Affinage

PLEKHA3

Pleckstrin homology domain-containing family A member 3 · UniProt Q9HB20

Length
300 aa
Mass
33.9 kDa
Annotated
2026-06-10
29 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PLEKHA3 (FAPP1) is a pleckstrin-homology (PH) domain adaptor that controls PI(4)P homeostasis and selective cargo exit at the trans-Golgi network (TGN) (PMID:15107860, PMID:30659099). Its PH domain is recruited to the TGN by coincidence detection of two ligands engaged at structurally distinct sites: PtdIns(4)P bound in a lipid-binding pocket and GTP-bound ARF engaged on the outer face of the β-barrel, allowing simultaneous and independent binding of both (PMID:11001876, PMID:21454700, PMID:24462251). Membrane recognition is sharpened by preferential targeting of PI(4)P-containing liquid-disordered bilayers and by a conserved hydrophobic wedge adjacent to the lipid pocket that penetrates the leaflet and can independently tubulate Golgi membranes, linking head-group recognition to membrane remodeling (PMID:20300118, PMID:22035800, PMID:25579996). Functionally, FAPP1 is required for post-Golgi carrier generation, as its displacement blocks cargo transfer to the plasma membrane and PH-domain overexpression impairs carrier fission (PMID:15107860). At ER-TGN contact sites FAPP1 binds the ER phosphatase Sac1 and positions it to dephosphorylate TGN PI(4)P in trans; FAPP1 depletion raises TGN PI(4)P and increases secretion of selected cargoes, defining FAPP1 as a gatekeeper of Golgi exit (PMID:30659099).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2000 High

    Established the molecular ligand of FAPP1 by showing its PH domain is a specific PtdIns(4)P reader, distinguishing it from PIP3-binding PH domains and providing the lipid-recognition basis for its function.

    Evidence In vitro phosphoinositide-binding assay with recombinant PH domains

    PMID:11001876

    Open questions at the time
    • Did not address subcellular localization or cellular function
    • No structural basis for the selectivity
  2. 2004 High

    Placed FAPP1 in a cellular pathway by showing it localizes to TGN carriers, binds both PI(4)P and ARF, and is required for post-Golgi cargo transport and carrier fission.

    Evidence Fluorescence localization, siRNA knockdown, PH-domain overexpression with cargo transport assays, co-IP

    PMID:15107860

    Open questions at the time
    • Did not resolve how PI(4)P and ARF are simultaneously engaged
    • Molecular mechanism of carrier fission unresolved
  3. 2005 Medium

    Defined which kinases generate the PI(4)P pools FAPP1 senses, distinguishing Golgi pools (PI4KIIalpha/PI4KIIIbeta) from a plasma-membrane pool (PI4KIIIalpha).

    Evidence GFP-fusion live-cell imaging with PI4-kinase siRNA and pharmacological inhibition

    PMID:15635101

    Open questions at the time
    • Functional consequence of plasma-membrane PI(4)P sensing not established
    • Single-lab imaging-based assignment
  4. 2005 Medium

    Clarified FAPP1's transport specificity by showing, in contrast to FAPP2, that FAPP1 depletion does not affect apical/basolateral transport in polarized cells.

    Evidence Adenovirus-mediated siRNA with transport assays in polarized MDCK cells

    PMID:16103222

    Open questions at the time
    • Negative result; does not exclude roles in non-polarized secretion
    • Cargo-specific dependencies not tested
  5. 2010 High

    Revealed how lipid recognition is coupled to membrane remodeling, showing a hydrophobic wedge in the PH domain that penetrates the bilayer and independently tubulates Golgi membranes.

    Evidence Solution NMR of micelle-bound PH domain, wedge mutagenesis, membrane tubulation assay

    PMID:20300118

    Open questions at the time
    • Tubulation shown in vitro; in-cell contribution to fission not directly quantified
    • Role of ARF in wedge insertion not addressed
  6. 2011 High

    Provided the high-resolution structural basis for coincidence detection, showing PI(4)P binds a defined pocket while ARF1 binds a distinct outer β-barrel site, permitting independent simultaneous engagement.

