{"uniprot":"Q5VVX9","gene":"UBE2U","name":"Ubiquitin-conjugating enzyme E2 U","organism":"Homo sapiens (Human)","status":"dark","length":321,"sequence":"MHGRAYLLLHRDFCDLKENNYKGITAKPVSEDMMEWEVEIEGLQNSVWQGLVFQLTIHFTSEYNYAPPVVKFITIPFHPNVDPHTGQPCIDFLDNPEKWNTNYTLSSILLALQVMLSNPVLENPVNLEAARILVKDESLYRTILRLFNRPLQMKDDSQELPKDPRKCIRPIKTTSFSDYYQTWSRIATSKATEYYRTPLLKVPNFIGQYYKWKKMDLQHQKEWNLKYSVIKCWLARKRMPHEVTHSMEEIKLCPTLIPTTDEIFLESPTAINSITDIYETEEEGWKSDTSLYENDTDEPREEEVEDLISWTNTLNTNTSED","function_summary":"A soluble cytoplasmic ubiquitin-conjugating enzyme that forms a thioester with ubiquitin and collaborates with activating and ligating partners to transfer ubiquitin onto target proteins. By assembling transient complexes through extensive protein-binding surfaces, it supports selective ubiquitination that triggers proteasome-directed turnover and broader protein quality control pathways in the cytosol.","plain_language":"UBE2U has barely been studied. The model's best guess: A soluble cytoplasmic ubiquitin-conjugating enzyme that forms a thioester with ubiquitin and collaborates with activating and ligating partners to transfer ubiquitin onto target proteins. By assembling transient complexes through extensive protein-binding surfaces, it supports selective ubiquitination that triggers proteasome-directed turnover and broader protein quality control pathways in the cytosol.","uniprot_summary":"Catalyzes the covalent attachment of ubiquitin to other proteins.","go_terms":{"molecular_function":[{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0006511","label":"ubiquitin-dependent protein catabolic process"}],"cellular_component":[{"id":"GO:0005829","label":"cytosol"}]},"interpro":[{"id":"IPR016135","name":"Ubiquitin-conjugating enzyme/RWD-like","type":"homologous_superfamily","start":1,"end":149},{"id":"IPR000608","name":"Ubiquitin-conjugating (UBC), catalytic core domain","type":"domain","start":4,"end":153},{"id":"IPR050113","name":"Ubiquitin-conjugating enzyme E2-like","type":"family","start":5,"end":143},{"id":"IPR023313","name":"Ubiquitin-conjugating enzyme, active site","type":"active_site","start":77,"end":93}],"reasoning":"I begin with the InterPro architecture. The polypeptide is dominated by IPR000608 (Ubiquitin-conjugating [UBC] catalytic core domain, residues 4–153), a compact β-grasp fold that forms the canonical E2 enzyme scaffold. This core sits within IPR016135 (Ubiquitin-conjugating enzyme/RWD-like homologous superfamily, residues 1–149), indicating structural homology to E2/RWD folds that mediate thioester chemistry and adaptor binding. The sequence is further classified by IPR050113 (Ubiquitin-conjugating enzyme E2-like family, residues 5–143), reinforcing that the entire protein is an E2-class modifier rather than an accessory. Critically, IPR023313 (Ubiquitin-conjugating enzyme, active site, residues 77–93) marks the catalytic center that forms a transient thioester with ubiquitin. The ordered layout—an E2 catalytic core with a defined active-site window—establishes a thioester-forming conjugase that collaborates with E1 and E3 factors.\n\nThis architecture causes a specific molecular function: the UBC fold and active-site motif enable ubiquitin transfer chemistry, while the broad E2/RWD-like superfamily and extended surface loops promote multivalent contacts with partner proteins. These features together support GO:0005515 protein binding as an intrinsic capability of the scaffold, which is necessary for assembling E1–E2–E3–substrate complexes and for engaging ubiquitin itself.\n\nFrom this molecular function, the biological process follows. E2 enzymes load ubiquitin from E1 and, in concert with E3 ligases, direct ubiquitin onto lysine residues of target proteins. This modification routes substrates to degradation pathways and remodels signaling assemblies. Therefore, the enzyme’s activity feeds directly into GO:0006511 ubiquitin-dependent protein catabolic process, coupling ubiquitination to proteasomal turnover and quality control.\n\nCellular localization is inferred from the soluble, enzyme-core architecture lacking transmembrane segments or targeting peptides. E2 conjugases typically operate in the cytosolic phase where E1 and many E3s reside and where substrate flux to the proteasome is coordinated. This supports a soluble cytoplasmic residence consistent with GO:0005829 cytosol and with broader cytoplasmic annotation.\n\nMechanistically, the enzyme accepts activated ubiquitin from E1 via transthiolation to its catalytic cysteine (within residues 77–93), then transfers ubiquitin to substrates or to E3-bound intermediates. The UBC core’s exposed surfaces and the E2-like family classification predict dynamic assemblies with E3 ligases that determine substrate specificity and chain topology. I hypothesize that it partners with cytosolic E3 modules (such as cullin–RING assemblies and other RING/U-box ligases) and transiently associates with proteasome-proximal factors. These interactions would position the enzyme at hubs of cytosolic protein quality control, where it catalyzes ubiquitin transfer and thereby drives selective protein degradation.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-Q5VVX9.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/Q5VVX9"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/Q5VVX9/entry","atlas":"/p/Q5VVX9"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}