Affinage

TBC1D5

TBC1 domain family member 5 · UniProt Q92609

Length
795 aa
Mass
89.0 kDa
Annotated
2026-04-28
19 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

TBC1D5 is a GTPase-activating protein (GAP) for Rab7 and Rab7b that integrates endosomal membrane identity with retromer-dependent trafficking and autophagy. TBC1D5 docks onto the VPS29 subunit of the retromer cargo-selective complex (VPS35/VPS29/VPS26) via a hydrophobic loop, and this interaction both positions TBC1D5 to inactivate Rab7-GTP on endosomal membranes and is required for retromer membrane uncoating, retrograde transport of CI-MPR, GLUT1 recycling, and ATG9 sorting to autophagosome formation sites (PMID:19531583, PMID:27827364, PMID:28602638, PMID:24603492). The TBC1D5–retromer interaction is competitively displaced by pathogen effectors (Legionella RidL, SARS-CoV-2 ORF3a) and modulated by LC3-positive autophagic membranes, which sequester TBC1D5 during metabolic stress to relieve retromer inhibition, while endosomal luminal pH sensed via NHE6 regulates TBC1D5 GAP activity to control Rab7 cycling and endosome maturation (PMID:29146912, PMID:38448435, PMID:28602638, PMID:29158324). Loss of TBC1D5 causes Rab7 hyperactivation, lysosomal accumulation of retromer, impaired Parkin-mediated mitophagy, and in Drosophila, excessive synaptic growth through elevated BMP receptor levels at the neuromuscular junction (PMID:29158324, PMID:36473687).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2009 High

    Establishing TBC1D5 as a retromer-associated Rab GAP resolved how Rab7 inactivation is coupled to retromer membrane dynamics, showing that TBC1D5 interacts with the VPS35/VPS29/VPS26 subcomplex and drives Rab7 dissociation from membranes.

    Evidence Co-immunoprecipitation, membrane fractionation, and dominant-negative Rab7 experiments in mammalian cells

    PMID:19531583

    Open questions at the time
    • No structural basis for the TBC1D5–retromer interaction
    • Rab7 substrate specificity not confirmed by in vitro GAP assay
    • Downstream cargo trafficking consequences not yet defined
  2. 2014 High

    Demonstrating that TBC1D5 associates with ATG9 and the ULK1 complex during autophagy established an unexpected link between retromer-associated Rab7 inactivation and autophagosome biogenesis, showing that TBC1D5 depletion mistraffics ATG9 to late endosomes.

    Evidence Co-immunoprecipitation with ATG9/ULK1/clathrin/AP2, siRNA knockdown, and immunofluorescence trafficking assays

    PMID:24603492

    Open questions at the time
    • Direct versus indirect interaction with ATG9 not resolved
    • Whether TBC1D5 GAP activity is required for ATG9 sorting not tested
    • How clathrin/AP2 association relates to Rab7 regulation unknown
  3. 2016 High

    The crystal structure of TBC1D5 bound to VPS29 revealed the precise molecular interface — a hydrophobic loop inserted into a conserved VPS29 pocket — explaining how TBC1D5 docks onto retromer and providing the structural template later exploited by pathogen effectors.

    Evidence X-ray crystallography of TBC1D5 GAP domain–VPS29 complex, ITC, pulldown, mutagenesis, and cellular trafficking assays

    PMID:27827364

    Open questions at the time
    • Full-length TBC1D5–retromer ternary complex structure not obtained
    • Whether the second loop contacting VPS35 is functionally essential was not resolved
    • Structural basis of GAP catalysis toward Rab7 not captured
  4. 2017 High

    Three studies collectively established that TBC1D5 is dynamically regulated: LC3-positive autophagic membranes sequester TBC1D5 from retromer to enable GLUT1 recycling during metabolic stress; retromer-TBC1D5 cooperatively controls Rab7 across ER, TGN, and mitochondria, and its loss impairs mitophagy; and Legionella RidL competitively displaces TBC1D5 from VPS29 to promote intracellular bacterial replication.

