Affinage

VPS33A

Vacuolar protein sorting-associated protein 33A · UniProt Q96AX1

Length
596 aa
Mass
67.6 kDa
Annotated
2026-06-11
19 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

VPS33A is a Sec1/Munc18 (SM)-family protein and a core subunit of the HOPS membrane-tethering complex that regulates SNARE-mediated fusion of late endosomes, multivesicular bodies, autophagosomes, and lysosome-related organelles with lysosomes (PMID:23901104, PMID:25783203, PMID:19158398). Crystallographic and structure-guided mutagenesis established that VPS16 recruits VPS33A to HOPS through residues 642–736 of VPS16, an interface necessary and sufficient for the interaction, and disruption of this binding prevents lysosome fusion with both endosomes and autophagosomes (PMID:23901104, PMID:25783203). VPS33A confers pathway specificity at the lysosomal fusion step by engaging defined SNARE complexes — it binds syntaxin 17 via a motif in the STX17 N-peptide to license the autophagic STX17–SNAP29–VAMP7 trans-SNARE complex, with an STX17 N-peptide phosphoserine acting as a late regulatory checkpoint, and it binds Stx11 to support the Snap23–Stx11–Vamp8 SNARE complex driving renin granule biogenesis (PMID:30655294, PMID:40855995). Proximity proteomics place VPS33A with both CORVET and HOPS subunits and with class III PI3-kinase complex components, distinguishing it from its paralog VPS33B (PMID:29778605). Loss-of-function alleles produce organelle-specific trafficking defects: the buff mouse D251E mutation blocks MVB–lysosome and autophagosome–lysosome fusion by altering HOPS-subunit and SNARE associations, causing melanosome, lysosome, and storage-granule biogenesis defects resembling Hermansky-Pudlak syndrome (PMID:12538872, PMID:19566896, PMID:26259518). A homozygous Arg498Trp mutation destabilizes VPS33A folding and reduces HOPS/CORVET abundance, causing lysosomal over-acidification, glycosaminoglycan and sphingolipid accumulation underlying a mucopolysaccharidosis-plus phenotype (PMID:31070736, PMID:28013294).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2003 Medium

    Established that a mammalian VPS33A defect causes a lysosome-related organelle biogenesis disease, linking the gene to vacuolar/lysosomal trafficking before its biochemistry was known.

    Evidence positional cloning of the buff mouse mutation

    PMID:12538872

    Open questions at the time
    • mechanistic role in the tethering complex inferred from yeast/Drosophila homology, not direct mammalian biochemistry
    • specific SNARE partners not yet identified
  2. 2009 Medium

    Resolved how VPS33A achieves pathway specificity, showing it acts at late endosome-to-lysosome and autophagosome-lysosome fusion via syntaxin binding rather than at early endosomes.

    Evidence Drosophila carnation null allele, mosaic analysis, and in vitro dSyntaxin16 binding; mouse buff urothelium ultrastructure and lysosomal enzyme assays; RANKL pull-down and VPS33A knockdown in osteoblasts

    PMID:19158398 PMID:19419298 PMID:19566896

    Open questions at the time
    • mammalian SNARE-binding specificity not directly tested in these studies
    • RANKL cargo interaction shown by pull-down without structural mapping
  3. 2013 High

    Defined the atomic basis of VPS33A's incorporation into HOPS, identifying the VPS16(642–736) interface as the recruitment determinant.

    Evidence X-ray crystallography of VPS33A alone and with VPS16, plus in vitro and cell-based interface mutagenesis

    PMID:23901104

    Open questions at the time
    • structure of the full HOPS complex with VPS33A not resolved
    • did not test functional consequence of interface disruption on fusion
  4. 2015 High

    Demonstrated functionally that VPS16-mediated recruitment to HOPS is required for fusion, and separated VPS33A/HOPS from the distinct VPS33B/VIPAR complex.

    Evidence structure-guided interface mutants tested in dextran-delivery and autophagosome-lysosome fusion rescue assays with siRNA depletion; co-IP comparisons

    PMID:25783203

    Open questions at the time
    • does not resolve how HOPS engages individual SNAREs at each membrane
    • in vitro reconstitution of fusion not performed
  5. 2015 Medium

    Showed that HOPS assembly controls autophagosomal SNARE engagement, explaining how the D251E mutation selectively impairs autophagy.

    Evidence co-IP of VPS33A(D251E) and Y440D mutants with HOPS subunits and the STX17–VAMP8–SNAP29 SNARE complex; autophagy and endocytic flux assays; buff brain histology

    PMID:26259518

    Open questions at the time
    • enhanced versus deficient SNARE association as the disease driver not biochemically dissected
    • single lab
  6. 2017 Medium

    Uncovered a role for VPS33A in lysosomal pH homeostasis and glycosaminoglycan catabolism, defining the mucopolysaccharidosis-plus disease mechanism.

