DEPDC5

Summary: DEPDC5 binds Rag GTPases and contributes to GATOR1 GAP activity.

Reason: IPR027244 maps the family to enabled GAP activity, but human experiments separate DEPDC5 Rag engagement from the NPRL2 catalytic module. The preferred GOA correction is to retain GO:0005096 with contributes_to rather than enables; the imported enables qualifier remains untouched here. GO:0031267 is the supported replacement for an enabled molecular function, while the core records contribution to GATOR1 GAP activity. Neither correction asserts autonomous DEPDC5 catalysis.

Proposed replacements: small GTPase binding

Summary: Binding to the ubiquitin-specific protease USP2.

Reason: IntAct intact:EBI-24681385 records a positive validated two-hybrid pair between O75140-2 (559 residues) and O75604, accompanied by array and pooling records. USP2 is a curated ubiquitin-specific protease; the partner class supports ubiquitin-specific protease binding, without assigning deubiquitinase activity or its regulation to DEPDC5. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Proposed replacements: ubiquitin-specific protease binding

Summary: Binding to the protein-folding chaperonin CCT3.

Reason: IntAct intact:EBI-24741275 records a positive validated two-hybrid pair between O75140-2 (559 residues) and P49368, accompanied by array and pooling records. CCT3 is a subunit of the TRiC protein-folding chaperonin, supporting protein-folding chaperone binding. The pair does not establish that DEPDC5 folds substrates or that the short product is a physiological TRiC client. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Proposed replacements: protein-folding chaperone binding

Summary: A validated short-product interaction with MAD2L1.

Reason: IntAct intact:EBI-24703582 records a positive validated two-hybrid pair between O75140-2 (559 residues) and Q13257, accompanied by array and pooling records. MAD2L1 is a spindle-checkpoint complex regulator. The pair does not establish a specific regulatory interaction, enzymatic activity or DEPDC5 checkpoint participation; retain the positive association as non-core. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Summary: Binding to a MEOX2 transcription-factor clone.

Reason: IntAct intact:EBI-24434236 records a positive validated two-hybrid pair between O75140-2 (559 residues) and Q6FHY5, accompanied by array and pooling records. The exact partner is the unreviewed 303-residue MEOX2 record Q6FHY5, matching reviewed MEOX2 except for one glutamine deletion outside its intact homeodomain. Direct human MEOX2 promoter-binding and reporter experiments establish its DNA-binding transcription-factor class. This supports a class-level binding refinement, without asserting that this clone has identical transcriptional activity or that DEPDC5 regulates transcription. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Proposed replacements: DNA-binding transcription factor binding

Summary: A validated short-product interaction with DPPA3.

Reason: IntAct intact:EBI-24665620 records a positive validated two-hybrid pair between O75140-2 (559 residues) and Q6W0C5, accompanied by array and pooling records. DPPA3 is a chromatin and epigenetic regulator. This isolated pair does not establish a more informative DEPDC5 molecular activity or participation in germ-cell reprogramming. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Summary: A validated short-product interaction with MTMR9.

Reason: IntAct intact:EBI-24656502 records a positive validated two-hybrid pair between O75140-2 (559 residues) and Q96QG7, accompanied by array and pooling records. MTMR9 is an inactive phosphatase that associates with active myotubularins. Binding it does not demonstrate phosphatase binding to an active enzyme, phosphatase regulation or a defined signaling-scaffold interaction by DEPDC5. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Summary: A validated short-product interaction with SYT17.

Reason: IntAct intact:EBI-24642109 records a positive validated two-hybrid pair between O75140-2 (559 residues) and Q9BSW7, accompanied by array and pooling records. SYT17 is a membrane-associated synaptotagmin-family protein; this pair does not establish a specific DEPDC5 molecular role in membrane traffic or neuronal signaling. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Summary: A validated short-product interaction with MAD2L2.

Reason: IntAct intact:EBI-24775208 records a positive validated two-hybrid pair between O75140-2 (559 residues) and Q9UI95, accompanied by array and pooling records. MAD2L2 participates in DNA polymerase-zeta and shieldin assemblies. The pair does not establish DEPDC5 participation in DNA repair, polymerase activity or binding a defined signaling scaffold. The heterologous assay establishes binding capacity, with no demonstrated native complex or transfer to other DEPDC5 products.

Summary: Cytosol and lysosomal membrane are supported, more specific locations.