    Evidence Co-IP, siRNA, live-cell imaging, FRAP, GTP-binding assays, flow cytometry for surface GLUT1, crystal structure of RidL–VPS29, infection assays

    PMID:28602638 PMID:29146912 PMID:29158324

    Open questions at the time
    • Quantitative kinetics of TBC1D5 redistribution between retromer and LC3 membranes not measured
    • Whether mitophagy defect is solely Rab7-dependent or involves additional TBC1D5 substrates unclear
    • RidL displacement shown in vitro and by co-localization but long-term consequences on host endosomal network not fully mapped
  5. 2018 High

    Identification of Rab7b as a second TBC1D5 substrate broadened the GAP's functional scope to retromer-dependent sorting of CI-MPR and sortilin, with retromer proteins enhancing TBC1D5 GAP activity toward Rab7b in vitro.

    Evidence In vitro GAP assay, siRNA screen, Co-IP, immunofluorescence, vesicle distribution quantification

    PMID:30111580

    Open questions at the time
    • Relative contribution of Rab7a versus Rab7b inactivation to retromer trafficking not dissected
    • No structural data for TBC1D5–Rab7b complex
    • Whether retromer enhancement of GAP activity is allosteric or proximity-based unknown
  6. 2020 Medium

    Two infection studies showed that TBC1D5-mediated Rab7 cycling is co-opted by pathogens beyond Legionella: HPV requires TBC1D5-driven Rab7 GTP hydrolysis for retromer disassembly and viral retrograde trafficking, and Coxiella burnetii kinase CstK recruits TBC1D5 to facilitate vacuolar biogenesis.

    Evidence Artificial protein inhibitors, siRNA knockdown, Rab7 mutants, infection/replication assays, yeast two-hybrid, CCV morphology quantification

    PMID:32303638 PMID:32521275

    Open questions at the time
    • Whether CstK phosphorylates TBC1D5 or modulates its GAP activity unknown
    • Mechanistic distinction between constitutive versus HPV-specific Rab7 cycling requirements not fully explained
    • Both studies from single laboratories
  7. 2022 Medium

    Genetic analysis in Drosophila demonstrated an in vivo developmental role: TBC1D5 constrains synaptic growth at the NMJ by maintaining retromer-Rab7-dependent retrieval of the BMP receptor Wit, linking endosomal Rab7 GAP function to intercellular signaling.

    Evidence Genetic null mutants, epistasis with Rab7 and retromer alleles, immunofluorescence, electron microscopy at the Drosophila NMJ

    PMID:36473687

    Open questions at the time
    • Whether mammalian TBC1D5 similarly regulates BMP signaling not tested
    • Direct biochemistry of Drosophila TBC1D5 GAP activity not performed
    • Single genetic model system
  8. 2023 Medium

    Demonstrating that autophagy can target retromer+TBC1D5 endosomes for bulk phagophore-mediated destruction revealed a second mode of autophagy–retromer crosstalk beyond TBC1D5 sequestration, requiring TBC1D5's retromer-binding capacity but not its LIR motif.

    Evidence mTOR inhibition, MTOR genetic KO, mutant TBC1D5 rescue, cargo recycling assays

    PMID:37938196

    Open questions at the time
    • Selectivity mechanism for targeting TBC1D5-containing endosomes to phagophores unknown
    • Whether this pathway operates during physiological starvation in vivo not shown
    • Single lab study
  9. 2024 Medium

    SARS-CoV-2 ORF3a was shown to sequester TBC1D5 via a Vps39-containing complex, displacing Rab7 and causing Rab7 hyperactivation that blocks CI-M6PR retrieval and lysosomal hydrolase delivery while promoting viral egress — establishing TBC1D5 as a convergent target of viral immune evasion.