    Evidence 1.9 Å crystal structure with NMR perturbation, mutagenesis, affinity measurements, tubulation assay

    PMID:21454700

    Open questions at the time
    • Membrane-bound ternary geometry not directly visualized
    • Regulation of binding by ARF nucleotide state in cells not shown
  7. 2011 Medium

    Demonstrated that head-group recognition itself drives remodeling, since stabilized PtdIns(4)P analogs are recognized and stimulate PH-domain membrane insertion and tubulation.

    Evidence Synthetic PI(4)P analogs with binding and membrane tubulation assays

    PMID:22035800

    Open questions at the time
    • In vitro analog system; physiological relevance of analogs limited
    • Single-lab study
  8. 2014 Medium

    Mapped the ARF-binding interface at a membrane surface, showing Arf1 switch I contacts the PH domain C-terminal extension at a site distinct from the PI(4)P pocket, confirming the coincidence-detection recruitment model.

    Evidence NMR chemical-shift perturbation at model membrane surface with structural modeling

    PMID:24462251

    Open questions at the time
    • Used yeast Arf1; human ARF1 contacts inferred
    • Affinity and stoichiometry on cellular membranes not measured
  9. 2015 Medium

    Refined membrane targeting selectivity, showing preference for PI(4)P in liquid-disordered membranes via a hydrophobic wedge adjacent to the recognition site, tuning FAPP1 to dynamic TGN zones.

    Evidence Liposome sedimentation, membrane partitioning, NMR with PI(4)P bicelles

    PMID:25579996

    Open questions at the time
    • Lipid-phase preference shown in reconstituted membranes
    • Functional impact on cargo selection not tested
  10. 2019 High

    Redefined FAPP1 as a PI(4)P-consuming gatekeeper rather than only a carrier-forming factor, showing it operates at ER-TGN contacts to position Sac1 for in-trans PI(4)P dephosphorylation and to limit secretion of selected cargoes.

    Evidence Reciprocal co-IP, in vitro Sac1 phosphatase assay, siRNA depletion with PI(4)P and cargo secretion readouts, super-resolution microscopy

    PMID:30659099

    Open questions at the time
    • Cargo-selectivity determinants of the gatekeeper function unresolved
    • How carrier-formation and PI(4)P-consumption roles are coordinated unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • How FAPP1 reconciles its membrane-tubulating carrier-formation activity with its Sac1-mediated PI(4)P-consuming gatekeeper role, and what determines which cargoes it gates, remains unresolved.
  • No model integrating tubulation and PI(4)P-consumption at the TGN
  • Physiological regulators switching between the two functions unidentified

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0008289 lipid binding 4 GO:0060090 molecular adaptor activity 2 GO:0140299 molecular sensor activity 2
Localization
GO:0005794 Golgi apparatus 3 GO:0005783 endoplasmic reticulum 1
Pathway
R-HSA-1430728 Metabolism 2 R-HSA-5653656 Vesicle-mediated transport 2
Partners
ARF1SACM1L

