{"uniprot":"Q8N7R7","gene":"CCNYL1","name":"Cyclin-Y-like protein 1","organism":"Homo sapiens (Human)","status":"dark","length":359,"sequence":"MGNTLTCCVSPNASPKLGRRAGSAELYCASDIYEAVSGDAVAVAPAVVEPAELDFGEGEGHHLQHISDREMPEDLALESNPSDHPRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLDDSTVSQPNLRTTVKCVTLAIYYHIKNRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTLVYLERLLTYAEIDICPTNWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFNINVPASVYAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKDLCRAAMRRSFSADNFIGIQRSKAILS","function_summary":"A human regulatory cyclin that assembles with and modulates cyclin-dependent kinases to coordinate cell-cycle control. Its cyclin fold provides the allosteric interface that tunes kinase activity, while N-terminal features likely guide targeting between membrane-proximal signaling sites, the cytoplasm, and the nucleus. By forming holoenzyme assemblies with kinases, it integrates plasma membrane–proximal cues with nucleocytoplasmic programs to regulate phosphorylation cascades that govern proliferation and checkpoint pathways.","plain_language":"CCNYL1 has barely been studied. The model's best guess: A human regulatory cyclin that assembles with and modulates cyclin-dependent kinases to coordinate cell-cycle control. Its cyclin fold provides the allosteric interface that tunes kinase activity, while N-terminal features likely guide targeting between membrane-proximal signaling sites, the cytoplasm, and the nucleus.","uniprot_summary":"Involved in cell cycle regulation.","go_terms":{"molecular_function":[{"id":"GO:0016538","label":"cyclin-dependent protein serine/threonine kinase regulator activity"},{"id":"GO:0005515","label":"protein binding"}],"biological_process":[{"id":"GO:0051726","label":"regulation of cell cycle"},{"id":"GO:0000079","label":"regulation of cyclin-dependent protein serine/threonine kinase activity"}],"cellular_component":[{"id":"GO:0005737","label":"cytoplasm"},{"id":"GO:0005886","label":"plasma membrane"},{"id":"GO:0005634","label":"nucleus"},{"id":"GO:0000307","label":"cyclin-dependent protein kinase holoenzyme complex"}]},"interpro":[{"id":"IPR036915","name":"Cyclin-like superfamily","type":"homologous_superfamily","start":191,"end":285},{"id":"IPR006671","name":"Cyclin, N-terminal","type":"domain","start":180,"end":285},{"id":"IPR013763","name":"Cyclin-like domain","type":"domain","start":193,"end":278},{"id":"IPR012399","name":"Cyclin Y","type":"family","start":1,"end":359}],"reasoning":"I begin with the InterPro architecture. The sequence is classified as IPR012399 (Cyclin Y family) spanning residues 1–359, establishing the overall identity and evolutionary context of a cyclin-class regulatory protein. Within its C-terminal half, three concordant cyclin-fold signatures appear: IPR006671 (Cyclin, N-terminal domain, residues 180–285), IPR013763 (Cyclin-like domain, residues 193–278), and IPR036915 (Cyclin-like superfamily, residues 191–285). The ordered layout—an N-terminal region that precedes and feeds into a canonical cyclin box fold—creates the hallmark bilobal cyclin architecture. This fold forms a conserved hydrophobic interface that binds and allosterically regulates cyclin-dependent kinases (CDKs). The concentration of cyclin-box signatures in the 180–285 region indicates that the principal regulatory core resides there, while the N-terminal family-specific region (1–180) likely mediates targeting and subcellular routing.\n\nThis cyclin-box architecture causes cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538). The cyclin fold is not catalytic; instead, it stabilizes and modulates CDK active sites, tuning substrate specificity and timing. The same surface that docks CDKs also supports multivalent contacts with other partners, consistent with protein binding (GO:0005515). Together, these molecular functions position the protein as a regulatory hub rather than an enzyme.\n\nBy modulating CDKs, the protein directly governs pathways that control progression and checkpoints, thereby driving regulation of the cell cycle (GO:0051726). More specifically, its cyclin-mediated control of CDKs constitutes regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079). The dual presence of cyclin motifs and a likely targeting N-terminus suggests it can switch between inhibitory and permissive states for CDKs depending on context.\n\nCellular localization follows from both the cyclin architecture and trafficking cues. The cyclin fold commonly operates in soluble compartments, supporting cytoplasmic residence (GO:0005737). The presence of a nuclear-localized regulatory axis and the need to coordinate transcriptional and checkpoint pathways argue for nuclear localization (GO:0005634). The protein’s family context and targeting features also point to membrane-proximal signaling. Association with membrane-tethered adaptors and cargo explains its presence at the plasma membrane (GO:0005886). Assembly with CDKs defines its participation in a cyclin-dependent protein kinase holoenzyme complex (GO:0000307). This ensemble of compartments reflects a dynamic cycle: membrane-associated signaling captures and modifies the cyclin–CDK module, which then operates in the cytoplasm and nucleus to enforce cell-cycle control.\n\nMechanistically, the cyclin-box core binds and tunes CDKs, while the N-terminal region likely recruits trafficking and membrane-associated partners. I hypothesize that the protein transiently assembles with CDK1 and CDK2 to form active holoenzymes, and with membrane-localized adaptors that govern endocytic or signaling routes. Candidate partners include adaptor protein complexes that govern endocytosis and recycling, small GTPases that specify membrane identity, and membrane-associated scaffolds. These assemblies would allow the cyclin–CDK module to shuttle between the plasma membrane and nucleocytoplasmic space, coupling extracellular cues to cell-cycle governance.","category":"dark","control_evaluation":null,"validation_plan":null,"structure":{"source":"AlphaFold DB","pdb":"/structures/AF-Q8N7R7.pdb","alphafold":"https://alphafold.ebi.ac.uk/entry/Q8N7R7"},"links":{"uniprot":"https://www.uniprot.org/uniprotkb/Q8N7R7/entry","atlas":"/p/Q8N7R7"},"provenance":{"model":"BioReason-Pro (ESM3 esm3-sm-open-v1)","source_list":"Pharos Tdark","note":"AI prediction, not experimentally verified"}}