Reason: The broad ARBA location is compatible with two experimentally supported pools. Mouse neuronal staining and human neural cultures support cytosolic DEPDC5 (PMID23542697); human tagged-DEPDC5 imaging and GATOR1 recruitment studies support the lysosomal surface (PMID23723238/28199306). Refine to cytosol and lysosomal membrane, both already represented among the source annotations. The human neural evidence remains preliminary and several KICSTOR localization assays use NPRL2 as the complex marker; no cell-type-independent distribution is asserted.

Proposed replacements: cytosol lysosomal membrane

Summary: DEPDC5 associates with the lysosomal surface.

Reason: The human-cell imaging in PMID23723238 places tagged DEPDC5 on the lysosomal surface, consistent with subsequent KICSTOR recruitment experiments and native lysosomal proteomics. Refine the organelle-level term to lysosomal membrane, already represented by other source rows; no membrane-spanning topology or lysosomal-lumen localization is implied.

Proposed replacements: lysosomal membrane

Summary: Native DEPDC5 is enriched with lysosomal membranes.

Reason: The original human placental lysosomal-membrane proteomics table lists DEPDC5 with 20 peptides, 18.4% sequence coverage and enrichment ratio 4.13. This supports membrane association, not integral-membrane topology. The historical 1572-residue isoform designation does not identify unique peptides specific to a current alternative product.

Summary: Ancestral lysosomal-membrane activity is supported on the human lineage.

Reason: The GO0005765 IBD is placed at PTN000995343 on the actual O75140 lineage. Its human experimental donor is legitimate target evidence for ancestral placement, not circular support. Direct human lysosomal-surface and GATOR1 recruitment experiments support the is_active_in qualifier.

Summary: KICSTOR positions GATOR1 activity at lysosomal membranes.

Reason: Endogenous-level FLAG-DEPDC5 proteomics and complex co-immunoprecipitation identify KICSTOR association. Tagged GATOR1 imaging and purified-lysosome experiments show that KICSTOR recruits the complex; several imaging assays use NPRL2 as the GATOR1 marker. Together with direct DEPDC5 localization in PMID23723238, these results support the recorded active location without assigning KICSTOR tether activity to DEPDC5.

Summary: The UniProt location mapping matches experimentally supported membrane association.

Reason: SL0157 maps the curated lysosomal-membrane location to GO0005765. Native proteomics and human GATOR1 localization/recruitment support this location, without implying transmembrane insertion.

Summary: The source supports DEPDC5 on the lysosomal surface.

Reason: The 2013 original reports tagged human DEPDC5 localization to the lysosomal surface and GATOR1 regulation of Rag-dependent mTORC1 signaling. The NAS evidence code is retained; this is not a claim that DEPDC5 is an integral membrane protein.

Summary: Reactome places DEPDC5-containing GATOR1 at the lysosomal membrane.

Reason: The exact event output contains a component path 9639281→9639274→9638242→9638222, terminating at the O75140 DEPDC5 physical entity with compartment GO0005765. This supports location of the complex component. The event ligand binds a Sestrin, CASTOR or SAMTOR protein; the model does not make DEPDC5 the amino-acid receptor or event catalyst.

Summary: Reactome places DEPDC5-containing GATOR1 at the lysosomal membrane.

Reason: The exact event output contains a component path 9639281→9639274→9638242→9638222, terminating at the O75140 DEPDC5 physical entity with compartment GO0005765. This supports location of the complex component. The event ligand binds a Sestrin, CASTOR or SAMTOR protein; the model does not make DEPDC5 the amino-acid receptor or event catalyst.

Summary: Reactome places DEPDC5-containing GATOR1 at the lysosomal membrane.

Reason: The exact event output contains a component path 9639274→9638242→9638222, terminating at the O75140 DEPDC5 physical entity with compartment GO0005765. This supports location of the complex component. The event ligand binds a Sestrin, CASTOR or SAMTOR protein; the model does not make DEPDC5 the amino-acid receptor or event catalyst.

Summary: Reactome places DEPDC5-containing GATOR1 at the lysosomal membrane.

Reason: The exact event output contains a component path 9639281→9639274→9638242→9638222, terminating at the O75140 DEPDC5 physical entity with compartment GO0005765. This supports location of the complex component. The event ligand binds a Sestrin, CASTOR or SAMTOR protein; the model does not make DEPDC5 the amino-acid receptor or event catalyst.

Summary: Cytosolic localization is supported outside the principal lysosomal GATOR1 context.

Reason: The original localization study reports mouse neuronal cell-body cytosol, often perinuclear, and corroborates the pattern in human neural cultures. Antibody controls include peptide blocking and omission of primary antibody, but the authors describe these as preliminary localization data. Retain this observed pool without replacing the principal lysosomal-membrane core location.

