{"doi":"10.1101/2023.09.28.559894","title":"Structural pathway for class III PI 3-kinase activation by the myristoylated GTP-binding pseudokinase VPS15","abstract":"Abstract The class III phosphatidylinositol (PI) 3-kinase complexes I and II (PI3KC3-C1 and -C2) are central to the initiation of macroautophagy and endosomal maturation, respectively. Through three-dimensional classification of a large cryo-EM dataset of human PI3KC3-C1 bound to the small GTPase RAB1A, we were able to map the structural pathway of enzyme activation. The inactive conformation is stabilized by an N -myristoyl modification of the pseudokinase (PK) subunit VPS15. The N -myristate is sequestered in the N-lobe of the VPS15 PK domain, which stabilizes a series of interactions whereby VPS15 sequesters and blocks the catalytic and membrane binding units of the VPS34 lipid kinase. In the activated conformation, the N -myristate and the VPS34 lipid kinase domain are liberated to interact with membranes and catalyze PI3P formation. The VPS15 PK domain contains a unique Arg at the gatekeeper position and binds tightly to GTP. GTP binding structurally stabilizes the N -myristate “in” conformation, which promotes the inactive conformation. This pathway provides a general mechanism for PI3KC3 activation in autophagy and endosome biogenesis and a roadmap for their pharmacological upregulation.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":400986,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.946,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1177673,"name":"Minghao Chen","orcid":"0000-0002-7668-3974","position":1,"is_corresponding":false},{"id":237132,"name":"Xuefeng Ren","orcid":"0000-0002-4822-4316","position":2,"is_corresponding":false},{"id":271123,"name":"Shanlin Rao","orcid":"0000-0003-4892-5523","position":3,"is_corresponding":false},{"id":1177674,"name":"Samantha N. Garcia","orcid":"0000-0001-5668-5609","position":4,"is_corresponding":false},{"id":1031790,"name":"Ainara Claveras Cabezudo","orcid":"0000-0003-1400-4929","position":5,"is_corresponding":false},{"id":261600,"name":"Anthony T. Iavarone","orcid":null,"position":6,"is_corresponding":false},{"id":240042,"name":"Gerhard Hummer","orcid":"0000-0001-7768-746X","position":7,"is_corresponding":false},{"id":237133,"name":"James H. Hurley","orcid":"0000-0001-5054-5445","position":8,"is_corresponding":false},{"id":888480,"name":"Annan SI Cook","orcid":"0000-0001-6415-9107","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":null,"created_at":"2026-07-19T01:20:08.195423Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}