Affinage

AGAP1

Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 · UniProt Q9UPQ3

Length
857 aa
Mass
94.5 kDa
Annotated
2026-04-28
19 papers in source corpus 13 papers cited in narrative 14 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

AGAP1 is a phosphoinositide-dependent Arf GTPase-activating protein that couples lipid-regulated Arf1 inactivation to endosomal sorting, cytoskeletal remodeling, and neuronal membrane trafficking. Its catalytic ArfGAP activity toward Arf1 is stimulated by PI(4,5)P₂ and phosphatidic acid via its PH domain, and allosterically enhanced by RhoA and the kinesin-13 family member Kif2A binding to its GLD domain (PMID:12388557, PMID:22453919, PMID:27531749). AGAP1 selectively associates with the AP-3 adaptor complex through PH-domain contacts with the δ and σ3 subunits, and this interaction is required for AP-3-dependent endosomal–lysosomal trafficking, including recycling of the M5 muscarinic receptor and regulation of dendritic spine morphology in neurons (PMID:12967569, PMID:20664521, PMID:27713690). AGAP1 also controls subcellular localization of the Rac-GAP FilGAP to intracellular vesicles, promotes exosome biogenesis in cancer cells, and functions upstream of the integrated stress response through its role in endolysosomal trafficking, as demonstrated by loss-of-function studies in Drosophila (PMID:31785816, PMID:37030635, PMID:37470098).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2002 High

    Establishing AGAP1 as a lipid-regulated ArfGAP resolved how phosphoinositide and phosphatidic acid signals are integrated to control Arf1 GTP hydrolysis, and identified the PH and GLD domains as critical regulatory elements.

    Evidence In vitro GAP assays with lipid vesicles and domain deletion mutants

    PMID:12388557

    Open questions at the time
    • Structural basis for synergistic lipid activation unknown
    • In vivo substrates beyond Arf1 not tested in endogenous settings
  2. 2003 High

    Demonstrating that AGAP1 specifically binds the AP-3 adaptor complex and controls LAMP1 trafficking established AGAP1 as a key regulator of the endosomal–lysosomal sorting pathway, distinct from AP-1-associated ArfGAPs.

    Evidence Co-immunoprecipitation of AGAP1 PH domain with AP-3 δ/σ3 subunits, siRNA knockdown, LAMP1 trafficking assays, and comparative analysis with AGAP2

    PMID:12967569 PMID:16079295

    Open questions at the time
    • Structural determinants of AP-3 selectivity versus AP-1 not defined at atomic level
    • Cargo repertoire beyond LAMP1 not systematically assessed
  3. 2004 High

    Mapping the Arf1 N-terminal helix (residues 2–17) as the AGAP1 interaction site and identifying critical lysines resolved how AGAP1 recognizes its primary substrate.

    Evidence In vitro GAP assays with Arf1 deletion/point mutants and peptide competition

    PMID:15212764

    Open questions at the time
    • No co-crystal structure of AGAP1–Arf1 complex
    • Whether the same interface is used in membrane-bound context is untested
  4. 2004 Medium

    Discovery that Src-mediated tyrosine phosphorylation of AGAP1 enhances its interaction with soluble guanylyl cyclase opened a link between Arf signaling and NO/cGMP pathways.

    Evidence Co-immunoprecipitation in vitro and in vivo with Src kinase phosphorylation assay

    PMID:15381706

    Open questions at the time
    • Functional consequence of sGC–AGAP1 interaction on cGMP production not shown
    • Phosphorylation sites on AGAP1 not mapped
    • Not independently replicated
  5. 2010 High

    Showing that AGAP1 bridges the M5 muscarinic receptor to AP-3 for endocytic recycling, and that this pathway modulates dopamine release in vivo, provided the first receptor-specific physiological role for AGAP1 in the nervous system.

    Evidence Co-IP of AGAP1–M5, receptor recycling assays in neurons, in vivo striatal dopamine release measurements upon pathway disruption

    PMID:20664521

    Open questions at the time
    • Whether other GPCRs use AGAP1/AP-3 for recycling is unknown
    • Mechanism by which AGAP1 recognizes M5 cytoplasmic domain not mapped
  6. 2012 High

    Identification of the GLD domain as an allosteric protein-binding module activated by RhoA resolved how Rho-family GTPase signals converge on Arf1 inactivation through AGAP1.

