Affinage

TRAPPC3

Trafficking protein particle complex subunit 3 · UniProt O43617

Length
180 aa
Mass
20.3 kDa
Annotated
2026-06-10
10 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

TRAPPC3 (BET3) is an essential, highly conserved core subunit of the TRAPP tethering complex that mediates ER-to-Golgi vesicular transport, acting after COPII budding but upstream of Rab1/Ypt1 GTPase activation and SNARE complex assembly (PMID:8590804, PMID:15728249). In the secretory pathway it is required for vesicle docking/fusion at the Golgi: loss of Bet3 function blocks SNARE complex formation and causes accumulation of dilated ER and small vesicles (PMID:8590804), and immunodepletion of cytosolic Bet3 blocks VSV-G transport in reconstituted assays, with epistasis placing its action between COPII and Rab1 (PMID:15728249). TRAPPC3 functions within a defined complex architecture: it partners with Bet5/TRAPPC1 (PMID:9611195) and forms a structurally characterized heterodimer with TPC6 that together recruits the Mum2 subunit, establishing the core subcomplex of TRAPP (PMID:16828797). The protein adopts an alpha/beta-plait fold and dimerizes, a property that predetermines equimolar TRAPP subunit stoichiometry, and presents a flat, positively charged surface with hydrophobic channels that directs Golgi-specific membrane targeting (PMID:15608655, PMID:15692564). A distinctive feature is its intrinsic self-palmitoylating activity: Bet3 stoichiometrically attaches palmitate from palmitoyl-CoA to cysteine 68, buried in a hydrophobic tunnel, in a reaction promoted by arginine 67 acting as a base catalyst to deprotonate the cysteine nucleophile (PMID:16908848, PMID:20372964). This irreversible modification serves a structural/stability role—deacylated Bet3 is thermally destabilized, fails to bind TPC6, and is degraded (PMID:16908848). Beyond the secretory pathway, Bet3 as a common TRAPP subunit is required for autophagy and the Cvt pathway in yeast, where it promotes autophagosome closure upstream of Ypt1 GTPase activation (PMID:25581738).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1995 High

    Established that Bet3 is required for ER-to-Golgi transport and acts upstream of SNARE complex assembly, defining its position in the secretory pathway.

    Evidence Temperature-sensitive bet3-1 mutants with transport assays, EM, and SNARE assembly readouts in yeast

    PMID:8590804

    Open questions at the time
    • Did not define the molecular complex Bet3 operates within
    • Mechanism of how Bet3 enables SNARE assembly unresolved
  2. 1998 High

    Defined Bet3 as a co-member of a discrete complex with Bet5, revealing it works through a multi-subunit assembly rather than alone.

    Evidence High-copy suppressor screen and genetic epistasis with BET5, BET1, SEC22, USO1, DSS4 in yeast

    PMID:9611195

    Open questions at the time
    • Full subunit composition of the complex not yet known
    • No structural or biochemical characterization of the complex
  3. 2004 High

    Solved the dimeric structure and identified a flat positively charged surface with hydrophobic channels as the molecular basis of Golgi-specific membrane targeting.

    Evidence X-ray crystallography of mouse Bet3 plus charge-inversion and channel-blocking mutagenesis with localization/trafficking phenotypes in yeast

    PMID:15608655

    Open questions at the time
    • Identity of the hydrophobic moiety inserting into the channel not determined here
    • Direct membrane binding not biochemically reconstituted
  4. 2005 High

    High-resolution human structure revealed palmitate covalently bound at Cys68 within the hydrophobic pocket and showed dimerization predetermines TRAPP stoichiometry, while palmitoylation is dispensable for viability and membrane association.

    Evidence 1.55 A crystal structure, mass spectrometry, C68S mutagenesis, and fractionation in yeast deletion strains

    PMID:15692564

    Open questions at the time
    • Functional role of palmitoylation left unresolved
    • How membrane association is achieved if not via palmitate
  5. 2005 High

    Demonstrated mammalian Bet3 acts as a cytosolic factor functioning after COPII but before Rab1, ordering its action within the transport cascade.

    Evidence Semi-intact cell reconstitution, antibody inhibition, immunodepletion/rescue, and gel filtration

    PMID:15728249

    Open questions at the time
    • Direct biochemical link to Rab1 activation not shown
    • Distinction between monomeric and TRAPP-bound pools functionally unresolved
  6. 2006 High

    Showed Bet3 has intrinsic self-palmitoylating enzymatic activity and assigned palmitoylation a structural/stability role essential for TPC6 binding and protein survival.

    Evidence In vitro [3H]palmitoyl-CoA assay, CD thermal stability, Co-IP with TPC6, and pulse-chase degradation

    PMID:16908848

    Open questions at the time
    • Physiological trigger or regulation of self-palmitoylation unknown
    • Whether palmitoylation status changes across cellular states not addressed
  7. 2006 High

    Defined the Bet3-TPC6 heterodimer as the core TRAPP subcomplex and mapped the TPC6 surface that recruits Mum2, building the architectural picture of complex assembly.

