{"gene":"TBC1D17","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":2007,"finding":"TBC1D17 was identified as a Rab GAP that specifically regulates Shiga toxin trafficking from the cell surface to the Golgi apparatus but not EGF uptake, placing it as a regulator of a discrete endosomal trafficking pathway.","method":"Functional screen of 39 predicted human Rab GAPs using Shiga toxin and EGF uptake assays in cells","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean functional screen with defined pathway readout, single lab, single primary method","pmids":["17562788"],"is_preprint":false},{"year":2012,"finding":"TBC1D17 acts as a GAP for Rab8, inactivating it through catalytic activity. Optineurin acts as an adaptor protein that bridges TBC1D17 and Rab8, mediating their interaction and colocalization. A non-catalytic region of TBC1D17 directly interacts with optineurin. TBC1D17 inhibits Rab8 recruitment to endocytic recycling tubules and thereby impairs transferrin receptor recycling from early endosomes. The glaucoma-associated E50K mutation in optineurin enhances TBC1D17-mediated Rab8 inactivation, causing defective transferrin receptor recycling.","method":"Co-immunoprecipitation, colocalization, catalytically inactive TBC1D17 mutant rescue, shRNA knockdown, live-cell imaging of Rab8 and transferrin receptor trafficking","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, catalytic mutant used, knockdown rescue, multiple orthogonal methods in single lab","pmids":["22854040"],"is_preprint":false},{"year":2014,"finding":"TBC1D17 localizes to autophagosomes and inhibits autophagy flux in a catalytic-activity-dependent manner. In the context of the E50K optineurin mutant, TBC1D17 activity mediates a block in autophagy flux leading to retinal cell death; knockdown of TBC1D17 rescues E50K-induced autophagy impairment and cell death.","method":"shRNA knockdown of TBC1D17, expression of catalytically inactive TBC1D17 mutant, colocalization with autophagosome markers, autophagy flux assays, cell viability assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — catalytic mutant and shRNA rescue used, multiple readouts, single lab","pmids":["24752605"],"is_preprint":false},{"year":2014,"finding":"TBC1D17 participates in mitophagy and forms both homodimers and heterodimers with TBC1D15. Together with TBC1D15, TBC1D17 regulates autophagosome biogenesis and morphology during mitophagy downstream of Parkin activation by inhibiting Rab7 activity at the interface between mitochondria and isolation membranes.","method":"Co-immunoprecipitation for dimer detection, Rab7 activity assays, autophagosome morphology analysis, epistasis with Parkin/PINK1 pathway","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, Rab GAP activity assay, functional mitophagy readouts, replicated in context of established PINK1-Parkin pathway","pmids":["24569479"],"is_preprint":false},{"year":2021,"finding":"TBC1D17 is a GAP for Rab5 and regulates transport of Glut1, Glut4, and transferrin receptor. AMPK phosphorylates TBC1D17 at Ser168, which promotes an intramolecular interaction between the N-terminal region (residues 1-306) and the TBC domain, enhancing auto-inhibition of TBC1D17 and thereby increasing Rab5 activity to promote GLUT4 translocation and glucose uptake. TBC1D17 interacts with Rab5 via its TBC domain and with AMPK via its N-terminal region.","method":"Co-immunoprecipitation, phosphorylation site mutagenesis (Ser168), in vitro AMPK phosphorylation assay, Rab5 activity assay, GLUT4 translocation assay in myoblasts and skeletal muscle, intramolecular interaction mapping","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro phosphorylation assay with mutagenesis, intramolecular domain interaction, functional glucose uptake readout, multiple orthogonal methods in single lab","pmids":["34045668"],"is_preprint":false},{"year":2024,"finding":"The central coiled-coil domain of optineurin and active (GTP-bound) Rab8a can simultaneously interact with the TBC domain of TBC1D17 to form a ternary complex. The optineurin leucine-zipper domain (LZD) and the TBC domain of TBC1D17 competitively bind to active Rab8a. The crystal structure of OPTN LZD in complex with active Rab8a was determined, revealing the molecular