    Evidence Two-hybrid screen, Co-IP, in vitro GAP assays with RhoA C-terminal peptides and GLD deletion mutants

    PMID:22453919

    Open questions at the time
    • Nucleotide-independence of RhoA binding is unusual and mechanistic basis is unclear
    • Cdc42 and Rac1 binding specificity not fully resolved
  7. 2016 High

    Demonstrating mutual enzymatic activation between AGAP1 and the kinesin Kif2A established a direct link between Arf signaling and microtubule dynamics during cell migration.

    Evidence In vitro GAP and ATPase assays, domain-mapping pulldowns, knockdown rescue with binding-deficient mutants in migration/spreading assays

    PMID:27531749

    Open questions at the time
    • In vivo relevance of Kif2A–AGAP1 complex in neurons not tested
    • Structural basis of mutual activation unknown
  8. 2016 Medium

    Localization of AGAP1 to dendritic spines and demonstration that its levels depend on dysbindin placed AGAP1 within a neuronal endosomal network relevant to schizophrenia-associated biology.

    Evidence Immunofluorescence in neurons, overexpression/knockdown morphological analysis, DTNBP1 null mouse comparison

    PMID:27713690

    Open questions at the time
    • Direct transcriptional or post-translational mechanism by which dysbindin regulates AGAP1 not defined
    • Causal role of AGAP1 reduction in schizophrenia-related phenotypes not established
  9. 2019 Medium

    Showing that AGAP1 controls FilGAP localization to intracellular vesicles and that AGAP1 loss redirects FilGAP to focal adhesions revealed a new mechanism by which AGAP1 indirectly regulates Rac-dependent cell spreading and invasion.

    Evidence Co-IP, colocalization, siRNA knockdown with epistatic rescue, cell spreading/invasion assays

    PMID:31785816

    Open questions at the time
    • Whether AGAP1 GAP activity is required for FilGAP relocalization or only scaffolding is unclear
    • Single-lab finding not yet independently replicated
  10. 2021 Medium

    The crystal structure of the GLD domain confirmed a conserved NTPase fold with G1–G5 loops, supporting the model that the GLD serves as a regulatory protein-interaction domain rather than an active GTPase.

    Evidence X-ray crystallography at 3.0 Å resolution

    PMID:33830075

    Open questions at the time
    • No co-structure with RhoA or Kif2A to reveal allosteric mechanism
    • Whether GLD binds nucleotide in vivo is unresolved
  11. 2023 Medium

    Two studies expanded AGAP1's functional scope: in cancer, mutant p53 stabilizes AGAP1 mRNA to promote exosome-mediated proliferation and metastasis; in Drosophila, loss of the AGAP1 ortholog CenG1a disrupts endolysosomal trafficking and constitutively activates the integrated stress response.

    Evidence RNA stability assays and proliferation/migration assays in cancer cells; Drosophila loss-of-function genetics with phospho-eIF2α readouts

    PMID:37030635 PMID:37470098

    Open questions at the time
    • Mechanism by which AGAP1 promotes exosome biogenesis is undefined
    • Whether ISR dysregulation upon AGAP1 loss is conserved in mammals is untested
    • Single-lab findings for each

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include the structural basis of AGAP1's allosteric regulation by the GLD domain, whether AGAP1 functions as a scaffold independent of its GAP activity in vivo, the full cargo repertoire of AGAP1/AP-3 trafficking, and whether AGAP1 dysfunction directly contributes to neuropsychiatric or cancer pathology in humans.
  • No full-length AGAP1 structure or AGAP1–partner co-structure available
  • No genetic disease association established by human family studies
  • Systematic identification of AGAP1-dependent cargoes not performed

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 4 GO:0060090 molecular adaptor activity 3 GO:0008289 lipid binding 1
Localization
GO:0005768 endosome 4 GO:0031410 cytoplasmic vesicle 2
Pathway
R-HSA-5653656 Vesicle-mediated transport 4 R-HSA-162582 Signal Transduction 3
Partners
AP3D1AP3S1ARF1CHRM5FILGAPGUCY1A1KIF2ARHOA
Complex memberships
AP-3 adaptor complex

