Affinage

VPS16

Vacuolar protein sorting-associated protein 16 homolog · UniProt Q9H269

Length
839 aa
Mass
94.7 kDa
Annotated
2026-06-11
21 papers in source corpus 9 papers cited in narrative 9 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

VPS16 is a scaffolding subunit of the class C VPS (HOPS/CORVET) membrane-tethering machinery that drives delivery of cargo to the lysosome/vacuole, first established by gene disruption in yeast that produced severe vacuolar protein-sorting defects and grossly abnormal vacuole morphology and showed Vps16p tightly integrated into a large sedimentable protein complex (PMID:8444873, PMID:11250079). Its defining mechanistic function is the direct recruitment of the SM (Sec1/Munc18) protein VPS33A: residues 642–736 of human VPS16 are necessary and sufficient to bind VPS33A, and a 2.6 Å co-crystal structure defines the interface whose mutation abolishes VPS33A recruitment to HOPS in vitro and in cells (PMID:23901104, PMID:23840694). This recruitment is mechanistically essential for fusion of late endosomes and autophagosomes with lysosomes, as interface mutants that cannot bind VPS33A fail to rescue these fusion events, whereas the paralogous VIPAR–VPS33B module forms a distinct complex that is dispensable for them (PMID:25783203). In mammalian cells the complex localizes to endosomal compartments and modulates transferrin recycling, and VPS16 sets the steady-state levels of partner HOPS/CORVET subunits including VPS33A (PMID:14623309, PMID:33938619). Bi-allelic VPS16 variants that deplete VPS16 protein coordinately reduce other subunits and cause defective endosomal trafficking with accumulation of autophagosomes and lysosomes, while loss of vps16 in zebrafish produces hypomyelination, neuronal cell death, and behavioral impairment, defining VPS16 as the basis of a lysosomal storage-like, hypomyelinating neurological disorder (PMID:33938619, PMID:39000367). A separately reported yeast activity as an inhibitor of the mRNA decapping enzyme Dcp1p (PMID:10523645) is not connected to the membrane-trafficking role in the available corpus.

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1993 Medium

    Established that VPS16 is a constituent of a large, tightly assembled protein complex required for vacuolar protein sorting, answering whether the gene acts in the lysosomal/vacuolar delivery pathway.

    Evidence Subcellular fractionation, gene disruption, and biochemical extraction in yeast

    PMID:8444873

    Open questions at the time
    • Complex composition and the identity of partner subunits not resolved
    • No structural or mechanistic basis for complex assembly
  2. 1999 Medium

    Reported a distinct activity in which yeast Vps16p inhibits the mRNA decapping enzyme Dcp1p, raising a possible second function unrelated to membrane trafficking.

    Evidence In vitro decapping assay, in vivo mRNA stability, and co-purification with Flag-Dcp1p in yeast

    PMID:10523645

    Open questions at the time
    • Not connected mechanistically to the trafficking complex role
    • No evidence this activity is conserved in the human protein
  3. 2001 Low

    Identified human VPS16 as the homolog of yeast class C VPS16, predicting conservation of the lysosomal delivery role in mammals.

    Evidence Molecular cloning, sequence and expression analysis

    PMID:11250079

    Open questions at the time
    • Sequence/expression only — no functional experiment on the human protein
    • No partner or localization data
  4. 2003 Medium

    Demonstrated that mammalian Vps16 engages syntaxins and Vps45 at endosomes and influences cargo recycling, placing the complex in endosomal trafficking.

    Evidence Co-immunoprecipitation, Western blot, and transferrin trafficking assays in mammalian cells

    PMID:14623309

    Open questions at the time
    • Direct versus indirect nature of syntaxin interactions not resolved
    • Mechanism by which recycling is inhibited not defined
  5. 2013 High

    Defined the atomic basis of VPS16-mediated SM-protein recruitment, showing that a discrete VPS16 C-terminal segment binds and incorporates VPS33A into HOPS.

    Evidence X-ray crystallography of VPS33A alone and bound to VPS16(642–736), interface mutagenesis, and cell-based co-IP (human and yeast structures)

    PMID:23840694 PMID:23901104

    Open questions at the time
    • Structure of the full HOPS holocomplex not determined
    • How VPS33A engages SNAREs within the assembled complex not shown
  6. 2015 High

    Established that VPS16-dependent recruitment of VPS33A is mechanistically essential for endosome- and autophagosome-lysosome fusion, distinguishing it from the separate VIPAR–VPS33B module.