basis of OPTN-Rab8a interaction and a unique effector binding mode.","method":"Crystal structure determination (OPTN LZD/active Rab8a complex), biochemical binding assays (pull-down, co-immunoprecipitation), mutagenesis of ALS-associated mutations","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with biochemical validation, mutagenesis, ternary complex reconstitution, single lab with multiple orthogonal methods","pmids":["39374890"],"is_preprint":false},{"year":2024,"finding":"SUMOylated FIS1 interacts with TBC1D17 under hypoxia, and this interaction suppresses hypoxia-induced mitophagy (HIM), identifying TBC1D17 as a fine-tuning negative regulator of HIM downstream of the SENP3-FIS1 axis.","method":"Co-immunoprecipitation of SUMOylated FIS1 with TBC1D17 under hypoxic conditions, mitophagy flux assays, cell death assays; validated in primary glioma stem cell-like cultures","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP with functional mitophagy readout, single lab, interaction validated in patient-derived cells but mechanistic follow-up limited","pmids":["39638786"],"is_preprint":false},{"year":2026,"finding":"Crystal structures of murine (2.20 Å) and human (3.34 Å) TBC domains of TBC1D17 were determined, revealing a heart-like shape and dimerization through a fragment near residues involved in GTP hydrolysis. Biochemical mapping showed that Rab5a interacts strongly with TBC1D17 fragments containing the annotated Rab-binding domain (RBD), whereas interactions with the TBC domain alone are much weaker, establishing the RBD as critical for Rab5a binding.","method":"X-ray crystallography (crystal structure), in vitro binding assays with truncation fragments of TBC1D17 for Rab5a interaction mapping","journal":"Protein science : a publication of the Protein Society","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure determination plus in vitro binding assays with domain mapping, multiple orthogonal methods in single study","pmids":["41999088"],"is_preprint":false}],"current_model":"TBC1D17 is a Rab GTPase-activating protein (RabGAP) that inactivates Rab8 (via an optineurin adaptor-mediated mechanism), Rab5 (regulating GLUT1/4 and transferrin receptor trafficking, subject to AMPK-mediated auto-inhibitory phosphorylation at Ser168), and Rab7 (in concert with TBC1D15 as a heterodimer during mitophagy); its TBC domain crystal structure has been resolved and a distinct Rab-binding domain (RBD) mediates high-affinity Rab5a binding, while its catalytic activity at autophagosome membranes controls autophagy flux and autophagic encapsulation of damaged mitochondria, with SUMOylated FIS1 interaction providing an additional regulatory input under hypoxia."},"narrative":{"mechanistic_narrative":"TBC1D17 is a Rab GTPase-activating protein (RabGAP) that controls distinct membrane trafficking and autophagic pathways by catalytically inactivating specific Rab GTPases [PMID:17562788, PMID:22854040]. It was first defined as a regulator of a discrete endosomal route, selectively governing Shiga toxin transport from the cell surface to the Golgi without affecting EGF uptake [PMID:17562788]. As a GAP for Rab8, TBC1D17 is bridged to its target by the adaptor optineurin, which binds a non-catalytic region of TBC1D17; this Rab8 inactivation blocks Rab8 recruitment to recycling tubules and impairs transferrin receptor recycling, an effect amplified by the glaucoma-associated optineurin E50K mutation [PMID:22854040]. Structural work resolved a ternary arrangement in which the optineurin coiled-coil and GTP-bound Rab8a engage the TBC domain, while the optineurin leucine-zipper and the TBC domain compete for active Rab8a [PMID:39374890]. TBC1D17 also acts as a GAP for Rab5, regulating GLUT1, GLUT4, and transferrin receptor trafficking; AMPK phosphorylation at Ser168 drives an intramolecular contact between the N-terminal region and the TBC domain that auto-inhibits TBC1D17, raising Rab5 activity to promote GLUT4 translocation and glucose uptake [PMID:34045668]. In autophagy, TBC1D17 localizes to autophagosomes and restrains autophagy flux through its catalytic activity, and it forms homo- and heterodimers with TBC1D15 to inhibit Rab7 at the mitochondria–isolation membrane interface during Parkin-driven mitophagy [PMID:24752605, PMID:24569479]. SUMOylated FIS1 binds TBC1D17 under hypoxia, positioning it as a negative regulator of hypoxia-induced mitophagy downstream of the SENP3–FIS1 axis [PMID:39638786]. Crystal structures of the TBC domain reveal a heart-like fold that dimerizes near catalytic residues, and a separate Rab-binding domain confers high-affinity Rab5a binding that the TBC domain alone cannot [PMID:39374890, PMID:41999088].","teleology":[{"year":2007,"claim":"Establishing whether TBC1D17 has a defined cellular substrate pathway, a functional screen placed it as a Rab GAP acting in a discrete retrograde endosome-to-Golgi route rather than a generic trafficking regulator.","evidence":"Functional screen of predicted human Rab GAPs using Shiga toxin and EGF uptake assays in cells","pmids":["17562788"],"confidence":"Medium","gaps":["Specific Rab substrate not identified in this study","Selectivity for Shiga toxin over EGF route mechanistically unexplained"]},{"year":2012,"claim":"To explain how TBC1D17 reaches a specific Rab, optineurin was identified as an adaptor that bridges TBC1D17 to Rab8, linking Rab8 inactivation to transferrin receptor recycling and to glaucoma-associated optineurin mutation.","evidence":"Co-IP, colocalization, catalytically inactive mutant rescue, shRNA knockdown, live-cell imaging of Rab8 and transferrin receptor","pmids":["22854040"],"confidence":"High","gaps":["Structural basis of the TBC1D17–optineurin–Rab8 interaction not defined","Whether other adaptors target TBC1D17 to additional Rabs unknown"]},{"year":2014,"claim":"Connecting TBC1D17 GAP activity to a degradative outcome, it was shown to localize to autophagosomes and to suppress autophagy flux, with knockdown rescuing E50K-induced cell death.","evidence":"shRNA knockdown, catalytically inactive mutant, autophagosome colocalization, autophagy flux and viability assays","pmids":["24752605"],"confidence":"Medium","gaps":["Rab substrate at autophagosomes not pinned down in this study","How TBC1D17 is recruited to autophagosome membranes unclear"]},{"year":2014,"claim":"Addressing how mitophagy membrane dynamics are controlled, TBC1D17 was shown to dimerize with TBC1D15 and inhibit Rab7 at the mitochondria–isolation membrane interface downstream of Parkin.","evidence":"Co-IP for dimer detection, Rab7 activity assays, autophagosome morphology analysis, epistasis with PINK1/Parkin","pmids":["24569479"],"confidence":"High","gaps":["Relative GAP contribution of TBC1D17 versus TBC1D15 within the heterodimer not resolved","Recruitment mechanism to the mitochondrial interface not defined"]},{"year":2021,"claim":"Revealing how TBC1D17 activity is regulated, AMPK phosphorylation at Ser168 was shown to trigger an auto-inhibitory intramolecular interaction, restraining Rab5 GAP activity to promote GLUT4 translocation and glucose uptake.","evidence":"In vitro AMPK phosphorylation, Ser168 mutagenesis, intramolecular interaction mapping, Rab5 activity and GLUT4 translocation assays in muscle","pmids":["34045668"],"confidence":"High","gaps":["Whether AMPK regulation extends to Rab8/Rab7-dependent functions untested","Structural detail of the N-terminal/TBC autoinhibited state not determined"]},{"year":2024,"claim":"Defining the architecture of the Rab8 module, structural and competition analyses showed optineurin and active Rab8a can form a ternary complex with the TBC domain, while the optineurin leucine-zipper and TBC domain compete for active Rab8a.","evidence":"Crystal structure of OPTN LZD/active Rab8a, pull-down and Co-IP binding assays, ALS-mutation mutagenesis","pmids":["39374890"],"confidence":"High","gaps":["Full TBC1D17/optineurin/Rab8a ternary structure not solved","Functional consequence of the competitive binding in cells not quantified"]},{"year":2024,"claim":"Identifying an additional regulatory input, SUMOylated FIS1 was found to bind TBC1D17 under hypoxia, positioning it as a fine-tuning negative regulator of hypoxia-induced mitophagy via the SENP3–FIS1 axis.","evidence":"Co-IP of SUMOylated FIS1 with TBC1D17 under hypoxia, mitophagy flux and cell death assays in patient-derived glioma stem-like cells","pmids":["39638786"],"confidence":"Medium","gaps":["Direct versus SUMO-dependent binding interface on TBC1D17 