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2002 AGAP1 is a phosphoinositide-dependent ArfGAP with activity toward Arf1>Arf5>Arf6; phosphatidylinositol 4,5-bisphosphate and phosphatidic acid synergistically stimulate its GAP activity; the PH domain is necessary for activity; and the GTP-binding protein-like (GLD) domain affects lipid dependence of GAP activity. In vitro GAP activity assays with lipid vesicles, domain deletion mutants The Journal of biological chemistry High 12388557
2002 Overexpressed AGAP1 localizes to endocytic punctate structures containing transferrin and Rab4 (endosomal markers), redistributes AP-1 from trans-Golgi to these structures, and inhibits PDGF-induced ruffle formation while also inducing loss of actin stress fibers. Overexpression with immunofluorescence and transferrin uptake assays in cultured cells The Journal of biological chemistry Medium 12388557
2003 AGAP1 directly associates with the AP-3 adaptor protein complex via its PH domain binding to the delta and sigma3 subunits of AP-3; AGAP1 overexpression changes cellular distribution of AP-3 and increases LAMP1 trafficking via the plasma membrane, while reduced AGAP1 expression renders AP-3 resistant to brefeldin A. Co-immunoprecipitation, colocalization, siRNA knockdown, overexpression with trafficking assays Developmental cell High 12967569
2004 AGAP1 interacts with Arf1 through the N-terminal amino acids 2–17 of Arf1, and lysines 15 and 16 of Arf1 are critical for productive interaction with AGAP1; peptides from amino acids 2–17 of Arf1 directly bind AGAP1 and inhibit its GAP activity. In vitro GAP activity assays with Arf1 deletion/point mutants, antibody sequestration, direct peptide binding Cellular signalling High 15212764
2004 AGAP1 physically interacts with both the alpha1 and beta1 subunits of soluble guanylyl cyclase (sGC) via its C-terminal portion, and tyrosine phosphorylation of AGAP1 by Src-like kinases potently increases this interaction. Co-immunoprecipitation in vitro and in vivo, tyrosine phosphorylation assay with Src kinase The Journal of biological chemistry Medium 15381706
2005 AGAP1 specifically associates with AP-3 (not AP-1) endosomes, distinguishing it from the closely related AGAP2 which specifically interacts with AP-1; this specificity underlies differential regulation of AP-3 versus AP-1 trafficking compartments. Co-immunoprecipitation, colocalization, overexpression trafficking assays comparing AGAP1 and AGAP2 Journal of cell science High 16079295
2010 AGAP1 directly and specifically interacts with the M5 muscarinic receptor and mediates binding of AP-3 to M5; this AGAP1-M5 interaction is required for AP-3-dependent endocytic recycling of M5 in neurons; disruption of this interaction in vivo reduces presynaptic M5-mediated dopamine release potentiation in the striatum. Co-immunoprecipitation, receptor recycling assays in neurons, in vivo pharmacological and genetic disruption with dopamine release measurements The EMBO journal High 20664521
2012 The GLD domain of AGAP1 functions as a protein-binding site that allosterically regulates ArfGAP catalytic activity; RhoA binds to the GLD domain via its C-terminus (nucleotide-independently) and increases AGAP1 GAP activity specifically toward Arf1; Rac1 and Cdc42 were identified as potential binding partners but Cdc42 C-terminal peptide did not bind or activate AGAP1. Two-hybrid screen, co-immunoprecipitation, in vitro GAP activity assays with RhoA and peptides, deletion mutants The Journal of biological chemistry High 22453919
2016 AGAP1 localizes to axons, dendrites, dendritic spines, and synapses in neurons, colocalizing preferentially with early and recycling endosome markers; overexpression and knockdown of AGAP1 alter neuronal endosomal trafficking and dendritic spine morphology; AGAP1 protein and mRNA levels are selectively reduced in DTNBP1 (dysbindin) null mice, placing AGAP1 downstream of dysbindin. Immunofluorescence in neurons, overexpression and siRNA knockdown with morphological readouts, comparison in DTNBP1 null mouse tissue Frontiers in cellular neuroscience Medium 27713690
2016 AGAP1 directly interacts with the kinesin-13 family member Kif2A via its GLD and PH domains binding the Kif2A motor domain; Kif2A increases AGAP1 GAP activity, and the GLD-PH domains of AGAP1 increase Kif2A ATPase activity; the Kif2A·AGAP1 complex functionally contributes to cytoskeleton remodeling during cell migration and spreading. Pulldown, in vitro GAP activity assay, in vitro ATPase assay, knockdown rescue experiments with mutants in cell migration/spreading assays The Journal of biological chemistry High 27531749
2019 AGAP1 binds to the C-terminus of FilGAP (a Rac-specific GAP) via its N-terminal GLD-containing region; AGAP1 controls subcellular localization of FilGAP to intracellular vesicles, and depletion of AGAP1 causes FilGAP to accumulate at focal adhesions, leading to suppressed cell spreading and increased cancer cell invasion that is reversed by co-depletion of FilGAP. Co-immunoprecipitation, colocalization, siRNA knockdown, cell spreading and invasion assays Biochemical and biophysical research communications Medium 31785816
2021 The crystal structure of the AGAP1 GLD domain (residues 70–235) was determined at 3.0 Å resolution; the domain contains conserved G1–G5 loops consistent with NTPase fold, supporting its role as a protein-binding regulatory domain rather than a nucleotide-hydrolyzing domain. X-ray crystallography Acta crystallographica. Section F, Structural biology communications Medium 33830075
2023 AGAP1 promotes exosome formation in cancer cells; the mutant p53-G245S interacts with hnRNPA2B1 to increase AGAP1 mRNA stability and protein translation, and elevated AGAP1 enhances exosome formation to promote cancer cell proliferation and metastasis. Whole-genome sequencing, RNA stability assays, co-immunoprecipitation, AGAP1 inhibitor (QS11) treatment, functional proliferation/migration assays Cancer letters Medium 37030635
2023 Loss of the Drosophila AGAP1 ortholog CenG1a results in reduced axon terminal size, increased neuronal endosome abundance, elevated autophagy, basal elevation of eIF2α phosphorylation, and inability to further activate the integrated stress response upon cytotoxic stress, placing AGAP1 function in endolysosomal trafficking upstream of the integrated stress response pathway. Drosophila loss-of-function genetics, immunofluorescence, phospho-eIF2α western blot, survival assays with environmental stressors Disease models & mechanisms Medium 37470098

