Affinage

AGAP1

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

Length
857 aa
Mass
94.5 kDa
Annotated
2026-06-09
20 papers in source corpus 14 papers cited in narrative 15 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

AGAP1 is a multidomain Arf GTPase-activating protein that couples phosphoinositide-regulated Arf1 inactivation to adaptor-mediated endosomal trafficking and cytoskeletal remodeling (PMID:12388557, PMID:12967569). Its catalytic GAP activity is intrinsic to the protein and selective for Arf1 over Arf5 and Arf6, requiring the PH domain and being synergistically stimulated by PI(4,5)P2 and phosphatidic acid; the N-terminal residues of Arf1 form a substrate interface unique to AGAP1 among Arf GAPs (PMID:12388557, PMID:15212764). The N-terminal GLD domain does not bind nucleotide in the canonical sense but serves as a protein-interaction scaffold whose crystal structure shows G1–G5 NTPase loops and a noncanonical GDP-binding site (R106-F107-K108) that allosterically tunes activity (PMID:22453919, PMID:33830075, PMID:42002626); RhoA binding to this region selectively potentiates Arf1-directed GAP activity (PMID:22453919). Through its PH domain AGAP1 binds the delta and sigma3 subunits of the AP-3 adaptor complex, a specific interaction that governs AP-3 distribution and endosomal-lysosomal cargo trafficking and distinguishes AGAP1 (AP-3 endosomes) from AGAP2 (AP-1 recycling endosomes) (PMID:12967569, PMID:16079295). In neurons AGAP1 localizes to dendritic spines and synapses on early and recycling endosomes, and by linking AP-3 to the M5 muscarinic receptor it drives M5 endocytic recycling and presynaptic dopamine release; its expression lies downstream of dysbindin and shapes dendritic spine morphology (PMID:20664521, PMID:27713690). AGAP1 also forms functional complexes with the kinesin Kif2A, reciprocally stimulating each partner's enzymatic activity to coordinate cell migration and spreading, and controls localization of the Rac-GAP FilGAP to intracellular vesicles to restrain cell invasion (PMID:27531749, PMID:31785816). Loss of AGAP1 perturbs endolysosomal homeostasis, elevates autophagy, and chronically activates the integrated stress response via eIF2alpha phosphorylation (PMID:37470098).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 2002 High

    Established AGAP1 as a catalytically active Arf GAP and defined how its activity is gated, answering whether it is an enzyme and what controls it.

    Evidence In vitro Arf GAP assays with domain-deletion mutants and lipid stimulation

    PMID:12388557

    Open questions at the time
    • Physiological Arf1 substrate pool in cells not defined
    • Structural basis of PH-domain lipid activation not resolved
  2. 2002 Medium

    Linked AGAP1 to endosomal membranes and the actin cytoskeleton, suggesting its GAP activity operates in a trafficking and morphology context.

    Evidence Overexpression with endocytic marker colocalization and actin imaging

    PMID:12388557

    Open questions at the time
    • Overexpression phenotypes may not reflect endogenous function
    • Mechanism connecting Arf1 inactivation to actin changes unclear
  3. 2003 High

    Identified the AP-3 adaptor complex as a specific direct partner, providing the molecular bridge between AGAP1 and cargo sorting.

    Evidence Direct binding mapped to delta/sigma3 subunits, plus gain- and loss-of-function on AP-3 distribution

    PMID:12967569

    Open questions at the time
    • How AP-3 binding integrates with GAP catalysis not resolved
    • Cargo repertoire beyond LAMP1 not mapped
  4. 2004 Medium

    Mapped the Arf1 substrate interface and an sGC interaction, refining substrate recognition and a possible signaling input.

    Evidence Arf1 N-terminal mutants in GAP assays; Co-IP and Src phosphorylation assays for sGC

    PMID:15212764 PMID:15381706

    Open questions at the time
    • Functional role of sGC association not established
    • Significance of Src tyrosine phosphorylation in cells unknown
  5. 2005 Medium

    Distinguished AGAP1 from paralog AGAP2 by adaptor specificity, showing related GAPs partition between distinct endosomal pathways.

    Evidence Comparative overexpression and distribution assays for AP-1 vs AP-3

    PMID:16079295

    Open questions at the time
    • Structural determinant of adaptor selectivity not identified
    • Functional consequences of mis-targeting not measured
  6. 2010 High

    Demonstrated a neuronal physiological role by tying AGAP1-AP-3 to M5 receptor recycling and dopamine release, moving from cell biology to circuit-level function.