Summary: Cytosolic localization is supported outside the principal lysosomal GATOR1 context.

Reason: The original localization study reports mouse neuronal cell-body cytosol, often perinuclear, and corroborates the pattern in human neural cultures. Antibody controls include peptide blocking and omission of primary antibody, but the authors describe these as preliminary localization data. Retain this observed pool without replacing the principal lysosomal-membrane core location.

Summary: Positive regulation of autophagy is a supported downstream GATOR1 role.

Reason: PTN000323637 lies on the human lineage. Its yeast and fission-yeast Iml1 donors have direct loss-of-function autophagy assays: alkaline-phosphatase delivery in budding yeast and Pgk1-GFP processing in fission yeast. These support the inherited regulatory role; autophagy is retained as a downstream context of TORC1 inhibition, not as an intrinsic autophagy-executing activity or a second core.

Summary: DEPDC5 directly engages Rag GTPases.

Reason: Human GATOR1 structures and biochemical binding experiments identify the DEPDC5 interface with RagA. This binding state can restrain the NPRL2–NPRL3 catalytic module; binding does not imply autonomous GAP activity. Engineered truncations are not treated as natural alternative products.

Summary: DEPDC5 contacts Rag GTPases through distinct interfaces.

Reason: The human GATOR1–Rag–Ragulator structures and biochemical analyses identify an auxiliary DEPDC5–RagC interface alongside its previously characterized RagA interaction. Substrate engagement and nucleotide-state coordination support small GTPase binding, while the catalytic arginine finger belongs to NPRL2.

Summary: DEPDC5 associates with a CUL3 ubiquitin-ligase complex as a reported substrate.

Reason: The accessible original extended-data captions report HA-DEPDC5 co-immunoprecipitation with CUL3/RBX1 and in-vitro ubiquitylation with KLHL22. The source qualifier is colocalizes_with, not constitutive membership or ligase activity. The subsequent 2025 challenge and reply dispute the degradation mechanism, including antibody and tagging effects; they do not directly negate this tagged association experiment. Retain the qualified association as non-core and keep the controversy explicit.

Summary: The inherited amino-acid-starvation response is supported.

Reason: The GO0034198 IBD at PTN000995343 lies on the human lineage and is grounded in human DEPDC5 and fly Iml1 experiments. Human GATOR1 perturbation and rescue experiments support nutrient-dependent mTORC1 shutoff, so the target has no demonstrated loss of this inherited response. The target appearing as its own donor is legitimate experimental grounding.

Summary: DEPDC5 assembly and Rag engagement are required for nutrient regulation.

Reason: DEPDC5-deficient human cells and reconstitution with structure-guided mutants test amino-acid-dependent mTORC1 regulation. Failure of GATOR1-assembly mutants to restore regulation supports this source-specific response annotation; it does not establish direct amino-acid binding by DEPDC5.

Summary: The DEPDC5 auxiliary Rag interface supports nutrient responses.

Reason: Human-cell nutrient assays of DEPDC5 truncation and interface mutants complement the structural and biochemical analysis. The mutants can preserve complex assembly while compromising nutrient responses, supporting DEPDC5 participation in amino-acid-starvation signaling without assigning it ligand-sensor or GEF activity.

Summary: DEPDC5 enables mTORC1 shutoff after amino-acid withdrawal.

Reason: Human DEPDC5 depletion prevents normal amino-acid-dependent mTORC1 inhibition in the original experiments. Together with the established GATOR1 complex mechanism, this supports participation in the starvation response rather than an unsupported inference from disease alone.

Summary: Negative regulation of TORC1 signaling is the specific supported signaling role.

Reason: The IPR000591 DEP-domain mapping identifies a broad signaling context but cannot determine a particular pathway by itself. Direct human GATOR1 evidence establishes the more informative negative regulation of TORC1 signaling. Refine to that existing term without transferring Wnt or heterotrimeric-G-protein roles from other DEP-domain proteins.

Proposed replacements: negative regulation of TORC1 signaling

Summary: GATOR and Rag complex associations are retained as non-core context.

Reason: The human co-IP evidence supports association of DEPDC5-containing GATOR1 with Rag and GATOR assemblies. This broad complex-association annotation is retained, while the core specifies the directly resolved Rag-binding activity and contribution to GATOR1 GAP activity. GATOR1–GATOR2 co-IP does not identify a separate DEPDC5-enabled molecular activity or establish direct contact with every co-purifying component. In the 2018 subunit experiments, NPRL3 is necessary and sufficient for GATOR2 association.

