Affinage

PIP5K1A

Phosphatidylinositol 4-phosphate 5-kinase type-1 alpha · UniProt Q99755

Length
562 aa
Mass
62.6 kDa
Annotated
2026-06-10
22 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PIP5K1A is a type I phosphatidylinositol 4-phosphate 5-kinase that generates plasma-membrane PI(4,5)P2 pools to coordinate growth-factor signaling, cytoskeletal dynamics, and receptor trafficking (PMID:28842595, PMID:33079727). Its catalytic domain forms a side-to-side dimer, and binding at adjacent dimerization/partner interfaces—including the DIX domain of Dishevelled—stimulates catalytic activity, with DIX engagement additionally enhancing substrate binding (PMID:26365782). Membrane recruitment and activation are controlled by multiple partners: PIP5K1A is recruited to c-Met in an Arf6-dependent manner upon HGF stimulation to drive PIP2/PIP3 production, Akt activation, and hepatocyte proliferation (PMID:28842595); CLIC1 relocates it to the leading edge to build PIP2-rich microdomains supporting integrin-mediated adhesion and migration (PMID:33079727); and DCLK1 suppresses its inhibitory threonine phosphorylation to promote membrane localization and PI3K-AKT activation under high matrix stiffness (PMID:41692802). These functions place PIP5K1A within KRAS-driven oncogenic signaling, where it is a KRAS-specific interactor whose depletion reduces oncogenic KRAS signaling and proliferation (PMID:30194290), and upstream of an Akt/GSK-3β–CDK2/cyclin D1 axis controlling cell-cycle progression (PMID:38838507). The kinase also produces dedicated PI(4,5)P2 with the scaffold EFR3A to enable AP2-dependent GPCR re-sensitization [PMID:bio_10.1101_2025.03.28.645988] and organizes membrane clusters that recruit RhoA during cytokinesis (PMID:42212321). Independent of its catalytic activity, PIP5K1A performs scaffolding roles: it competitively binds the KEAP1 Kelch domain to stabilize NRF2 and suppress ferroptosis (PMID:40405713), and binds nuclear XPO5 to restrict pre-let-7 miRNA export (PMID:37655623).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2015 High

    Established the structural basis for how PIP5K1A catalytic activity is switched on, showing dimerization and partner binding at defined interfaces stimulate the kinase.

    Evidence X-ray crystallography of zebrafish catalytic domain with site-directed mutagenesis and in vitro kinase assays

    PMID:26365782

    Open questions at the time
    • Structure is of the isolated catalytic domain, not the full-length human enzyme on a membrane
    • How DIX binding mechanistically enhances substrate binding is not resolved at atomic detail
  2. 2017 High

    Defined a receptor-coupled activation route, showing Arf6-dependent recruitment to c-Met links PIP5K1A lipid production to Akt activation and proliferation in vivo.

    Evidence siRNA knockdown in HepG2, recruitment co-IP, lipid measurement, and Pip5k1a knockout mouse hepatectomy model

    PMID:28842595

    Open questions at the time
    • Direct binding interface between PIP5K1A and c-Met/Arf6 not mapped
    • Whether PIP3 is produced directly or via downstream PI3K is not fully delineated
  3. 2018 High

    Identified PIP5K1A as a selective effector of oncogenic KRAS, establishing it as a vulnerability in KRAS-driven cancers.

    Evidence BioID interactome, CRISPR loss-of-function screen, co-IP binding mapping, proliferation assays in pancreatic cancer lines

    PMID:30194290

    Open questions at the time
    • Structural basis of KRAS-specific (vs NRAS/HRAS) binding not resolved
    • Whether the effect requires PIP5K1A catalytic activity not directly tested
  4. 2019 Low

    Probed the membrane-engagement mechanism, predicting monomeric PIP5K1A binds PI4P membranes via a reorientation step while dimers cannot engage both active sites simultaneously.

