological_process":[{"id":"GO:0016579","label":"protein deubiquitination"},{"id":"GO:0006511","label":"ubiquitin-dependent protein catabolic process"},{"id":"GO:1904037","label":"positive regulation of epithelial cell apoptotic process"}],"cellular_component":[{"id":"GO:0005730","label":"nucleolus"}]},"interpro":[{"id":"IPR038765","name":"Papain-like cysteine peptidase superfamily","type":"homologous_superfamily","start":79,"end":387},{"id":"IPR001394","name":"Peptidase C19, ubiquitin carboxyl-terminal hydrolase","type":"domain","start":80,"end":372},{"id":"IPR028889","name":"Ubiquitin specific protease USP, catalytic domain","type":"domain","start":80,"end":375},{"id":"IPR050164","name":"Ubiquitin carboxyl-terminal hydrolases","type":"family","start":59,"end":376},{"id":"IPR018200","name":"Ubiquitin specific protease, conserved site","type":"conserved_site","start":81,"end":96},{"id":"IPR018200","name":"Ubiquitin specific protease, conserved site","type":"conserved_site","start":317,"end":335}],"reasoning":"I begin with the InterPro architecture. The core of the protein is a papain-like cysteine peptidase scaffold: IPR038765 (Papain-like cysteine peptidase superfamily, residues 79–387) frames the overall fold. Nested within this scaffold are multiple USP-family signatures that define a ubiquitin-specific protease catalytic core: IPR001394 (Peptidase C19, ubiquitin carboxyl-terminal hydrolase, residues 80–372), IPR028889 (Ubiquitin specific protease USP, catalytic domain, residues 80–375), and IPR050164 (Ubiquitin carboxyl-terminal hydrolases family, residues 59–376). Two conserved catalytic elements punctuate this core: IPR018200 (Ubiquitin specific protease, conserved site, residues 81–96) and IPR018200 again at residues 317–335. This ordered layout—USP catalytic domain embedded in a papain-like fold with N- and C-terminal catalytic-site motifs—creates a thiol protease active site that cleaves isopeptide bonds at ubiquitin C-termini. This architecture causes cysteine-type deubiquitinase activity, aligning with GO:0004843.\n\nFrom this catalytic foundation, I infer molecular functions and auxiliary binding capacities. The papain-like USP core directly supports GO:0004843 cysteine-type deubiquitinase activity and GO:0019783 ubiquitin-like protein peptidase activity. The presence of non-catalytic surfaces typical of USPs often mediates additional ligand interactions; here, two such modalities are indicated: GO:0005540 hyaluronic acid binding and GO:0003723 RNA binding. Hyaluronan binding can arise from basic, solvent-exposed patches that engage polyanionic glycans, while RNA-binding capacity is consistent with nucleolar residency and RNA-rich assemblies.\n\nThese molecular activities propagate to biological processes. By hydrolyzing ubiquitin from substrates, the enzyme executes GO:0016579 protein deubiquitination and modulates GO:0006511 ubiquitin-dependent protein catabolic process by rescuing or remodeling ubiquitylated proteins. In epithelial contexts, selective deubiquitination can tip cell-fate pathways toward apoptosis—either by stabilizing pro-apoptotic factors or by remodeling signaling complexes—supporting GO:1904037 positive regulation of epithelial cell apoptotic process. The nucleolar association and RNA-binding capacity further suggest roles in ribosome biogenesis surveillance and stress-responsive ubiquitin signaling.\n\nCellular localization follows from both catalytic logic and binding preferences. The nucleolus (GO:0005730) is a hub for ribosome assembly and RNA-rich granules; USP-family enzymes frequently partition to nucleoli where they tune ubiquitin signaling on RNA-processing and assembly factors. The absence of transmembrane features and the soluble papain-like fold point to a non-membranous, intranuclear environment, with nucleolar enrichment driven by RNA/hyaluronan-binding surfaces and substrate availability.\n\nMechanistically, I propose that the enzyme operates as a nucleolus-enriched deubiquitinase that edits ubiquitin signals on ribosome biogenesis and stress-response factors. Its papain-like active site removes ubiquitin to stabilize key nucleolar substrates, while auxiliary RNA/hyaluronan-binding surfaces concentrate it at RNA-rich assemblies. This positioning allows it to influence epithelial apoptosis by coupling nucleolar proteostasis to cell-fate pathways. Likely interaction partners include ubiquitin itself and polyubiquitylated substrates; nucleolar organizers and ribosome assembly factors; and E3/E2 ubiquitin-conjugation machinery that it counterbalances through deubiquitination.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-D6R9N7.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/D6R9N7"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/D6R9N7/entry","atlas":"/p/D6R9N7"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}