not mapped","Whether the FIS1 interaction modulates GAP catalytic activity unknown"]},{"year":2026,"claim":"Resolving the substrate-recognition logic, crystal structures of the TBC domain revealed a heart-shaped fold that dimerizes near catalytic residues, and binding mapping established a distinct Rab-binding domain as critical for high-affinity Rab5a interaction.","evidence":"X-ray crystallography of murine and human TBC domains plus in vitro Rab5a binding with truncation fragments","pmids":["41999088"],"confidence":"High","gaps":["Structure of the RBD–Rab5a complex not determined","Functional role of TBC domain dimerization in catalysis untested"]},{"year":null,"claim":"It remains unresolved how the multiple Rab substrates (Rab5, Rab7, Rab8), adaptor and regulatory inputs (optineurin, AMPK, SUMOylated FIS1), and dimerization states are integrated to select among endosomal recycling, autophagy, and mitophagy outputs in a given cellular context.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model coordinating Rab5/Rab7/Rab8 GAP activities","Context determinants of substrate choice unknown","In vivo physiological phenotypes of TBC1D17 loss not characterized in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,3,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,3,4]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,5]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2,3,6]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,4]}],"complexes":[],"partners":["OPTN","RAB8A","RAB5","RAB7","TBC1D15","PRKAA","FIS1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9HA65","full_name":"TBC1 domain family member 17","aliases":[],"length_aa":648,"mass_kda":72.7,"function":"Probable RAB GTPase-activating protein that inhibits RAB8A/B function. Reduces Rab8 recruitment to tubules emanating from the endocytic recycling compartment (ERC) and inhibits Rab8-mediated endocytic trafficking, such as that of transferrin receptor (TfR) (PubMed:22854040). Involved in regulation of autophagy","subcellular_location":"Cytoplasmic vesicle, autophagosome; Cytoplasm; Recycling endosome","url":"https://www.uniprot.org/uniprotkb/Q9HA65/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TBC1D17","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TBC1D17","total_profiled":1310},"omim":[{"mim_id":"616659","title":"TBC1 DOMAIN FAMILY, MEMBER 17; TBC1D17","url":"https://www.omim.org/entry/616659"},{"mim_id":"612662","title":"TBC1 DOMAIN FAMILY, MEMBER 15; TBC1D15","url":"https://www.omim.org/entry/612662"},{"mim_id":"602432","title":"OPTINEURIN; OPTN","url":"https://www.omim.org/entry/602432"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":132.3}],"url":"https://www.proteinatlas.org/search/TBC1D17"},"hgnc":{"alias_symbol":["FLJ12168"],"prev_symbol":[]},"alphafold":{"accession":"Q9HA65","domains":[{"cath_id":"2.30.29.230","chopping":"2-21_29-62_118-190","consensus_level":"medium","plddt":74.5803,"start":2,"end":190},{"cath_id":"1.10.472.80","chopping":"191-204_271-311_456-596","consensus_level":"medium","plddt":89.2453,"start":191,"end":596},{"cath_id":"1.10.8.270","chopping":"331-450","consensus_level":"high","plddt":95.8285,"start":331,"end":450}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9HA65","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9HA65-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9HA65-F1-predicted_aligned_error_v6.png","plddt_mean":72.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TBC1D17","jax_strain_url":"https://www.jax.org/strain/search?query=TBC1D17"},"sequence":{"accession":"Q9HA65","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9HA65.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9HA65/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9HA65"}},"corpus_meta":[{"pmid":"24569479","id":"PMC_24569479","title":"Mitochondrial Rab GAPs govern autophagosome biogenesis during mitophagy.","date":"2014","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/24569479","citation_count":267,"is_preprint":false},{"pmid":"17562788","id":"PMC_17562788","title":"Specific Rab GTPase-activating proteins define the Shiga toxin and epidermal growth factor uptake pathways.","date":"2007","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17562788","citation_count":126,"is_preprint":false},{"pmid":"22854040","id":"PMC_22854040","title":"Optineurin mediates a negative regulation of Rab8 by the GTPase-activating protein TBC1D17.