    Evidence Coarse-grained and atomistic molecular dynamics simulations

    PMID:31204251

    Open questions at the time
    • Computational only — predicted binding modes lack experimental validation
    • Proposed conformational change or bilayer distortion for dimer binding untested
    • No link to in-cell membrane behavior
  5. 2021 High

    Showed how PIP5K1A is spatially targeted during migration, with CLIC1 delivering it to the leading edge to build adhesion-promoting PIP2 microdomains.

    Evidence Comparative proteomics, co-IP, fractionation/live imaging, siRNA with adhesion and mouse lung metastasis readouts

    PMID:33079727

    Open questions at the time
    • Mechanism by which CLIC1 selects PIP5K1A/PIP5K1C is not detailed
    • How PIP2 microdomains organize integrin clustering at molecular level unresolved
  6. 2023 Medium

    Revealed a kinase-independent nuclear function, showing PIP5K1A blocks XPO5–pre-let-7 binding to restrict miRNA export.

    Evidence Co-IP, kinase-dead mutant analysis, C. elegans lin-28/let-7 epistasis, quantitative miRNA measurement

    PMID:37655623

    Open questions at the time
    • Single lab; nuclear localization mechanism of PIP5K1A not established
    • Whether interaction with XPO5 is direct vs complex-mediated unconfirmed
    • Generality across miRNAs beyond let-7 untested
  7. 2024 Medium

    Placed PIP5K1A upstream of an Akt/GSK-3β–CDK2/cyclin D1 cell-cycle axis and identified rupatadine as a kinase inhibitor.

    Evidence Kinase activity assay, bio-layer interferometry, western blot, proliferation assays, xenograft

    PMID:38838507

    Open questions at the time
    • Single lab; direct kinase substrates linking to GSK-3β not defined
    • Specificity of rupatadine for PIP5K1A vs other PIP kinases not fully characterized
  8. 2025 Medium

    Demonstrated a second kinase-independent scaffolding role, with PIP5K1A competing for the KEAP1 Kelch domain to stabilize NRF2 and suppress ferroptosis.

    Evidence Co-IP, ubiquitination assays, kinase-dead mutant, siRNA with lipid peroxidation readouts, ISA-2011B inhibition

    PMID:40405713

    Open questions at the time
    • Single lab; binding stoichiometry/affinity with KEAP1 not quantified
    • Whether this competes with endogenous KEAP1 substrates beyond NRF2 unknown
  9. 2025 Medium

    Linked a dedicated PIP5K1A PI(4,5)P2 pool to GPCR re-sensitization, acting with EFR3A to sort AT1R into an AP2 compartment.

    Evidence Genetic perturbation of PIP5K1A/EFR3A, PI(4,5)P2 reporters, re-sensitization assays, AP2 co-localization imaging (preprint)

    PMID:bio_10.1101_2025.03.28.645988

    Open questions at the time
    • Preprint, not yet peer-reviewed
    • Direct PIP5K1A–EFR3A interaction interface not mapped
    • Generality across other GPCRs untested
  10. 2026 Medium

    Dissected structural determinants linking PIP5K1A membrane anchoring to RhoA recruitment and cytokinesis.

    Evidence Structure-function mutagenesis (Q169, PIPB motif, activation loop), live imaging, maternal depletion/overexpression in porcine embryos, RhoA co-localization

    PMID:42212321

    Open questions at the time
    • Single lab in porcine embryo system; human relevance not directly shown
    • Mechanism by which PIP2 clusters recruit RhoA not fully resolved
  11. 2026 Medium

    Identified a phosphoregulatory partner, showing DCLK1 inhibits PIP5K1A threonine phosphorylation to promote its membrane localization and PI3K-AKT signaling under stiff matrix.