Summary: Perinuclear cytoplasmic staining is an observed secondary localization.

Reason: PMID23542697 reports predominantly perinuclear neuronal cell-body staining in mouse brain and corroborating human neural cultures. Retain this location as a contextual pool, with the original study’s antibody-based and preliminary scope; no distinct perinuclear enzymatic function is inferred.

Summary: Perinuclear cytoplasmic staining is an observed secondary localization.

Reason: PMID23542697 reports predominantly perinuclear neuronal cell-body staining in mouse brain and corroborating human neural cultures. Retain this location as a contextual pool, with the original study’s antibody-based and preliminary scope; no distinct perinuclear enzymatic function is inferred.

Summary: Negative TORC1 regulation is an inherited core role.

Reason: PTN000323637 carries the GO1904262 IBD on the human lineage, with experimental yeast, fission-yeast, fly and human grounding. The independently characterized human GATOR1 mechanism strongly supports the inherited inhibitory role. Differences in nutrient context or catalytic subunit assignment do not invalidate this process-level transfer.

Summary: DEPDC5 organizes inhibitory GATOR1 regulation of mTORC1.

Reason: Human structures, biochemical assays and knockout-cell reconstitution link DEPDC5 assembly and Rag engagement to nutrient-dependent mTORC1 inhibition. The protein contributes to the complex’s GAP mechanism; its isolated binding state can inhibit catalytic access and is not itself the catalytic reaction.

Summary: DEPDC5 Rag contacts contribute to suppression of mTORC1.

Reason: Human-cell interface-mutant experiments and biochemical comparisons link the DEPDC5 auxiliary RagC interface to productive GATOR1 nucleotide-state control and suppression of mTORC1. The proposed membrane orientation switch remains a model, distinct from the measured inhibitory process.

Summary: DEPDC5 is required for GATOR-dependent Sestrin suppression of mTORC1.

Reason: DEPDC5 knockdown in human cells weakens SESN2-dependent inhibition of S6K/4EBP phosphorylation. This supports the GATOR1 inhibitory process in the Sestrin pathway, while the source locates Sestrin association through GATOR2 rather than demonstrating direct Sestrin–DEPDC5 binding.

Summary: DEPDC5-dependent negative mTORC1 regulation is supported despite a disputed degradation model.

Reason: The original public extended-data experiments test KLHL22 perturbation in DEPDC5-depleted human cells and support DEPDC5-dependent mTORC1 regulation. The 2025 challenge and reply dispute amino-acid/KLHL22-induced DEPDC5 degradation, including antibody and tag effects. Preserve this broader inhibitory-process annotation, independently established by GATOR1 studies, without treating the contested degradation model as settled.

Summary: DEPDC5-containing GATOR1 inhibits the amino-acid-sensing mTORC1 branch.

Reason: The original human-cell perturbations and complex-level RagA/B GAP assays establish the GATOR1 inhibitory mechanism. Retain the source NAS code and process annotation, without assigning autonomous GAP catalysis to DEPDC5.

Summary: DEPDC5 is the conserved large GATOR1 subunit.

Reason: The GO1990130 IBD at PTN000323637 lies on the human lineage. Direct yeast and fission-yeast complex purification/co-immunoprecipitation support the Iml1–Npr2–Npr3 assembly, and independent human structures establish DEPDC5–NPRL2–NPRL3 GATOR1. The human self donor is valid experimental grounding.

Summary: Human DEPDC5 is a structural subunit of GATOR1.

Reason: Purified human DEPDC5–NPRL2–NPRL3 complexes and their structures directly establish membership. DEPDC5 forms the large organizing subunit; complex membership and contribution to GAP activity do not make it the catalytic NPRL2 arginine-finger subunit.

Summary: Human DEPDC5 is a structural subunit of GATOR1.

Reason: Purified human DEPDC5–NPRL2–NPRL3 complexes and their structures directly establish membership. DEPDC5 forms the large organizing subunit; complex membership and contribution to GAP activity do not make it the catalytic NPRL2 arginine-finger subunit.

Summary: The source distinguishes GATOR1 from Sestrin-bound GATOR2.

Reason: Human-cell co-immunoprecipitation experiments use DEPDC5, NPRL2 and NPRL3 as GATOR1 and distinguish this assembly from GATOR2. FLAG-DEPDC5 does not co-precipitate endogenous Sestrin2 in the reported experiment; Sestrin–GATOR2 association is not substituted for a DEPDC5 interaction. Independent structures corroborate the GATOR1 membership.