Affinage

VPS16

Vacuolar protein sorting-associated protein 16 homolog · UniProt Q9H269

Length
839 aa
Mass
94.7 kDa
Annotated
2026-04-28
20 papers in source corpus 8 papers cited in narrative 8 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

VPS16 is a scaffold subunit of the HOPS and CORVET tethering complexes that is essential for endolysosomal trafficking, autophagosome–lysosome fusion, and vacuolar/lysosomal biogenesis. Its C-terminal region (residues 642–736) directly binds the SM-family protein VPS33A through an extensive interface resolved by X-ray crystallography in both yeast and human systems, and this interaction is necessary and sufficient to recruit VPS33A into the HOPS complex and to enable late endosome–lysosome and autophagosome–lysosome fusion (PMID:23901104, PMID:23840694, PMID:25783203). VPS16 also stabilizes other HOPS/CORVET subunits; bi-allelic loss of VPS16 causes coordinate depletion of complex members, accumulation of autophagosomes and lysosomes, and impaired endosomal trafficking, all rescued by VPS16 re-expression (PMID:33938619). In yeast, Vps16p additionally modulates mRNA decapping by inhibiting Dcp1p activity (PMID:10523645).

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 1993 High

    Establishing that Vps16p is a component of a large protein complex required for vacuolar protein sorting answered the foundational question of whether VPS16 acts alone or as part of a multi-subunit machine in the endolysosomal pathway.

    Evidence Subcellular fractionation, gene disruption, and overexpression in S. cerevisiae

    PMID:8444873

    Open questions at the time
    • Identity of other complex components unknown
    • Mechanism by which complex promotes vacuolar sorting undefined
    • No mammalian homolog characterized
  2. 1999 Medium

    Discovery that Vps16p inhibits the mRNA decapping enzyme Dcp1p revealed an unexpected non-trafficking function, raising the question of whether VPS16 moonlights in mRNA metabolism.

    Evidence In vitro decapping assay and mRNA stability measurements in vps16 mutant yeast

    PMID:10523645

    Open questions at the time
    • Direct physical interaction between Vps16p and Dcp1p not demonstrated
    • Not replicated in mammalian systems
    • Relationship between decapping and vacuolar sorting functions unclear
  3. 2003 Medium

    Identification of mammalian VPS16 as a class C Vps complex member that localizes to endosomes and interacts with syntaxins extended the yeast paradigm to mammalian endolysosomal trafficking.

    Evidence Co-immunoprecipitation, transferrin trafficking assay, and subcellular localization in mammalian cells

    PMID:14623309

    Open questions at the time
    • Architecture of the mammalian complex not defined
    • Specific binding partners within the complex not mapped
    • Single-lab Co-IP without reciprocal validation
  4. 2013 High

    Crystal structures of the VPS33A–VPS16 interface in both human and yeast systems answered how VPS33 is recruited into the HOPS complex, revealing that VPS16 residues 642–736 are necessary and sufficient for this interaction.

    Evidence X-ray crystallography at 2.6 Å resolution with interface mutagenesis validated in vitro and in cells (two independent labs, human and yeast)

    PMID:23840694 PMID:23901104

    Open questions at the time
    • Full HOPS complex architecture not resolved
    • How VPS16 contacts other HOPS subunits beyond VPS33 not structurally defined
    • Functional consequence of interface disruption on membrane fusion not yet tested
  5. 2015 High

    Structure-guided mutagenesis demonstrated that the VPS16–VPS33A interaction is essential for both late endosome–lysosome and autophagosome–lysosome fusion, establishing VPS16 as functionally required for HOPS-dependent membrane fusion events.

    Evidence Crystal-structure-guided interface mutants tested in siRNA-rescue experiments with dextran delivery and autophagosome–lysosome fusion assays in mammalian cells

    PMID:25783203

    Open questions at the time
    • SNARE-pairing mechanism downstream of VPS33A recruitment not resolved
    • Whether VPS16 has fusogenic roles independent of VPS33A not addressed
    • Contribution of CORVET versus HOPS not dissected
  6. 2021 High

    Patient-derived cells with bi-allelic VPS16 reduction showed that VPS16 stabilizes all HOPS/CORVET subunits and is required for normal endosomal trafficking, autophagy flux, and lysosome homeostasis, establishing VPS16 as a master scaffold of the complex.