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/22854040","citation_count":57,"is_preprint":false},{"pmid":"24752605","id":"PMC_24752605","title":"E50K-OPTN-induced retinal cell death involves the Rab GTPase-activating protein, TBC1D17 mediated block in autophagy.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24752605","citation_count":55,"is_preprint":false},{"pmid":"29951055","id":"PMC_29951055","title":"Altered Functions and Interactions of Glaucoma-Associated Mutants of Optineurin.","date":"2018","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29951055","citation_count":52,"is_preprint":false},{"pmid":"34045668","id":"PMC_34045668","title":"AMPK-mediated phosphorylation enhances the auto-inhibition of TBC1D17 to promote Rab5-dependent glucose uptake.","date":"2021","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/34045668","citation_count":43,"is_preprint":false},{"pmid":"26302410","id":"PMC_26302410","title":"Defects in autophagy caused by glaucoma-associated mutations in optineurin.","date":"2015","source":"Experimental eye research","url":"https://pubmed.ncbi.nlm.nih.gov/26302410","citation_count":40,"is_preprint":false},{"pmid":"34432599","id":"PMC_34432599","title":"C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/34432599","citation_count":35,"is_preprint":false},{"pmid":"39638786","id":"PMC_39638786","title":"SENP3-FIS1 axis promotes mitophagy and cell survival under hypoxia.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/39638786","citation_count":11,"is_preprint":false},{"pmid":"39374890","id":"PMC_39374890","title":"Molecular Basis of the Recognition of the Active Rab8a by Optineurin.","date":"2024","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/39374890","citation_count":6,"is_preprint":false},{"pmid":"39539253","id":"PMC_39539253","title":"Proteomics reveals that nanoplastics with different sizes induce hepatocyte apoptosis in mice through distinct mechanisms involving mitophagy dysregulation and cell cycle 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specifically regulates Shiga toxin trafficking from the cell surface to the Golgi apparatus but not EGF uptake, placing it as a regulator of a discrete endosomal trafficking pathway.\",\n      \"method\": \"Functional screen of 39 predicted human Rab GAPs using Shiga toxin and EGF uptake assays in cells\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean functional screen with defined pathway readout, single lab, single primary method\",\n      \"pmids\": [\"17562788\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TBC1D17 acts as a GAP for Rab8, inactivating it through catalytic activity. Optineurin acts as an adaptor protein that bridges TBC1D17 and Rab8, mediating their interaction and colocalization. A non-catalytic region of TBC1D17 directly interacts with optineurin. TBC1D17 inhibits Rab8 recruitment to endocytic recycling tubules and thereby impairs transferrin receptor recycling from early endosomes. The glaucoma-associated E50K mutation in optineurin enhances TBC1D17-mediated Rab8 inactivation, causing defective transferrin receptor recycling.\",\n      \"method\": \"Co-immunoprecipitation, colocalization, catalytically inactive TBC1D17 mutant rescue, shRNA knockdown, live-cell imaging of Rab8 and transferrin receptor trafficking\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, catalytic mutant used, knockdown rescue, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"22854040\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TBC1D17 localizes to autophagosomes and inhibits autophagy flux in a catalytic-activity-dependent manner. In the context of the E50K optineurin mutant, TBC1D17 activity mediates a block in autophagy flux leading to retinal cell death; knockdown of TBC1D17 rescues E50K-induced autophagy impairment and cell death.