    Evidence exome sequencing of Arg498Trp patients, lysosomal pH measurement, GAG quantification, and RNAi knockdown

    PMID:28013294

    Open questions at the time
    • molecular link between VPS33A loss and over-acidification not defined
    • endocytic/autophagic pathways reported unaffected, conflicting with other models of the same mutation
  7. 2018 Medium

    Mapped the proximity interactome of VPS33A, distinguishing it from VPS33B and placing it with both CORVET/HOPS and class III PI3-kinase machinery.

    Evidence BioID proximity biotinylation-mass spectrometry with gel filtration and reciprocal validation

    PMID:29778605

    Open questions at the time
    • proximity does not establish direct binary interactions
    • functional significance of PI3KC3 association not tested
  8. 2019 Medium

    Identified an N-peptide phosphorylation checkpoint on STX17 controlling fusion competency, and confirmed Arg498Trp destabilizes folding and depletes HOPS/CORVET.

    Evidence FLIM-FRET in live HeLa cells with STX17 N-peptide and phosphomimetic mutants; crystal-structure-based stability prediction with proteasome-inhibitor rescue and lipidomics

    PMID:30655294 PMID:31070736

    Open questions at the time
    • kinase responsible for STX17 N-peptide phosphorylation not identified
    • VAMP7 versus VAMP8 usage differs between studies
  9. 2025 Medium

    Extended VPS33A's SNARE-engaging role to a new lysosome-related organelle, showing it supports renin granule biogenesis via Stx11.

    Evidence buff mouse analysis, As4.1 knockdown, co-IP of VPS33A with Stx11, renin assays, and electron microscopy

    PMID:40855995

    Open questions at the time
    • how D251E enhances Stx11 binding yet impairs the Snap23–Stx11–Vamp8 complex mechanistically unresolved
    • single lab
  10. 2024 Low

    Genetic epistasis implicated VPS33A domain 3a in SNARE complex assembly during endosomal trafficking.

    Evidence C. elegans suppressor screen of vps-45 temperature-sensitive lethality

    PMID:38585203

    Open questions at the time
    • genetic interaction in ortholog with no biochemical follow-up
    • domain 3a contribution not tested in mammalian VPS33A
  11. 2026 Low

    Positioned VPS33A upstream of ULK1 in a pro-autophagic axis relevant to cancer drug sensitivity.

    Evidence siRNA knockdown and ULK1 overexpression rescue with LC3 flux, proliferation assays, and xenograft in cholangiocarcinoma cells

    PMID:41718964

    Open questions at the time
    • no direct VPS33A–ULK1 biochemical interaction shown
    • mechanism by which VPS33A loss reduces ULK1 levels unknown
    • single lab

Open questions

Synthesis pass · forward-looking unresolved questions
  • How HOPS-incorporated VPS33A selects among distinct SNARE sets at different organelles and how phosphoregulation is coordinated across pathways remains unresolved.
  • no reconstituted fusion assay defining VPS33A's catalytic contribution to SNARE zippering
  • kinase/phosphatase governing STX17 N-peptide switch unidentified
  • structure of VPS33A within an assembled HOPS-SNARE intermediate lacking

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 2 GO:0098772 molecular function regulator activity 2 GO:0140096 catalytic activity, acting on a protein 2
Localization
GO:0005764 lysosome 2 GO:0005768 endosome 2 GO:0005829 cytosol 2
Pathway
R-HSA-5653656 Vesicle-mediated transport 3 R-HSA-9612973 Autophagy 3 R-HSA-9609507 Protein localization 2
Partners
SNAP29STX11STX17VAMP7VPS11VPS16VPS39VPS41
Complex memberships
CORVETHOPS