    Evidence siRNA depletion, fluorescent dextran delivery, structure-guided interface mutagenesis with rescue, and co-IP in mammalian cells

    PMID:25783203

    Open questions at the time
    • Step in the fusion reaction directly catalyzed by the VPS16–VPS33A interface not pinpointed
    • Distinct cargo/compartment roles of HOPS versus CORVET not delineated
  7. 2021 High

    Showed VPS16 acts as a stability scaffold setting the levels of HOPS/CORVET subunits, and that its loss causes a human trafficking disease with lysosome/autophagosome accumulation.

    Evidence Patient fibroblast biochemistry, VPS16 re-expression rescue, transferrin trafficking, and zebrafish knockdown with IHC

    PMID:33938619

    Open questions at the time
    • Whether destabilization reflects failed complex assembly versus enhanced degradation not resolved
    • Tissue-specific basis of myelination defects not defined
  8. 2024 Medium

    Confirmed in vivo that VPS16 is required for myelination and neuronal survival, linking the trafficking defect to a neurological phenotype.

    Evidence Zebrafish vps16 knockout with immunohistochemistry and behavioral assays

    PMID:39000367

    Open questions at the time
    • Cell-autonomous versus non-autonomous origin of hypomyelination not established
    • Molecular link between lysosomal fusion failure and neuronal death not defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How VPS16 coordinates HOPS versus CORVET assembly and whether the reported decapping-inhibitor activity has any role in human cells remain unresolved.
  • No structure of the full holocomplex or of CORVET-specific assembly
  • Human relevance of the Dcp1p-inhibitor activity untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0005198 structural molecule activity 2
Localization
GO:0005764 lysosome 2 GO:0005768 endosome 1
Pathway
R-HSA-5653656 Vesicle-mediated transport 3 R-HSA-9612973 Autophagy 2
Partners
SYNTAXINSVPS33AVPS45
Complex memberships
CORVETHOPSclass C VPS complex

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1993 Yeast Vps16p associates with a sedimentable particulate protein complex; this association is resistant to detergent and salt extraction but can be disrupted by 6 M urea or alkali buffer, indicating tight integration into a large protein complex. Loss of VPS16 causes severe defects in vacuolar protein sorting and grossly abnormal vacuole morphology. Subcellular fractionation, gene disruption, biochemical extraction The Journal of biological chemistry Medium 8444873
1999 Yeast Vps16p functions as an inhibitor of the mRNA decapping enzyme Dcp1p; mutations in VPS16 reduce decapping activity in vitro and stabilize mRNAs in vivo. Extracts from vps16 mutant strains inhibit purified Flag-Dcp1p activity, and Vps16p mutations enhance the interaction of Dcp1p with the Hsp70 family member Ssa1p/2p. In vitro decapping assay, mRNA stability assay in vivo, co-purification with Flag-Dcp1p Molecular and cellular biology Medium 10523645
2001 Human VPS16 is the homolog of yeast class C VPS16, and like its yeast counterpart is predicted to function in lysosomal protein delivery as part of the class C VPS complex. Molecular cloning, sequence analysis, expression analysis Gene Low 11250079
2003 Mouse Vps16 (mVps16) interacts with multiple syntaxins and with Vps45p in mammalian cells; the mammalian class C VPS complex localizes to endosomal compartments. Overexpression of mammalian class C VPS proteins does not affect transferrin internalization but inhibits transferrin recycling. Co-immunoprecipitation, Western blot, transferrin trafficking assay Biochemical and biophysical research communications Medium 14623309
2013 The crystal structure of human VPS33A was determined, confirming it as an SM (Sec1/Munc18) family member. VPS16 residues 642–736 are necessary and sufficient to recruit VPS33A to the HOPS complex; the crystal structure of VPS33A bound to VPS16(642–736) was solved at 2.6 Å. Mutations at the binding interface disrupt the VPS33A–VPS16 interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS. X-ray crystallography (2.6 Å), in vitro binding assay, interface mutagenesis, cell-based co-immunoprecipitation Proceedings of the National Academy of Sciences of the United States of America High 23901104
2013 The crystal structure of yeast Vps33 alone (2.6 Å) and in complex with a C-terminal portion of Vps16 (2.6 Å) was solved, revealing the structural basis for Vps33–Vps16 interaction. Vps33 has the same basic three-domain SM-protein architecture but with domain 1 displaced by 15 Å and rotated 40° relative to other SM families. Binding to Vps16 causes only subtle conformational changes in Vps33. X-ray crystallography (2.6 Å resolution) PloS one High 23840694
2015 VPS16 is required for fusion of endosomes and autophagosomes with lysosomes in mammalian cells. The crystal structure of the VPS16/VPS33A complex was used to design interface mutants that disrupt VPS33A binding; these mutants fail to rescue lysosome fusion with endosomes or autophagosomes, demonstrating that VPS16-mediated recruitment of VPS33A to HOPS is mechanistically essential for lysosomal fusion. Depletion of VIPAR (VPS16 paralog) or VPS33B had no effect on these fusion events, and immunoprecipitation showed VIPAR and VPS33B form a distinct complex separate from HOPS. siRNA depletion, fluorescent dextran delivery assay, structure-guided mutagenesis, co-immunoprecipitation Traffic (Copenhagen, Denmark) High 25783203
2021 Bi-allelic VPS16 variants reduce VPS16 protein levels by ~85% in patient fibroblasts and cause coordinate reduction of other HOPS/CORVET subunits including VPS33A; re-expression of VPS16 restores levels of other subunits. Patient fibroblasts show defective endosomal trafficking of transferrin and accumulation of autophagosomes and lysosomal compartments, all rescued by VPS16 re-expression. Zebrafish with disrupted vps16 show impaired myelination and accumulation of lysosomes/autophagosomes in brain glia. Patient fibroblast biochemistry (Western blot, protein quantification), VPS16 re-expression rescue, transferrin trafficking assay, zebrafish vps16 knockdown with IHC EMBO molecular medicine High 33938619
2024 Loss of Vps16 function in zebrafish causes hypomyelination, increased neuronal cell death, systemic defects, and behavioral/cognitive impairment, demonstrating a required role for Vps16 in myelination and neuronal survival in vivo. Zebrafish vps16 knockout, immunohistochemistry, behavioral assays (visuomotor response, acoustic/tap stimuli, memory test) International journal of molecular sciences Medium 39000367