\",\n      \"method\": \"shRNA knockdown of TBC1D17, expression of catalytically inactive TBC1D17 mutant, colocalization with autophagosome markers, autophagy flux assays, cell viability assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — catalytic mutant and shRNA rescue used, multiple readouts, single lab\",\n      \"pmids\": [\"24752605\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TBC1D17 participates in mitophagy and forms both homodimers and heterodimers with TBC1D15. Together with TBC1D15, TBC1D17 regulates autophagosome biogenesis and morphology during mitophagy downstream of Parkin activation by inhibiting Rab7 activity at the interface between mitochondria and isolation membranes.\",\n      \"method\": \"Co-immunoprecipitation for dimer detection, Rab7 activity assays, autophagosome morphology analysis, epistasis with Parkin/PINK1 pathway\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, Rab GAP activity assay, functional mitophagy readouts, replicated in context of established PINK1-Parkin pathway\",\n      \"pmids\": [\"24569479\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TBC1D17 is a GAP for Rab5 and regulates transport of Glut1, Glut4, and transferrin receptor. AMPK phosphorylates TBC1D17 at Ser168, which promotes an intramolecular interaction between the N-terminal region (residues 1-306) and the TBC domain, enhancing auto-inhibition of TBC1D17 and thereby increasing Rab5 activity to promote GLUT4 translocation and glucose uptake. TBC1D17 interacts with Rab5 via its TBC domain and with AMPK via its N-terminal region.\",\n      \"method\": \"Co-immunoprecipitation, phosphorylation site mutagenesis (Ser168), in vitro AMPK phosphorylation assay, Rab5 activity assay, GLUT4 translocation assay in myoblasts and skeletal muscle, intramolecular interaction mapping\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro phosphorylation assay with mutagenesis, intramolecular domain interaction, functional glucose uptake readout, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"34045668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The central coiled-coil domain of optineurin and active (GTP-bound) Rab8a can simultaneously interact with the TBC domain of TBC1D17 to form a ternary complex. The optineurin leucine-zipper domain (LZD) and the TBC domain of TBC1D17 competitively bind to active Rab8a. The crystal structure of OPTN LZD in complex with active Rab8a was determined, revealing the molecular basis of OPTN-Rab8a interaction and a unique effector binding mode.\",\n      \"method\": \"Crystal structure determination (OPTN LZD/active Rab8a complex), biochemical binding assays (pull-down, co-immunoprecipitation), mutagenesis of ALS-associated mutations\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with biochemical validation, mutagenesis, ternary complex reconstitution, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"39374890\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SUMOylated FIS1 interacts with TBC1D17 under hypoxia, and this interaction suppresses hypoxia-induced mitophagy (HIM), identifying TBC1D17 as a fine-tuning negative regulator of HIM downstream of the SENP3-FIS1 axis.\",\n      \"method\": \"Co-immunoprecipitation of SUMOylated FIS1 with TBC1D17 under hypoxic conditions, mitophagy flux assays, cell death assays; validated in primary glioma stem cell-like cultures\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP with functional mitophagy readout, single lab, interaction validated in patient-derived cells but mechanistic follow-up limited\",\n      \"pmids\": [\"39638786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Crystal structures of murine (2.20 Å) and human (3.34 Å) TBC domains of TBC1D17 were determined, revealing a heart-like shape and dimerization through a fragment near residues involved in GTP hydrolysis. Biochemical mapping showed that Rab5a interacts strongly with TBC1D17 fragments containing the annotated Rab-binding domain (RBD), whereas interactions with the TBC domain alone are much weaker, establishing the RBD as critical for Rab5a binding.