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2013 Crystal structure of human VPS33A confirmed its identity as a Sec1/Munc18 (SM) family member. VPS16 recruits VPS33A to the HOPS complex via residues 642–736 of VPS16, which are necessary and sufficient for the VPS33A–VPS16 interaction. Mutations at the binding interface disrupt the interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS. X-ray crystallography (crystal structures of VPS33A alone and in complex with VPS16(642–736)); in vitro binding assays; cell-based interaction assays with interface mutants Proceedings of the National Academy of Sciences of the United States of America High 23901104
2015 Recruitment of VPS33A to HOPS by VPS16 is required for lysosome fusion with endosomes and autophagosomes. VPS16 and VPS33A interface mutants (designed from the crystal structure) that no longer bind each other fail to rescue lysosome–endosome and lysosome–autophagosome fusion in cells depleted of endogenous proteins. VPS33B and VIPAR, paralogs of VPS33A and VPS16 respectively, form a complex distinct from HOPS and are not required for these fusion events. Crystal-structure-guided mutagenesis; fluorescent dextran delivery to lysosomes assay (endocytic pathway); autophagosome–lysosome fusion assay; immunoprecipitation; siRNA depletion Traffic (Copenhagen, Denmark) High 25783203
2009 Drosophila VPS33A (carnation/Car) is specifically required for late endosome-to-lysosome fusion and autophagosome–lysosome fusion, but not early endosome function. Car binds dSyntaxin16 (present on lysosomes) in vitro, whereas dVps33B binds the early endosomal Avl Syntaxin, explaining their distinct pathway specificities. dVps33B cannot substitute for Car function. Null allele generation; eye-specific genetic mosaic analysis; fluorescence microscopy of endocytic receptors and autophagosomes; in vitro Syntaxin-binding assay Molecular biology of the cell High 19158398
2003 Mouse buff (bf) mutation maps to Vps33a, identifying VPS33A as the first mammalian defect in the class C vacuole/prevacuole-associated t-SNARE complex. The mutation causes defective biogenesis of melanosomes, lysosomes, and storage granules, phenotypically resembling Hermansky-Pudlak syndrome. Positional cloning; genetic mapping; sequence analysis of buff mutant Proceedings of the National Academy of Sciences of the United States of America Medium 12538872
2009 VPS33A (buff mouse point mutation D251E) is required for fusion of uroplakin-degrading multivesicular bodies (MVBs) with lysosomes in bladder urothelial umbrella cells. In buff mice, fusiform vesicles are replaced by accumulating Rab27b-negative MVBs, accompanied by increased lysosomal enzyme activities, indicating a block at the MVB–lysosome fusion step. Histological and ultrastructural analysis of buff mouse urothelium; fluorescence microscopy; lysosomal enzyme activity assays; protein quantification Traffic (Copenhagen, Denmark) Medium 19566896
2009 VPS33A interacts with the cytoplasmic tail of RANKL (identified by pull-down) and mediates transport of RANKL from the Golgi apparatus to secretory lysosomes in osteoblastic cells. Knockdown of VPS33A reduces lysosomal storage of RANKL and causes its accumulation in the Golgi, and disrupts regulated cell-surface expression of RANKL. Protein pull-down assay; siRNA knockdown; immunofluorescence microscopy; cell-surface expression assay Journal of bone and mineral research Medium 19419298
2015 The VPS33A(D251E) mutation in buff mice selectively impairs autophagosome–lysosome fusion without compromising the endocytic pathway. Mechanistically, VPS33A(D251E) shows enhanced association with the autophagic SNARE complex (STX17–VAMP8–SNAP29) and enhanced interactions with HOPS subunits VPS41, VPS39, VPS18, and VPS11 (but not VPS16). Reduction of VPS33A–HOPS subunit interactions (via VPS33A(Y440D)) also reduces STX17 association, indicating that HOPS assembly controls autophagosomal SNARE engagement. These defects cause Purkinje cell loss. Co-immunoprecipitation; autophagy flux assays; endocytic pathway assays; histological analysis of buff mouse brain; behavioral testing Autophagy Medium 26259518
2019 The Arg498Trp missense mutation in VPS33A destabilizes protein folding (predicted by 3D crystal structure), reducing abundance of full-length VPS33A and other HOPS/CORVET components. Proteasome inhibitor treatment rescues the mutant protein from degradation. Patient fibroblasts show vacuolation, disordered endosomal/lysosomal compartments, abnormal lactosylceramide trafficking, and elevated β-D-galactosylsphingosine despite normal cognate lysosomal hydrolase activities. Crystal structure analysis; immunoblotting; proteasome inhibitor treatment; confocal microscopy; lipidomic screening; glycosaminoglycan urinary analysis Human molecular genetics Medium 31070736
2017 A homozygous VPS33A Arg498Trp mutation causes lysosomal over-acidification and heparan sulphate accumulation (plasma HS ~60× normal) in patient-derived and VPS33A-depleted cells, without affecting endocytic or autophagic pathways, revealing a novel role for VPS33A in controlling lysosomal pH homeostasis and glycosaminoglycan catabolism. Whole exome/Sanger sequencing; lysosomal pH measurement; GAG quantification; RNAi knockdown in cells; endocytic and autophagic pathway assays Human molecular genetics Medium 28013294
2019 VPS33A interacts with syntaxin 17 (Stx17) via a VPS33A-binding motif in the Stx17 N-peptide to regulate autophagosome–lysosome fusion. FLIM-FRET in live HeLa cells revealed that Stx17 heterotrimerizes with SNAP29 and VAMP7 (not VAMP8) at the autophagosome. A phosphoserine in the Stx17 N-peptide acts as a master-switch controlling fusion competency, providing a late regulatory checkpoint for autophagy completion. FLIM-FRET in live HeLa cells; Stx17 N-peptide binding assays; phosphomimetic/phospho-null mutant analysis The Journal of biological chemistry Medium 30655294
2018 BioID proximity biotinylation revealed that VPS33A co-localizes with components of both CORVET and HOPS complexes and with class III PI3-kinase (PI3KC3) complex subunits (PIK3C3, PIK3R4, NRBF2, UVRAG, RUBICON), while VPS33B does not associate with CORVET/HOPS subunits and instead interacts with CCDC22 (a CCC complex member). The VPS33B–VIPAR complex is considerably smaller than CORVET/HOPS. BioID proximity biotinylation–mass spectrometry; gel filtration fractionation; reciprocal interaction validation Journal of molecular biology Medium 29778605
2025 VPS33A (as part of the HOPS complex) is required for renin granule (RG) biogenesis in juxtaglomerular cells. The buff mouse VPS33A(D251E) mutation produces smaller RGs and reduced active renin. VPS33A interacts with Stx11 (SNARE), and this interaction is enhanced by the D251E mutation, impairing the SNARE complex (Snap23–Stx11–Vamp8) required for RG biogenesis. Mouse model analysis (buff mice); siRNA knockdown in As4.1 cells; co-immunoprecipitation of VPS33A with Stx11; renin content assay; electron microscopy Journal of cell science Medium 40855995
2024 A domain 3a mutation in C. elegans VPS33A (M376I) suppresses the temperature-sensitive lethality caused by loss of VPS45, another SM protein involved in endosomal SNARE-mediated membrane fusion. This genetic epistasis places VPS33A domain 3a as functionally important for SNARE complex assembly in endosomal trafficking. Genetic suppressor screen in C. elegans; temperature-sensitive lethality assay microPublication biology Low 38585203
2026 VPS33A knockdown reduces ULK1 protein levels, suppresses autophagic flux, and increases CCA cell sensitivity to pemigatinib. ULK1 overexpression restores autophagy and reverses the enhanced drug sensitivity caused by VPS33A depletion, placing VPS33A upstream of ULK1 in a pro-autophagic axis. siRNA knockdown; ULK1 overexpression; GFP-RFP-LC3 autophagic flux assay; CCK-8/EdU proliferation assays; in vivo xenograft Digestive diseases and sciences Low 41718964