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 The PH domain of FAPP1 (PLEKHA3) specifically binds phosphatidylinositol-4-phosphate (PtdIns(4)P) in vitro, with distinct selectivity from PtdIns(3,4,5)P3 and other phosphoinositides. In vitro phosphoinositide-binding assay using recombinant PH domains The Biochemical journal High 11001876
2004 FAPP1 localizes to the trans-Golgi network (TGN) on nascent carriers and interacts with both PtdIns(4)P and the small GTPase ARF through its PH domain; knockdown or displacement of FAPP1 inhibits cargo transfer to the plasma membrane, and overexpression of FAPP-PH impairs carrier fission, establishing FAPP1 as an essential component of a PtdIns(4)P- and ARF-regulated machinery controlling post-Golgi carrier generation. Subcellular localization (fluorescence microscopy), siRNA knockdown, overexpression with cargo transport assays, co-immunoprecipitation Nature cell biology High 15107860
2005 The FAPP1 PH domain detects PI(4)P in distinct cellular compartments including the Golgi and plasma membrane; PI4KIIalpha and PI4KIIIbeta regulate Golgi PI(4)P pools sensed by FAPP1-PH, whereas plasma membrane PI(4)P pool detected by FAPP1-PH is specifically regulated by PI4KIIIalpha. GFP-fusion live-cell imaging, siRNA knockdown of individual PI4 kinases, pharmacological inhibition (wortmannin, PAO) Molecular biology of the cell Medium 15635101
2010 The FAPP1 PH domain contains a prominent hydrophobic wedge that independently tubulates Golgi membranes by penetrating into the lipid leaflet; the mechanism involves electrostatic approach, phosphoinositide sampling, and perpendicular bilayer penetration. Solution NMR structure of micelle-bound FAPP1-PH domain, mutagenesis of hydrophobic wedge residues, membrane tubulation assay EMBO reports High 20300118
2011 Crystal structure of the FAPP1 PH domain at 1.9 Å resolution reveals a seven-stranded β-barrel with a lipid-binding pocket; PtdIns(4)P binding is enhanced in acidic environment and required for membrane penetration and tubulation; ARF1 binds to the outer side of the β-barrel at a site distinct from the lipid-binding pocket, allowing simultaneous and independent binding of both ligands. X-ray crystallography (1.9 Å), NMR resonance perturbation analysis, site-directed mutagenesis, binding affinity measurements, membrane tubulation assay The Journal of biological chemistry High 21454700
2011 Metabolically stabilized analogs of PtdIns(4)P (methylenephosphonate and phosphorothioate derivatives) are recognized by the FAPP1 PH domain and stimulate membrane insertion and tubulation activity of the PH domain, demonstrating that the head group recognition drives membrane remodeling. Chemical synthesis of PtdIns(4)P analogs, binding assays, membrane tubulation assay Chemistry & biology Medium 22035800
2014 At a model membrane surface, yeast Arf1 (yArf1) interacts with the FAPP1-PH domain primarily through contacts between switch I residues of Arf1 and the C-terminal extension of the PH domain; the Arf1 binding site is distinct from the PI4P binding site, supporting coincidence detection of activated ARF and PI4P as the membrane recruitment mechanism. NMR chemical shift perturbation analysis at model membrane surface, structural modeling Structure Medium 24462251
2015 The FAPP1-PH domain preferentially targets PI4P-containing liquid disordered membranes over liquid ordered membranes; membrane penetration is mediated by an exposed conserved hydrophobic wedge adjacent to the PI4P recognition site, providing selectivity for dynamic TGN membrane zones. Liposome sedimentation assays, membrane partitioning assays, NMR spectroscopy with PI4P-containing bicelles Journal of molecular biology Medium 25579996
2019 FAPP1 localizes at ER-TGN contact sites (ERTGoCS), physically interacts with the ER phosphatase Sac1, and promotes Sac1's in-trans dephosphorylation of PI4P at the TGN in vitro; depletion of FAPP1 increases TGN PI4P levels and increases secretion of selected cargoes (e.g., ApoB100), establishing FAPP1 as a PI4P detector/adaptor that positions Sac1 to consume TGN PI4P and thereby acts as a gatekeeper of Golgi exit. Co-immunoprecipitation (FAPP1–Sac1 interaction), in vitro phosphatase assay (Sac1 activity with/without FAPP1), FAPP1 depletion (siRNA) with PI4P level measurement and cargo secretion assay, super-resolution microscopy for ERTGoCS localization The Journal of cell biology High 30659099
2005 FAPP1 depletion (siRNA) had no effect on apical or basolateral transport in polarized MDCK cells, in contrast to FAPP2 depletion which specifically reduced apical transport. RNA interference, adenovirus-mediated siRNA, transport assays in polarized MDCK cells The Journal of cell biology Medium 16103222
2005 A protein named FASP1 (FAPP1-associated protein-1) was identified as a binding partner of pp5644; FASP1 is described as being associated with FAPP1, and co-localizes with pp5644 in the cytoplasm of HeLa cells. Yeast two-hybrid, GST pull-down, co-immunoprecipitation, co-localization by fluorescence microscopy Molecular and cellular biochemistry Low 15881666