\",\n      \"method\": \"X-ray crystallography (crystal structure), in vitro binding assays with truncation fragments of TBC1D17 for Rab5a interaction mapping\",\n      \"journal\": \"Protein science : a publication of the Protein Society\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure determination plus in vitro binding assays with domain mapping, multiple orthogonal methods in single study\",\n      \"pmids\": [\"41999088\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TBC1D17 is a Rab GTPase-activating protein (RabGAP) that inactivates Rab8 (via an optineurin adaptor-mediated mechanism), Rab5 (regulating GLUT1/4 and transferrin receptor trafficking, subject to AMPK-mediated auto-inhibitory phosphorylation at Ser168), and Rab7 (in concert with TBC1D15 as a heterodimer during mitophagy); its TBC domain crystal structure has been resolved and a distinct Rab-binding domain (RBD) mediates high-affinity Rab5a binding, while its catalytic activity at autophagosome membranes controls autophagy flux and autophagic encapsulation of damaged mitochondria, with SUMOylated FIS1 interaction providing an additional regulatory input under hypoxia.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TBC1D17 is a Rab GTPase-activating protein (RabGAP) that controls distinct membrane trafficking and autophagic pathways by catalytically inactivating specific Rab GTPases [#0, #1]. It was first defined as a regulator of a discrete endosomal route, selectively governing Shiga toxin transport from the cell surface to the Golgi without affecting EGF uptake [#0]. As a GAP for Rab8, TBC1D17 is bridged to its target by the adaptor optineurin, which binds a non-catalytic region of TBC1D17; this Rab8 inactivation blocks Rab8 recruitment to recycling tubules and impairs transferrin receptor recycling, an effect amplified by the glaucoma-associated optineurin E50K mutation [#1]. Structural work resolved a ternary arrangement in which the optineurin coiled-coil and GTP-bound Rab8a engage the TBC domain, while the optineurin leucine-zipper and the TBC domain compete for active Rab8a [#5]. TBC1D17 also acts as a GAP for Rab5, regulating GLUT1, GLUT4, and transferrin receptor trafficking; AMPK phosphorylation at Ser168 drives an intramolecular contact between the N-terminal region and the TBC domain that auto-inhibits TBC1D17, raising Rab5 activity to promote GLUT4 translocation and glucose uptake [#4]. In autophagy, TBC1D17 localizes to autophagosomes and restrains autophagy flux through its catalytic activity, and it forms homo- and heterodimers with TBC1D15 to inhibit Rab7 at the mitochondria–isolation membrane interface during Parkin-driven mitophagy [#2, #3]. SUMOylated FIS1 binds TBC1D17 under hypoxia, positioning it as a negative regulator of hypoxia-induced mitophagy downstream of the SENP3–FIS1 axis [#6]. Crystal structures of the TBC domain reveal a heart-like fold that dimerizes near catalytic residues, and a separate Rab-binding domain confers high-affinity Rab5a binding that the TBC domain alone cannot [#5, #7].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing whether TBC1D17 has a defined cellular substrate pathway, a functional screen placed it as a Rab GAP acting in a discrete retrograde endosome-to-Golgi route rather than a generic trafficking regulator.\",\n      \"evidence\": \"Functional screen of predicted human Rab GAPs using Shiga toxin and EGF uptake assays in cells\",\n      \"pmids\": [\"17562788\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific Rab substrate not identified in this study\", \"Selectivity for Shiga toxin over EGF route mechanistically unexplained\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"To explain how TBC1D17 reaches a specific Rab, optineurin was identified as an adaptor that bridges TBC1D17 to Rab8, linking Rab8 inactivation to transferrin receptor recycling and to glaucoma-associated optineurin mutation.\",\n      \"evidence\": \"Co-IP, colocalization, catalytically inactive mutant rescue, shRNA knockdown, live-cell imaging of Rab8 and transferrin receptor\",\n      \"pmids\": [\"22854040\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the TBC1D17–optineurin–Rab8 interaction not defined\", \"Whether other adaptors target TBC1D17 to additional Rabs unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connecting TBC1D17 GAP activity to a degradative outcome, it was shown to localize to autophagosomes and to suppress autophagy flux, with knockdown rescuing E50K-induced cell death.