    Evidence Reciprocal Co-IP, neuronal recycling assays, in vivo dopamine release after genetic manipulation

    PMID:20664521

    Open questions at the time
    • Whether other GPCRs use this route not tested
    • Behavioral consequences not directly addressed
  7. 2012 High

    Reassigned the GLD domain as a protein-interaction module and identified RhoA as an allosteric activator, explaining cross-talk between Rho and Arf signaling.

    Evidence Y2H, Co-IP, in vitro GAP assays with RhoA peptides, nucleotide binding assay

    PMID:22453919

    Open questions at the time
    • RhoA nucleotide-state independence biological meaning unclear
    • Whether RhoA binding occurs at endogenous levels not shown
  8. 2016 Medium

    Placed AGAP1 in synaptic endosomal trafficking and downstream of dysbindin, connecting it to a neurodevelopmental pathway.

    Evidence Neuronal imaging, overexpression/knockdown spine and endosome readouts, Western blot in DTNBP1-null mice

    PMID:27713690

    Open questions at the time
    • Mechanism by which dysbindin regulates AGAP1 levels unknown
    • Causal link between spine defects and behavior not established
  9. 2016 High

    Revealed a Kif2A-AGAP1 functional complex with reciprocal enzymatic activation, extending AGAP1 function to motor-driven cytoskeletal remodeling.

    Evidence Interaction screen, domain-mapped Co-IP, in vitro GAP and ATPase assays, knockdown with interaction-dependent rescue

    PMID:27531749

    Open questions at the time
    • In vivo relevance of mutual activation not tested
    • Subcellular site of Kif2A-AGAP1 action not defined
  10. 2019 Medium

    Showed AGAP1 sequesters the Rac-GAP FilGAP onto vesicles to limit cell invasion, linking AGAP1 to invasion control through GAP localization.

    Evidence Co-IP, colocalization, double-knockdown spreading/migration/invasion assays

    PMID:31785816

    Open questions at the time
    • Whether FilGAP sequestration requires AGAP1 catalytic activity unclear
    • In vivo invasion role not tested
  11. 2021 Medium

    Provided a crystal structure of the GLD domain, confirming NTPase-like architecture without detectable nucleotide binding.

    Evidence X-ray crystallography of GLD residues 70-235 at 3.0 Å

    PMID:33830075

    Open questions at the time
    • No functional validation in this study
    • Apo structure does not reveal regulatory ligand
  12. 2023 Medium

    Connected AGAP1 loss to integrated stress response activation and endolysosomal dysfunction in vivo, defining a stress-sensitization phenotype.

    Evidence Drosophila CenG1a loss-of-function genetics with morphology, autophagy, phospho-eIF2alpha, and survival readouts

    PMID:37470098

    Open questions at the time
    • Direct molecular trigger of eIF2alpha phosphorylation unknown
    • Conservation of stress phenotype in mammals not confirmed
  13. 2023 Low

    Proposed a mutant-p53/hnRNPA2B1 axis that elevates AGAP1 to promote exosome-driven cancer progression.

    Evidence Sequencing, Co-IP, mRNA stability assay, QS11 inhibitor functional assays

    PMID:37030635

    Open questions at the time
    • Mechanistic chain partly inferred from correlation and inhibitor data at abstract-level detail
    • Direct effect of AGAP1 on exosome biogenesis not biochemically defined
  14. 2026 High

    Resolved a noncanonical GDP-binding site in the GLD domain and tied it to tumor suppression, linking AGAP1 structure to metabolic and oncogenic signaling.

    Evidence GLD-GDP crystal structure at 2.5 Å, structure-based mutagenesis, RNA-seq, metabolic assays, xenograft and metastasis mouse models with AGAP1 knockout

    PMID:42002626

    Open questions at the time
    • How GDP occupancy regulates GAP catalysis mechanistically not resolved
    • Tumor-suppressor role appears context-dependent versus other oncogenic reports

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved how AGAP1's catalytic Arf1 inactivation, GLD-domain protein scaffolding, and noncanonical nucleotide sensing are integrated into a single regulatory mechanism across its trafficking, cytoskeletal, and cancer functions.
  • No unified structure of full-length AGAP1 with substrate and partners
  • Whether AGAP1 is pro- or anti-tumorigenic appears cell-context dependent