    Evidence X-ray crystallography of Bet3-Tpc6B and Mum2 recruitment pull-downs

    PMID:16828797

    Open questions at the time
    • Functional distinction between Tpc6A and Tpc6B iso-complexes unclear
    • How the core subcomplex nucleates the full TRAPP not resolved
  8. 2010 Medium

    Defined the catalytic mechanism of self-palmitoylation, identifying Arg67-mediated base catalysis of Cys68 and additional surface acyl-CoA binding sites beyond the tunnel.

    Evidence R67 mutagenesis, pH-dependent in vitro palmitoylation, fluorescence acyl-CoA binding in vitro

    PMID:20372964

    Open questions at the time
    • Function of the additional surface acyl-CoA binding sites unknown
    • In vitro mechanism not validated in cellular context
  9. 2015 Medium

    Extended Bet3 function beyond secretion to autophagy and the Cvt pathway, placing it upstream of Ypt1 activation in autophagosome closure.

    Evidence bet3ts yeast with GFP-Atg8 and Ape1 maturation assays, protease protection, and rescue by active Ypt1

    PMID:25581738

    Open questions at the time
    • Whether mammalian TRAPPC3 plays the same autophagy role untested
    • Direct mechanism by which Bet3/TRAPP activates Ypt1 in autophagy not shown

Open questions

Synthesis pass · forward-looking unresolved questions
  • How TRAPPC3 mechanistically couples its tethering/scaffolding role to GEF-mediated Rab1/Ypt1 activation, and whether its self-palmitoylation is dynamically regulated in vivo, remain unresolved.
  • No direct demonstration of TRAPPC3-dependent Rab GEF activation in mammals
  • Regulation of self-palmitoylation across cellular states uncharacterized
  • No disease association established in the available corpus

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008289 lipid binding 2 GO:0016740 transferase activity 2 GO:0060090 molecular adaptor activity 2 GO:0140096 catalytic activity, acting on a protein 2
Localization
GO:0005794 Golgi apparatus 2 GO:0005829 cytosol 1
Pathway
R-HSA-5653656 Vesicle-mediated transport 2 R-HSA-9612973 Autophagy 1
Partners
TRAPPC1TRAPPC6ATRAPPC6B
Complex memberships
TRAPP