Source papers

Stage 0 corpus · 29 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2000 Identification of pleckstrin-homology-domain-containing proteins with novel phosphoinositide-binding specificities. The Biochemical journal 480 11001876
2004 FAPPs control Golgi-to-cell-surface membrane traffic by binding to ARF and PtdIns(4)P. Nature cell biology 451 15107860
2006 Legionella pneumophila exploits PI(4)P to anchor secreted effector proteins to the replicative vacuole. PLoS pathogens 245 16710455
2005 A plasma membrane pool of phosphatidylinositol 4-phosphate is generated by phosphatidylinositol 4-kinase type-III alpha: studies with the PH domains of the oxysterol binding protein and FAPP1. Molecular biology of the cell 220 15635101
2008 Imaging phosphatidylinositol 4-phosphate dynamics in living plant cells. The Plant journal : for cell and molecular biology 142 18785997
2005 FAPP2 is involved in the transport of apical cargo in polarized MDCK cells. The Journal of cell biology 83 16103222
2019 The activity of Sac1 across ER-TGN contact sites requires the four-phosphate-adaptor-protein-1. The Journal of cell biology 70 30659099
2011 Molecular basis of phosphatidylinositol 4-phosphate and ARF1 GTPase recognition by the FAPP1 pleckstrin homology (PH) domain. The Journal of biological chemistry 67 21454700
2010 Structural basis of wedging the Golgi membrane by FAPP pleckstrin homology domains. EMBO reports 65 20300118
2014 Discovery of novel membrane binding structures and functions. Biochemistry and cell biology = Biochimie et biologie cellulaire 45 25394204
2005 High-affinity interaction of the N-terminal myristoylation motif of the neuronal calcium sensor protein hippocalcin with phosphatidylinositol 4,5-bisphosphate. The Biochemical journal 35 16053445
2014 Interaction of Fapp1 with Arf1 and PI4P at a membrane surface: an example of coincidence detection. Structure (London, England : 1993) 33 24462251
2015 Structural basis of dynamic membrane recognition by trans-Golgi network specific FAPP proteins. Journal of molecular biology 30 25579996
2014 Copy number variants in short children born small for gestational age. Hormone research in paediatrics 29 25300501
2010 Requirement for Golgi-localized PI(4)P in fusion of COPII vesicles with Golgi compartments. Molecular biology of the cell 23 21119004
2013 Membranes and mammalian glycolipid transferring proteins. Chemistry and physics of lipids 20 24220498
2006 Neuronal calcium sensor-1 and phosphatidylinositol 4-kinase beta stimulate extracellular signal-regulated kinase 1/2 signaling by accelerating recycling through the endocytic recycling compartment. Molecular biology of the cell 19 16837555
2019 Endocytic Markers Associated with the Internalization and Processing of Aspergillus fumigatus Conidia by BEAS-2B Cells. mSphere 18 30728282
2018 Regulation of glucosylceramide synthesis by Golgi-localized phosphoinositide. Biochemical and biophysical research communications 11 29627573
2019 Tethering of Multi-Vesicular Bodies and the Tonoplast to the Plasma Membrane in Plants. Frontiers in plant science 10 31396242
2019 Novel GFP-fused protein probes for detecting phosphatidylinositol-4-phosphate in the plasma membrane. Animal cells and systems 7 31231579
2023 Genome-wide association study identifies variants associated with semen volume in white-feathered broilers. Animal genetics 6 37705287
2022 Origin and Evolution of the Multifaceted Adherens Junction Component Plekha7. Frontiers in cell and developmental biology 6 35399503
2011 Metabolically stabilized derivatives of phosphatidylinositol 4-phosphate: synthesis and applications. Chemistry & biology 6 22035800
2005 P5644 interacts with phosphatidylinositol-4-phosphate adaptor protein-1 associated protein-1. Molecular and cellular biochemistry 6 15881666
2016 NMR of Membrane Proteins: Beyond Crystals. Advances in experimental medicine and biology 4 27553233
2025 Ursodeoxycholic acid alleviates multiple sclerosis via TGR5-dependent microglial regulation in mice. European journal of pharmacology 2 40653076
2025 Genetic insights into cardiac conduction disorders from genome-wide association studies. Human genomics 1 40022259
2011 Secondary structure and 1H, 13C, 15N resonance assignments of the Golgi-specific PH domain of FAPP1. Biomolecular NMR assignments 0 21298564

Missed literature

Know a paper Affinage missed for PLEKHA3? Flag it for the maintainers and the community.

No submissions yet.