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0098772 molecular function regulator activity 2 GO:0140096 catalytic activity, acting on a protein 2 GO:0008289 lipid binding 1
Localization
GO:0005768 endosome 2 GO:0005886 plasma membrane 2 GO:0031410 cytoplasmic vesicle 2
Pathway
R-HSA-5653656 Vesicle-mediated transport 3 R-HSA-112316 Neuronal System 2 R-HSA-8953854 Metabolism of RNA 1
Partners
AP3D1AP3S1CHRM5FILGAPGUCY1A1GUCY1B1KIF2ARHOA
Complex memberships
AP-3 adaptor complex

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2002 AGAP1 has Arf GAP activity with substrate preference Arf1 > Arf5 > Arf6; this activity requires the pleckstrin homology (PH) domain and is synergistically stimulated by phosphatidylinositol 4,5-bisphosphate and phosphatidic acid. Deletion of the GTP-binding protein-like (GLD) domain altered lipid dependence of GAP activity. In vitro Arf GAP activity assays, domain deletion mutants, lipid stimulation assays The Journal of biological chemistry High 12388557
2002 Overexpressed AGAP1 associates with and induces punctate endocytic structures containing transferrin and Rab4, redistributes AP1 from trans-Golgi to these endosomal structures, inhibits PDGF-induced actin ruffles, and induces loss of actin stress fibers — effects distinct from other ASAP family Arf GAPs. Overexpression with immunofluorescence, colocalization with endocytic markers, actin cytoskeleton imaging The Journal of biological chemistry Medium 12388557
2003 AGAP1 directly associates with the AP-3 adaptor protein complex via its PH domain binding the delta and sigma3 subunits of AP-3; this interaction is specific (other Arf GAPs and coat proteins are not affected), and AGAP1 overexpression alters AP-3 cellular distribution and increases LAMP1 trafficking via the plasma membrane, while reduced AGAP1 expression renders AP-3 resistant to brefeldin A. Direct binding assay, colocalization, overexpression and knockdown with coat protein distribution readout Developmental cell High 12967569
2004 AGAP1 interacts with both the alpha1 and beta1 subunits of soluble guanylyl cyclase (sGC) through its carboxyl-terminal portion; this interaction is confirmed in vitro and in vivo, and is potentiated by tyrosine phosphorylation of AGAP1 by Src-like kinases. Co-immunoprecipitation (in vitro and in vivo), yeast two-hybrid or equivalent binding assay, phosphorylation assay with Src kinase The Journal of biological chemistry Medium 15381706
2004 Amino acids 2–17 of Arf1 are critical for productive interaction with AGAP1 (as well as ASAP1 and Arf GAP1), but the specific contribution of individual residues (e.g., Lys15/16 important for AGAP1 and ASAP1 but not Arf GAP1; Leu8 important for Arf GAP1 but not AGAP1) differs among Arf GAP subtypes, defining a unique interface between Arf1 and AGAP1. Antibody sequestration of Arf1 N-terminus, deletion and point mutant Arf1 proteins, in vitro GAP activity assays Cellular signalling Medium 15212764
2005 AGAP1 specifically regulates AP-3 endosomes while the closely related AGAP2 specifically regulates AP-1 recycling endosomes, establishing that these two related Arf GAPs have distinct adaptor protein complex specificity. Comparative overexpression, colocalization, intracellular distribution assays for AP-1 and AP-3 Journal of cell science Medium 16079295
2010 AGAP1 directly physically interacts with the M5 muscarinic acetylcholine receptor (specific among MR subtypes and AGAP subtypes) and mediates binding of AP-3 to M5; this interaction is required for endocytic recycling of M5 in neurons, and its disruption or elimination of AP-3 decreases presynaptic M5-mediated dopamine release potentiation in the striatum. Co-immunoprecipitation (direct interaction), neuronal recycling assays, in vivo dopamine release measurements after genetic manipulation The EMBO journal High 20664521
2012 The GLD domain of AGAP1 does not bind nucleotides but instead acts as a protein-binding site; RhoA (but not Cdc42) binds to AGAP1/AGAP2 via RhoA's C-terminus independently of nucleotide state, and RhoA or its C-terminal peptide allosterically increases AGAP1 GAP activity specifically toward Arf1. Yeast two-hybrid screen, co-immunoprecipitation, in vitro GAP activity assay with RhoA peptides, nucleotide binding assay The Journal of biological chemistry High 22453919
2016 AGAP1 localizes to axons, dendrites, dendritic spines, and synapses in neurons, colocalizing with early and recycling endosome markers; overexpression and knockdown of AGAP1 both affect neuronal endosomal trafficking and dendritic spine morphology. AGAP1 protein and mRNA levels are selectively reduced in mice carrying null allele of DTNBP1 (dysbindin gene), placing AGAP1 downstream of dysbindin. Immunofluorescence, live-cell imaging, overexpression and siRNA knockdown with spine morphology and endosomal trafficking readouts, Western blot in DTNBP1 knockout mice Frontiers in cellular neuroscience Medium 27713690