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1995 Yeast Bet3p (TRAPPC3 ortholog) is required for ER-to-Golgi vesicular transport; in bet3-1 temperature-sensitive mutants, the SNARE docking/fusion complex fails to form, and the cells accumulate dilated ER and small vesicles, placing Bet3p upstream of SNARE complex assembly. Temperature-sensitive mutant isolation via synthetic lethal screen with BET1; transport assays (invertase, alpha-factor, carboxypeptidase Y); electron microscopy; SNARE complex assembly assay Molecular biology of the cell High 8590804
1998 High-copy suppressor screen established that Bet3p acts in the same complex as Bet5p (BET5) to mediate a late stage in ER-to-Golgi transport; Bet3p and Bet5p are co-members of a novel complex required for vesicle targeting/fusion at the Golgi. High-copy suppressor screen; temperature-sensitive bet5-1 mutant generation by PCR mutagenesis; secretory pathway transport assays (CPY, alpha-factor); genetic epistasis with BET1, SEC22, USO1, DSS4, ANP1 Genetics High 9611195
2004 Crystal structure of mouse Bet3 (TRAPPC3 ortholog) reveals a dimeric architecture with hydrophobic channels; the channel entrances lie on a flat, positively charged putative membrane-interacting surface. Charge-inversion mutations on this surface and a channel-blocking mutation each caused conditional lethality, incorrect Golgi localization, and membrane trafficking defects in yeast, defining the molecular mechanism of Golgi-specific targeting via charged surface interactions and insertion of a hydrophobic moiety into the channels. X-ray crystallography (mouse Bet3); site-directed mutagenesis of conserved surface residues and channel residues in yeast Bet3p; growth assays; fluorescence localization; membrane trafficking assays Nature structural & molecular biology High 15608655
2005 Crystal structure of human BET3 at 1.55 Å resolution reveals an alpha/beta-plait fold with a hydrophobic pocket burying a palmitate covalently linked via thioester bond to cysteine 68. BET3 forms dimers in crystal and solution, predetermining equimolar TRAPP subunit stoichiometry. Palmitoylation is neither required for viability nor sufficient for membrane association; membrane association likely depends on protein-protein contacts within TRAPP. X-ray crystallography (1.55 Å); mass spectrometry identifying palmitoylation; site-directed mutagenesis (C68S, Bet3p C80S); subcellular fractionation; membrane extraction assays in yeast deletion strains The EMBO journal High 15692564
2005 Mammalian Bet3 (TRAPPC3) functions as a cytosolic factor required for ER-to-Golgi transport; antibody inhibition and immunodepletion of Bet3 from cytosol block VSV-G transport in a semi-intact cell reconstitution system, rescued by recombinant GST-Bet3. Epistasis experiments place Bet3 action after COPII but before Rab1, alpha-SNAP, and the EGTA-sensitive stage. Gel filtration reveals Bet3 exists in a high-molecular-weight pool (likely TRAPP complex) and a monomeric pool. Semi-intact cell ER-to-Golgi transport reconstitution assay; antibody inhibition; immunodepletion and rescue; gel filtration chromatography; western blotting Journal of cell science High 15728249
2006 Human BET3 (TRAPPC3) possesses unique self-palmitoylating activity: purified Bet3 rapidly and stoichiometrically attaches [3H]palmitate from palmitoyl-CoA to cysteine 68 in vitro at physiological pH and concentrations. The fatty acid must insert into the hydrophobic tunnel for stable attachment (blocked by A82 mutations). Palmitoylation is not reversible even upon Golgi disassembly. Palmitoylation has a structural/stability role: chemically deacylated Bet3 shows reduced melting temperature by CD spectroscopy and fails to bind TRAPP subunit TPC6, leading to its degradation in cells. In vitro palmitoylation assay with [3H]palmitoyl-CoA; site-directed mutagenesis (C68S, A82 variants); CD spectroscopy (thermal stability); co-immunoprecipitation (Bet3 with TPC6); pulse-chase degradation assay Proceedings of the National Academy of Sciences of the United States of America High 16908848
2006 Crystal structure of human Bet3-Tpc6B heterodimer defines the core subcomplex architecture of TRAPP; Tpc6B contains a conserved patch with uncharged pockets forming a putative Golgi anchoring interface. Both Bet3-Tpc6A and Bet3-Tpc6B iso-complexes recruit TRAPP subunit Mum2, with the alpha1-alpha2 loop regions of Tpc6 identified as the Mum2 binding site. X-ray crystallography of Bet3-Tpc6B complex; structural comparison with Tpc6A; pull-down/co-complex assembly assays recruiting Mum2; expression analysis in mouse organs Journal of molecular biology High 16828797
2010 Arginine 67 of Bet3 promotes self-palmitoylation by helping to deprotonate cysteine 68 so it can act as a nucleophile in the acylation reaction; this effect is compensated by raising pH, consistent with a base-catalysis mechanism. Long-chain acyl-CoAs (but not short-chain) bind Bet3 with micromolar affinity; Bet3 contains three Pal-CoA binding sites, reduced to two when the tunnel is obstructed, indicating surface binding sites exist in addition to the tunnel site. Site-directed mutagenesis (R67); in vitro palmitoylation assays at varied pH; fluorescence spectroscopy (acyl-CoA binding); structural analysis of non-acylated Bet3 Cellular and molecular life sciences : CMLS Medium 20372964
2015 Yeast Bet3 (TRAPPC3 ortholog), as a common TRAPP subunit, is required for autophagy and the Cvt pathway; in bet3ts cells, autophagosome closure is defective (GFP-Atg8 dispersed in cytoplasm; prApe1 protease-accessible but not matured). Overexpression of active Ypt1 GTPase (but not Ypt31) partially rescues autophagic defects of bet3ts cells, placing Bet3 upstream of Ypt1 activation in autophagy via TRAPP complexes. Temperature-sensitive bet3ts yeast mutant; GFP-Atg8 processing and localization assays; Ape1 maturation assay; protease protection assay; genetic rescue by active Ypt1/Ypt31 Cell biology international Medium 25581738

Source papers

Stage 0 corpus · 10 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1995 BET3 encodes a novel hydrophilic protein that acts in conjunction with yeast SNAREs. Molecular biology of the cell 61 8590804
2004 Crystal structure of bet3 reveals a novel mechanism for Golgi localization of tethering factor TRAPP. Nature structural & molecular biology 55 15608655
2005 Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization. The EMBO journal 53 15692564
2006 Unique self-palmitoylation activity of the transport protein particle component Bet3: a mechanism required for protein stability. Proceedings of the National Academy of Sciences of the United States of America 44 16908848
2005 Mammalian Bet3 functions as a cytosolic factor participating in transport from the ER to the Golgi apparatus. Journal of cell science 33 15728249
2006 Structure of the Bet3-Tpc6B core of TRAPP: two Tpc6 paralogs form trimeric complexes with Bet3 and Mum2. Journal of molecular biology 30 16828797
1998 A high copy suppressor screen reveals genetic interactions between BET3 and a new gene. Evidence for a novel complex in ER-to-Golgi transport. Genetics 27 9611195
2024 The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea. Communications biology 13 38472392
2010 Characterization of the self-palmitoylation activity of the transport protein particle component Bet3. Cellular and molecular life sciences : CMLS 8 20372964
2015 Bet3 participates in autophagy through GTPase Ypt1 in Saccharomyces cerevisiae. Cell biology international 5 25581738

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