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 AGAP1, an endosome-associated, phosphoinositide-dependent ADP-ribosylation factor GTPase-activating protein that affects actin cytoskeleton. The Journal of biological chemistry 93 12388557
2003 Specific regulation of the adaptor protein complex AP-3 by the Arf GAP AGAP1. Developmental cell 76 12967569
2010 AGAP1/AP-3-dependent endocytic recycling of M5 muscarinic receptors promotes dopamine release. The EMBO journal 64 20664521
2005 Evaluation of the chromosome 2q37.3 gene CENTG2 as an autism susceptibility gene. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 55 15892143
2005 The Arf GAPs AGAP1 and AGAP2 distinguish between the adaptor protein complexes AP-1 and AP-3. Journal of cell science 55 16079295
2023 Mutant p53 activates hnRNPA2B1-AGAP1-mediated exosome formation to promote esophageal squamous cell carcinoma progression. Cancer letters 32 37030635
2004 AGAP1, a novel binding partner of nitric oxide-sensitive guanylyl cyclase. The Journal of biological chemistry 31 15381706
2004 Differences between AGAP1, ASAP1 and Arf GAP1 in substrate recognition: interaction with the N-terminus of Arf1. Cellular signalling 30 15212764
2021 Osteosarcoma Cell-Derived Exosomal miR-1307 Promotes Tumorgenesis via Targeting AGAP1. BioMed research international 26 33834074
2016 The Endosome Localized Arf-GAP AGAP1 Modulates Dendritic Spine Morphology Downstream of the Neurodevelopmental Disorder Factor Dysbindin. Frontiers in cellular neuroscience 20 27713690
2012 GTP-binding protein-like domain of AGAP1 is protein binding site that allosterically regulates ArfGAP protein catalytic activity. The Journal of biological chemistry 13 22453919
2018 A de novo 2q37.2 deletion encompassing AGAP1 and SH3BP4 in a patient with autism and intellectual disability. European journal of medical genetics 12 30472483
2019 AGAP1 regulates subcellular localization of FilGAP and control cancer cell invasion. Biochemical and biophysical research communications 11 31785816
2023 AGAP1-associated endolysosomal trafficking abnormalities link gene-environment interactions in neurodevelopmental disorders. Disease models & mechanisms 8 37470098
2016 Direct Functional Interaction of the Kinesin-13 Family Member Kinesin-like Protein 2A (Kif2A) and Arf GAP with GTP-binding Protein-like, Ankyrin Repeats and PH Domains1 (AGAP1). The Journal of biological chemistry 5 27531749
2023 Circular RNA AGAP1 Stimulates Immune Escape and Distant Metastasis in Renal Cell Carcinoma. Molecular biotechnology 4 37202649
2021 Crystal structure of the GTP-binding protein-like domain of AGAP1. Acta crystallographica. Section F, Structural biology communications 3 33830075
2025 Sex-dependent epigenetic disruption of YY1 binding by prenatal BPA exposure downregulates Matr3 and alters Agap1 splicing in the offspring hippocampus. Biology of sex differences 1 40790242
2023 AGAP1-associated endolysosomal trafficking abnormalities link gene-environment interactions in a neurodevelopmental disorder. bioRxiv : the preprint server for biology 1 36778426