    Evidence Patient fibroblast complementation, western blotting of subunit levels, transferrin uptake, autophagosome/lysosome imaging, and zebrafish vps16 knockdown with rescue

    PMID:33938619

    Open questions at the time
    • Structural basis for VPS16-dependent stabilization of non-VPS33 subunits unknown
    • Whether partial VPS16 loss differentially affects HOPS versus CORVET not resolved
    • Tissue-specific consequences of VPS16 deficiency not fully explored

Open questions

Synthesis pass · forward-looking unresolved questions
  • A complete structural model of HOPS/CORVET with all VPS16 contact surfaces, the mechanism by which VPS16 stabilizes non-VPS33 subunits, and whether the yeast mRNA decapping role is conserved in mammals remain unresolved.
  • Full HOPS/CORVET holocomplex structure with VPS16 contacts not available
  • Mechanism of coordinate subunit stabilization by VPS16 undefined
  • Conservation of VPS16 decapping function beyond yeast untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 4
Localization
GO:0005764 lysosome 2 GO:0005768 endosome 2
Pathway
R-HSA-5653656 Vesicle-mediated transport 4 R-HSA-9612973 Autophagy 2
Partners
VPS11VPS18VPS33A
Complex memberships
CORVETHOPS

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1993 Yeast Vps16p associates with a sedimentable, large protein complex (resistant to detergent and salt, extractable with urea/alkali), is essential for vacuolar protein sorting, and is required for normal vacuole morphology; it localizes to a particulate cell fraction. Subcellular fractionation, gene disruption, overexpression saturation assay, polyclonal antiserum detection The Journal of biological chemistry High 8444873
1999 Yeast Vps16p inhibits the mRNA decapping enzyme Dcp1p; mutations in VPS16 reduce decapping activity in vitro and stabilize mRNAs in vivo, and extracts from vps16 mutants inhibit purified Dcp1p activity; enhanced interaction of Dcp1p with Hsp70 (Ssa1p/2p) is observed in vps16 mutants. In vitro decapping assay, mRNA stability assay, co-purification of Dcp1p with Ssa1p/2p Molecular and cellular biology Medium 10523645
2001 Human VPS16, VPS11, VPS18, and VPS33 were molecularly cloned and identified as homologs of the yeast class C VPS genes required for lysosomal protein delivery. Molecular cloning, sequence analysis, expression profiling Gene Medium 11250079
2003 Mammalian Vps16 (mVps16) is a component of the class C Vps complex; mammalian class C Vps proteins interact with multiple syntaxins and Vps45, localizing to endosomal compartments, and their overexpression inhibits transferrin recycling without affecting internalization. Co-immunoprecipitation, transferrin trafficking assay, subcellular localization Biochemical and biophysical research communications Medium 14623309
2013 Crystal structure of human VPS33A alone and in complex with VPS16 (residues 642–736) was determined at 2.6 Å resolution; VPS16 residues 642–736 are necessary and sufficient to recruit VPS33A to the HOPS complex, and mutations at the binding interface disrupt the interaction both in vitro and in cells, preventing VPS33A incorporation into HOPS. X-ray crystallography, 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 Crystal structure of yeast Vps33 alone and bound to a C-terminal portion of Vps16 determined at 2.6 Å; the Vps33–Vps16 interface is extensive but binding causes only subtle conformational change in Vps33; this confirms Vps33 as an SM-family protein that is stably integrated into HOPS via Vps16. X-ray crystallography PloS one High 23840694
2015 VPS16 recruits VPS33A to the HOPS complex, and this interaction is essential for lysosome fusion with late endosomes and autophagosomes; VPS16/VPS33A interface mutants (designed from the crystal structure) that cannot bind each other fail to rescue endosome–lysosome or autophagosome–lysosome fusion in cells depleted of endogenous proteins. Additionally, VIPAR and VPS33B form a separate complex distinct from HOPS and are not required for these fusion events. Crystal-structure-guided mutagenesis, fluorescent dextran delivery assay (endosome–lysosome fusion), autophagosome–lysosome fusion assay, siRNA depletion, co-immunoprecipitation Traffic (Copenhagen, Denmark) High 25783203
2021 Bi-allelic reduction (~85%) of VPS16 protein similarly reduces levels of other HOPS/CORVET subunits including VPS33A; re-expression of VPS16 restores subunit levels and rescues defects in transferrin uptake/endosomal trafficking, autophagosome accumulation, and lysosomal compartment accumulation, demonstrating VPS16 as a scaffold required for HOPS/CORVET complex stability. Patient-derived fibroblast complementation, western blotting, transferrin trafficking assay, autophagosome/lysosome imaging, zebrafish vps16 knockdown model EMBO molecular medicine High 33938619

Source papers

Stage 0 corpus · 20 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) 125 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 81 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
2022 Overexpression of VPS16 correlates with tumor progression and chemoresistance in colorectal cancer. Biochemical and biophysical research communications 6 35367832
2024 Hypomyelinated vps16 Mutant Zebrafish Exhibit Systemic and Neurodevelopmental Pathologies. International journal of molecular sciences 4 39000367
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
2025 The Plasmodium falciparum homolog of Vps16 interacts with the core members of the Vps-C tethering complex. mSphere 0 40626728