\",\n      \"evidence\": \"shRNA knockdown, catalytically inactive mutant, autophagosome colocalization, autophagy flux and viability assays\",\n      \"pmids\": [\"24752605\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Rab substrate at autophagosomes not pinned down in this study\", \"How TBC1D17 is recruited to autophagosome membranes unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Addressing how mitophagy membrane dynamics are controlled, TBC1D17 was shown to dimerize with TBC1D15 and inhibit Rab7 at the mitochondria–isolation membrane interface downstream of Parkin.\",\n      \"evidence\": \"Co-IP for dimer detection, Rab7 activity assays, autophagosome morphology analysis, epistasis with PINK1/Parkin\",\n      \"pmids\": [\"24569479\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative GAP contribution of TBC1D17 versus TBC1D15 within the heterodimer not resolved\", \"Recruitment mechanism to the mitochondrial interface not defined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealing how TBC1D17 activity is regulated, AMPK phosphorylation at Ser168 was shown to trigger an auto-inhibitory intramolecular interaction, restraining Rab5 GAP activity to promote GLUT4 translocation and glucose uptake.\",\n      \"evidence\": \"In vitro AMPK phosphorylation, Ser168 mutagenesis, intramolecular interaction mapping, Rab5 activity and GLUT4 translocation assays in muscle\",\n      \"pmids\": [\"34045668\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether AMPK regulation extends to Rab8/Rab7-dependent functions untested\", \"Structural detail of the N-terminal/TBC autoinhibited state not determined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defining the architecture of the Rab8 module, structural and competition analyses showed optineurin and active Rab8a can form a ternary complex with the TBC domain, while the optineurin leucine-zipper and TBC domain compete for active Rab8a.\",\n      \"evidence\": \"Crystal structure of OPTN LZD/active Rab8a, pull-down and Co-IP binding assays, ALS-mutation mutagenesis\",\n      \"pmids\": [\"39374890\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full TBC1D17/optineurin/Rab8a ternary structure not solved\", \"Functional consequence of the competitive binding in cells not quantified\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identifying an additional regulatory input, SUMOylated FIS1 was found to bind TBC1D17 under hypoxia, positioning it as a fine-tuning negative regulator of hypoxia-induced mitophagy via the SENP3–FIS1 axis.\",\n      \"evidence\": \"Co-IP of SUMOylated FIS1 with TBC1D17 under hypoxia, mitophagy flux and cell death assays in patient-derived glioma stem-like cells\",\n      \"pmids\": [\"39638786\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus SUMO-dependent binding interface on TBC1D17 not mapped\", \"Whether the FIS1 interaction modulates GAP catalytic activity unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Resolving the substrate-recognition logic, crystal structures of the TBC domain revealed a heart-shaped fold that dimerizes near catalytic residues, and binding mapping established a distinct Rab-binding domain as critical for high-affinity Rab5a interaction.\",\n      \"evidence\": \"X-ray crystallography of murine and human TBC domains plus in vitro Rab5a binding with truncation fragments\",\n      \"pmids\": [\"41999088\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of the RBD–Rab5a complex not determined\", \"Functional role of TBC domain dimerization in catalysis untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how the multiple Rab substrates (Rab5, Rab7, Rab8), adaptor and regulatory inputs (optineurin, AMPK, SUMOylated FIS1), and dimerization states are integrated to select among endosomal recycling, autophagy, and mitophagy outputs in a given cellular context.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model coordinating Rab5/Rab7/Rab8 GAP activities\", \"Context determinants of substrate choice unknown\", \"In vivo physiological phenotypes of TBC1D17 loss not characterized in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 3, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 3, 4]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2, 3, 6]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"OPTN\", \"RAB8A\", \"RAB5\", \"RAB7\", \"TBC1D15\", \"PRKAA\", \"FIS1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}