    Evidence Co-immunoprecipitation, dominant-negative Rab7 mutant, viral replication assays, CI-M6PR trafficking assay

    PMID:38448435

    Open questions at the time
    • Direct binding interface between ORF3a–Vps39 complex and TBC1D5 not structurally resolved
    • Whether other coronaviruses use the same mechanism not tested
    • Contribution of TBC1D5 sequestration versus other ORF3a activities to viral pathogenesis not dissected

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of TBC1D5's catalytic mechanism toward Rab7, the quantitative contribution of Rab7a versus Rab7b inactivation to specific trafficking itineraries, whether endosomal pH directly regulates TBC1D5 GAP activity in vivo, and the physiological importance of TBC1D5 post-translational modifications.
  • No structure of TBC1D5 in complex with Rab7-GTP
  • pH-dependent regulation awaits peer-reviewed confirmation
  • Post-translational regulation (phosphorylation) mentioned but functionally undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 3 GO:0140096 catalytic activity, acting on a protein 2
Localization
GO:0005768 endosome 3 GO:0031410 cytoplasmic vesicle 2
Pathway
R-HSA-5653656 Vesicle-mediated transport 4 R-HSA-9612973 Autophagy 4 R-HSA-9609507 Protein localization 3
Partners
ATG9ANHE6RAB7ARAB7BVPS26VPS29VPS35
Complex memberships
Retromer cargo-selective complex (VPS35/VPS29/VPS26)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 TBC1D5 is a Rab GAP protein that interacts with the retromer cargo-selective subcomplex (VPS35/VPS29/VPS26) and negatively regulates its endosomal recruitment by causing Rab7 to dissociate from the membrane. Co-immunoprecipitation, membrane fractionation, dominant-negative Rab7 experiments Journal of cell science High 19531583
2016 Crystal structure of the TBC1D5 GAP domain bound to VPS29 reveals that a loop from TBC1D5 binds a conserved hydrophobic pocket on VPS29 opposite the VPS29-VPS35 interface; a distinct loop may also contact VPS35. TBC1D5 is a high-affinity ligand of the retromer cargo-selective complex and loss of TBC1D5 causes defective retromer-dependent receptor trafficking. X-ray crystallography, complementary biochemical assays (pulldown, ITC), cellular trafficking assays, mutagenesis Nature communications High 27827364
2014 TBC1D5 associates with ATG9 and the active ULK1 complex during autophagy, and also interacts with clathrin and the AP2 complex. Depletion of TBC1D5 leads to missorting of ATG9 to late endosomes upon autophagy induction, demonstrating TBC1D5 regulates ATG9 vesicular trafficking toward autophagosome formation sites. Co-immunoprecipitation, siRNA knockdown, immunofluorescence/trafficking assays EMBO reports High 24603492
2017 Retromer and its associated RAB7-specific GAP TBC1D5 together control the activity state and localization of RAB7 across multiple membrane compartments including ER, TGN, and mitochondria. Loss of TBC1D5 or retromer causes RAB7 hyperactivation and lysosomal accumulation, impairing ATG9a sorting and autophagosome formation around damaged mitochondria during Parkin-mediated mitophagy. siRNA knockdown, live-cell imaging, FRAP, immunofluorescence, GTP-binding assays The EMBO journal High 29158324
2017 During metabolic stress, LC3+ autophagic compartments bind and sequester TBC1D5 away from retromer, releasing TBC1D5's inhibitory interaction with retromer and enabling retromer recruitment to endosomal membranes and GLUT1 plasma membrane translocation. In autophagy-deficient cells, TBC1D5 maintains inhibitory interactions with retromer, causing GLUT1 mis-sorting into endolysosomes. Co-immunoprecipitation, siRNA knockdown, flow cytometry (surface GLUT1), immunofluorescence, rescue experiments Molecular cell High 28602638
2017 The Legionella pneumophila effector RidL binds to the VPS29 retromer subunit at the same hydrophobic pocket as TBC1D5, thereby displacing TBC1D5 from retromer and from LCVs. TBC1D5 displacement promotes intracellular bacterial growth. Crystal structure of RidL-VPS29 complex, in vitro binding assays, mutagenesis, cell-based co-localization and displacement assays, infection assays Nature communications High 29146912