2016 Kif2A (kinesin-13 family) binds to the GLD and PH domains of AGAP1 via its motor domain; Kif2A increases AGAP1 GAP activity, and AGAP1's GLD+PH domain increases Kif2A ATPase activity. Knockdown of either Kif2A or AGAP1 slows cell migration and accelerates cell spreading; rescue experiments establish that physical interaction between the two proteins is required for their joint regulation of cytoskeletal remodeling. Protein interaction screen, co-immunoprecipitation, domain mapping, in vitro GAP and ATPase assays, siRNA knockdown with cell migration and spreading rescue experiments The Journal of biological chemistry High 27531749
2019 AGAP1 binds to the C-terminus of FilGAP (a Rac-specific GAP) via its own N-terminal GLD domain; AGAP1 controls subcellular localization of FilGAP to intracellular vesicles, away from focal adhesions. Depletion of AGAP1 causes FilGAP accumulation at focal adhesions and actin structures, suppresses cell spreading, and promotes cancer cell invasion in an extracellular matrix — effects dependent on FilGAP. Co-immunoprecipitation, colocalization by immunofluorescence, siRNA knockdown with cell spreading, migration, and invasion assays Biochemical and biophysical research communications Medium 31785816
2021 Crystal structure of the AGAP1 GLD domain (residues 70–235) resolved at 3.0 Å; the structure reveals conserved G1–G5 loops consistent with NTPase classification; nucleotide binding is not detected but protein partners or other domains may regulate its activity. X-ray crystallography, gel-filtration chromatography purification Acta crystallographica. Section F, Structural biology communications Medium 33830075
2023 Loss of AGAP1 function in Drosophila (CenG1a mutant) causes reduced axon terminal size, increased neuronal endosome abundance, elevated autophagy, and basal elevation of phospho-eIF2α (integrated stress response activation); CenG1a-mutant flies show increased lethality from cytotoxic environmental stressors, suggesting AGAP1 deficiency chronically activates the integrated stress response and sensitizes cells to secondary insults. Drosophila loss-of-function genetics, neuronal morphology quantification, endosome abundance imaging, autophagy markers, eIF2α phosphorylation western blot, survival assays with environmental stressors Disease models & mechanisms Medium 37470098
2023 Mutant p53 (G245S) interacts with hnRNPA2B1, which increases AGAP1 mRNA stability and thus protein translation; elevated AGAP1 then promotes exosome formation, enhancing cancer cell proliferation and metastasis. Whole-genome sequencing, co-immunoprecipitation, mRNA stability assay, AGAP1 inhibitor (QS11) functional assay Cancer letters Low 37030635
2026 Crystal structure of AGAP1 GLD domain in complex with GDP at 2.5 Å identifies a noncanonical GDP-binding site defined by residues R106-F107-K108; mutagenesis disrupting this site enhances TNBC cell proliferation and migration, activates glycolysis/TCA cycle and PI3K-AKT signaling; knockout of AGAP1 promotes tumor growth and metastasis in xenograft and pulmonary metastasis mouse models. X-ray crystallography, structure-based mutagenesis, RNA-seq, ECAR/OCR/glucose uptake assays, xenograft and pulmonary metastasis mouse models, AGAP1 knockout Cellular and molecular life sciences : CMLS High 42002626

Source papers

Stage 0 corpus · 20 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 94 12388557
2003 Specific regulation of the adaptor protein complex AP-3 by the Arf GAP AGAP1. Developmental cell 78 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 34 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 21 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 15 22453919
2019 AGAP1 regulates subcellular localization of FilGAP and control cancer cell invasion. Biochemical and biophysical research communications 13 31785816
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
2023 AGAP1-associated endolysosomal trafficking abnormalities link gene-environment interactions in neurodevelopmental disorders. Disease models & mechanisms 9 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 4 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
2026 AGAP1 and noncanonical GDP binding regulate triple-negative breast cancer development. Cellular and molecular life sciences : CMLS 0 42002626

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