Source papers

Stage 0 corpus · 21 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
1993 The VPS16 gene product associates with a sedimentable protein complex and is essential for vacuolar protein sorting in yeast. The Journal of biological chemistry 103 8444873
2020 Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities. Annals of neurology 94 32808683
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
2001 Molecular cloning and characterization of human VPS18, VPS 11, VPS16, and VPS33. Gene 59 11250079
2013 Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*. PloS one 51 23840694
2016 Homozygous mutation of VPS16 gene is responsible for an autosomal recessive adolescent-onset primary dystonia. Scientific reports 48 27174565
1999 Mutations in VPS16 and MRT1 stabilize mRNAs by activating an inhibitor of the decapping enzyme. Molecular and cellular biology 29 10523645
2021 Bi-allelic VPS16 variants limit HOPS/CORVET levels and cause a mucopolysaccharidosis-like disease. EMBO molecular medicine 27 33938619
2021 Homozygous missense VPS16 variant is associated with a novel disease, resembling mucopolysaccharidosis-plus syndrome in two siblings. Clinical genetics 21 34013567
2021 Transcript-Specific Loss-of-Function Variants in VPS16 Are Enriched in Patients With Dystonia. Neurology. Genetics 16 34901436
2021 Mutation screening of VPS16 gene in patients with isolated dystonia. Parkinsonism & related disorders 15 33482438
2003 Identification of mouse Vps16 and biochemical characterization of mammalian class C Vps complex. Biochemical and biophysical research communications 15 14623309
2023 Dominant VPS16 Pathogenic Variants: Not Only Isolated Dystonia. Movement disorders clinical practice 11 38291845
2024 Hypomyelinated vps16 Mutant Zebrafish Exhibit Systemic and Neurodevelopmental Pathologies. International journal of molecular sciences 6 39000367
2022 Overexpression of VPS16 correlates with tumor progression and chemoresistance in colorectal cancer. Biochemical and biophysical research communications 6 35367832
2025 VPS16-Related Dystonia: Expanding the Clinical Spectrum and Therapeutic Insights. Movement disorders clinical practice 2 40970427
2025 Expanding the Genetic and Phenotypic Spectrum of DYT-VPS16: The Importance of Splice-Site Variants. Movement disorders : official journal of the Movement Disorder Society 2 41200738
2024 Familial Mediterranean fever gene variations could trigger VPS16-associated early-onset dystonia and diabetes mellitus: clinical identification of a family with MEFV and VPS16 genetic variation association. Rheumatology advances in practice 2 39055541
2026 [Case report: VPS16 - a new cause of generalized dystonia]. Ideggyogyaszati szemle 0 42233462
2025 The Plasmodium falciparum homolog of Vps16 interacts with the core members of the Vps-C tethering complex. mSphere 0 40626728

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