2018 TBC1D5 inhibits Rab7a GTPase activity (GAP function), and pharmacological or genetic inhibition of TBC1D5 enhances Rab7a activation, leading to increased retromer recruitment to endosomes and gain of retromer function. siRNA knockdown, GTP-loading assays, endosomal recruitment assays, cargo trafficking assays Journal of cell science Medium 29777037
2018 TBC1D5 localizes to Rab7b-positive vesicles, physically interacts with Rab7b, and has in vitro GAP activity toward Rab7b that is further enhanced by retromer proteins. Loss of TBC1D5 reduces the number of CI-MPR- and sortilin-positive vesicles, phenocopying constitutively active Rab7b. siRNA screen, in vitro GAP assay, Co-immunoprecipitation, immunofluorescence, vesicle distribution quantification Journal of cell science High 30111580
2020 During HPV entry, retromer binding to the HPV L2 capsid protein recruits TBC1D5 to retromer at the endosome membrane; TBC1D5 then stimulates Rab7-GTP hydrolysis to drive retromer disassembly from HPV and delivery to the retrograde pathway. HPV trafficking specifically requires Rab7 GTP/GDP cycling, unlike constitutive retromer cargoes. Artificial protein inhibitors, siRNA knockdown, infection assays, co-localization, dominant-negative and constitutively active Rab7 mutants Cell reports Medium 32521275
2020 The Coxiella burnetii secreted kinase CstK physically interacts with TBC1D5, co-localizes with TBC1D5 in non-infected cells, and TBC1D5 is recruited to Coxiella-containing vacuoles (CCVs). TBC1D5 depletion significantly impairs CCV development, indicating TBC1D5 is functionally required for vacuole biogenesis during infection. Yeast two-hybrid, co-immunoprecipitation, immunofluorescence, siRNA knockdown with CCV morphology readout The Journal of biological chemistry Medium 32303638
2022 In Drosophila NMJ, TBC1D5 (ortholog) coordinates with retromer and Rab7 to constrain synaptic growth; loss of TBC1D5 increases BMP type II receptor Wishful Thinking (Wit) levels at the NMJ, upregulating BMP signaling and causing excessive satellite boutons and branch formation. Disruption of TBC1D5-Rab7 or TBC1D5-retromer interactions phenocopies TBC1D5 loss. Genetic null mutants, epistasis analysis, immunofluorescence, electron microscopy, Western blot Journal of genetics and genomics Medium 36473687
2023 Autophagy targets retromer+TBC1D5 endosomes for bulk destruction by phagophores in a manner requiring TBC1D5 and its ability to bind retromer (but not TBC1D5's C-terminal LIR motif or its nutrient-regulated dephosphorylation), leading to impaired endosomal recycling of retromer cargoes to the plasma membrane and TGN. mTOR inhibition, MTOR genetic KO, immunofluorescence, cargo recycling assays, mutant TBC1D5 rescue experiments Autophagy Medium 37938196
2024 SARS-CoV-2 ORF3a, in complex with Vps39, sequesters TBC1D5 and displaces Rab7 from the TBC1D5 complex, thereby disrupting Rab7 GTP hydrolysis and causing Rab7 hyperactivation. This impairs CI-M6PR retrieval from late endosomes to TGN and blocks lysosomal hydrolase transport, while promoting viral egress. Co-immunoprecipitation, dominant-negative Rab7 mutant, viral replication assays, immunofluorescence, CI-M6PR trafficking assay Nature communications Medium 38448435
2021 In ischemic/hypoxic cardiomyocytes, reduced TBC1D5 levels block the Rab7 membrane GTPase cycle, which impedes retromer binding to microtubules and motor proteins, impairing retrograde transport and leading to decreased CI-MPR levels and abnormal distribution of lysosomal cathepsins. Ischemia/hypoxia cell model, Western blot, immunofluorescence, co-immunoprecipitation, subcellular fractionation Frontiers in cardiovascular medicine Low 35004909
2024 NHE6-mediated proton efflux from the endosomal lumen activates late endosomal Rab7 by potently inactivating the Rab7 GAP TBC1D5 in a pH-dependent manner. NHE6 physically interacts with TBC1D5 in a complex with Rab7, and epistatic knockdown of TBC1D5 in NHE6-null neurons rescues Rab7 GTPase cycling and endosome maturation. Co-immunoprecipitation, pH-dependent GAP activity assays, NHE6-null mouse neurons, epistatic siRNA knockdown, endosome maturation assays bioRxivpreprint Medium bio_10.1101_2024.12.09.627558