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. Traffic (Copenhagen, Denmark) 127 25783203
2003 The mouse organellar biogenesis mutant buff results from a mutation in Vps33a, a homologue of yeast vps33 and Drosophila carnation. Proceedings of the National Academy of Sciences of the United States of America 107 12538872
2013 Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. Proceedings of the National Academy of Sciences of the United States of America 82 23901104
2009 The SM protein Car/Vps33A regulates SNARE-mediated trafficking to lysosomes and lysosome-related organelles. Molecular biology of the cell 79 19158398
2017 Mutation in VPS33A affects metabolism of glycosaminoglycans: a new type of mucopolysaccharidosis with severe systemic symptoms. Human molecular genetics 55 28013294
2015 Impairment of autophagosome-lysosome fusion in the buff mutant mice with the VPS33A(D251E) mutation. Autophagy 44 26259518
2019 The lysosomal disease caused by mutant VPS33A. Human molecular genetics 32 31070736
2017 A probable new syndrome with the storage disease phenotype caused by the VPS33A gene mutation. Clinical dysmorphology 32 27547915
2009 Involvement of vps33a in the fusion of uroplakin-degrading multivesicular bodies with lysosomes. Traffic (Copenhagen, Denmark) 32 19566896
2019 A VPS33A-binding motif on syntaxin 17 controls autophagy completion in mammalian cells. The Journal of biological chemistry 31 30655294
2009 Vps33a mediates RANKL storage in secretory lysosomes in osteoblastic cells. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 31 19419298
2018 Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B. Journal of molecular biology 23 29778605
2009 The Vps33a gene regulates behavior and cerebellar Purkinje cell number. Brain research 22 19254700
2022 Juvenile mucopolysaccharidosis plus disease caused by a missense mutation in VPS33A. Human mutation 12 36153662
2022 Mucopolysaccharidosis-Plus Syndrome: Report on a Polish Patient with a Novel VPS33A Variant with Comparison with Other Described Patients. International journal of molecular sciences 10 36232726
2025 Cellular and molecular changes in mucopolysaccharidosis-plus syndrome caused by a homozygous c.599G > C (p.Arg200Pro) variant of the VPS33A gene. Journal of applied genetics 3 40758165
2026 VPS33A Promotes Pemigatinib Resistance in Cholangiocarcinoma via Autophagy. Digestive diseases and sciences 1 41718964
2025 Impaired biogenesis of renin granules in juxtaglomerular cells of Vps33a (D251E) mutant mice. Journal of cell science 0 40855995
2024 Domain 3a mutation of VPS33A suppresses larval arrest phenotype in the loss of VPS45 in Caenorhabditis elegans. microPublication biology 0 38585203

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