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. Journal of cell science 304 19531583
2017 Control of RAB7 activity and localization through the retromer-TBC1D5 complex enables RAB7-dependent mitophagy. The EMBO journal 158 29158324
2014 TBC1D5 and the AP2 complex regulate ATG9 trafficking and initiation of autophagy. EMBO reports 146 24603492
2017 Autophagy-Dependent Shuttling of TBC1D5 Controls Plasma Membrane Translocation of GLUT1 and Glucose Uptake. Molecular cell 119 28602638
2016 Structural and mechanistic insights into regulation of the retromer coat by TBC1d5. Nature communications 90 27827364
2018 Inhibition of TBC1D5 activates Rab7a and can enhance the function of the retromer cargo-selective complex. Journal of cell science 63 29777037
2017 Structural insights into Legionella RidL-Vps29 retromer subunit interaction reveal displacement of the regulator TBC1D5. Nature communications 42 29146912
2018 TBC1D5 controls the GTPase cycle of Rab7b. Journal of cell science 38 30111580
2024 SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle. Nature communications 36 38448435
2020 TBC1D5-Catalyzed Cycling of Rab7 Is Required for Retromer-Mediated Human Papillomavirus Trafficking during Virus Entry. Cell reports 33 32521275
2020 The secreted protein kinase CstK from Coxiella burnetii influences vacuole development and interacts with the GTPase-activating host protein TBC1D5. The Journal of biological chemistry 13 32303638
2023 Autophagy captures the retromer-TBC1D5 complex to inhibit receptor recycling. Autophagy 9 37938196
2024 Enhancing Rab7 Activity by Inhibiting TBC1D5 Expression Improves Mitophagy in Alzheimer's Disease Models. Journal of Alzheimer's disease : JAD 8 38848175
2024 TBC1D5 reverses the capability of HIF-2α in tumor progression and lipid metabolism in clear cell renal cell carcinoma by regulating the autophagy. Journal of translational medicine 7 38419050
2020 miR-10 involved in salinity-induced stress responses and targets TBC1D5 in the sea cucumber, Apostichopus japonicas. Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 7 31904427
2012 Integration of H-2Z1, a somatosensory cortex-expressed transgene, interferes with the expression of the Satb1 and Tbc1d5 flanking genes and affects the differentiation of a subset of cortical interneurons. The Journal of neuroscience : the official journal of the Society for Neuroscience 7 22623674
2022 GTPase-activating protein TBC1D5 coordinates with retromer to constrain synaptic growth by inhibiting BMP signaling. Journal of genetics and genomics = Yi chuan xue bao 6 36473687
2021 Impaired Retrograde Transport Due to Lack of TBC1D5 Contributes to the Trafficking Defect of Lysosomal Cathepsins in Ischemic/Hypoxic Cardiomyocytes. Frontiers in cardiovascular medicine 0 35004909
2020 Gender-Discordant Monochorionic-Diamniotic Twins Both With 45,X/46,X, Idic(Y) Mosaicism and a Novel Deletion Within the TBC1D5 Gene. Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society 0 32364436