    Evidence Co-IP, phosphorylation analysis, subcellular fractionation, in vitro/in vivo pancreatic tumor models with DCLK1 perturbation

    PMID:41692802

    Open questions at the time
    • Single lab; the kinase/phosphatase acting on the threonine site not identified
    • Whether DCLK1 acts directly or recruits a phosphatase unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the catalytic and scaffolding (KEAP1-, XPO5-binding) activities of PIP5K1A are partitioned across subcellular compartments and integrated with its many activating partners remains unresolved.
  • No unifying model for how partner choice (DIX, KRAS, Arf6, CLIC1, DCLK1) dictates output
  • Full-length human enzyme structure on membrane lacking
  • Mechanism of nuclear targeting for kinase-independent roles unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 3 GO:0008289 lipid binding 2 GO:0060089 molecular transducer activity 2
Localization
GO:0005886 plasma membrane 4 GO:0005634 nucleus 1 GO:0005829 cytosol 1
Pathway
R-HSA-162582 Signal Transduction 3 R-HSA-1643685 Disease 3 R-HSA-5653656 Vesicle-mediated transport 1 R-HSA-8953854 Metabolism of RNA 1

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2015 Crystal structure of the catalytic domain of zebrafish PIP5K1A resolved at 3.3 Å reveals a side-to-side dimer. Mutagenesis identified two adjacent interfaces for dimerization and interaction with the DIX domain of Dishevelled. Binding at these interfaces (either through dimerization or DIX interaction) stimulates PIP5K1A catalytic activity; DIX binding additionally enhances substrate binding. X-ray crystallography, site-directed mutagenesis, in vitro kinase activity assays Nature communications High 26365782
2018 PIP5K1A is a KRAS-specific interactor (not shared with NRAS or HRAS), binding to a unique region in KRAS. PIP5K1A depletion specifically reduces oncogenic KRAS signaling and proliferation, and sensitizes pancreatic cancer cell lines to MAPK inhibitors. BirA proximity-dependent biotin identification (BioID) interactome, CRISPR-Cas9 loss-of-function screen, co-immunoprecipitation mapping of binding region, cell proliferation assays Nature communications High 30194290
2017 Upon HGF stimulation, PIP5K1A is recruited to c-Met in an Arf6 activity-dependent manner, where it generates PIP2 and subsequently PIP3 to activate Akt and drive hepatocyte proliferation. In vivo, Pip5k1a knockout mice show suppressed hepatocyte proliferation and liver regeneration after partial hepatectomy. siRNA knockdown in HepG2 cells, co-immunoprecipitation/recruitment assay to c-Met, PI3P/PIP2/PIP3 measurement, Pip5k1a knockout mouse hepatectomy model Scientific reports High 28842595
2021 CLIC1 recruits PIP5K1A and PIP5K1C from the cytoplasm to the leading edge of the plasma membrane in response to migration stimuli, where PIP5K1A generates a PIP2-rich microdomain that induces integrin-mediated cell-matrix adhesion formation and cytoskeletal extension signaling. Comparative proteomics, co-immunoprecipitation, subcellular fractionation/live imaging of protein recruitment, siRNA knockdown with adhesion and metastasis readouts, mouse lung metastasis model The Journal of clinical investigation High 33079727
2019 Multiscale molecular dynamics simulations show that monomeric PIP5K1A binds specifically to PI4P-containing membranes (not zwitterionic or anionic membranes lacking PIPs), with initial encounter followed by reorientation to a productive binding pose; dimeric PIP5K1A cannot bind via both active sites simultaneously, suggesting conformational change or bilayer distortion is needed. Coarse-grained and atomistic molecular dynamics simulations Structure Low 31204251
2023 PIP5K1A interacts with nuclear export protein XPO5 in the nucleus to regulate mature let-7 miRNA levels by blocking XPO5 binding to pre-let-7, thereby reducing nuclear export of pre-miRNA; this role is kinase-independent. The ortholog PPK-1 in C. elegans functions in the lin-28/let-7 heterochronic pathway. Co-immunoprecipitation (PIP5K1A–XPO5 interaction), kinase-dead mutant analysis, C. elegans genetic pathway analysis, quantitative miRNA level measurement in human cells Nucleic acids research Medium 37655623
2025 PIP5K1A competitively binds the Kelch domain of KEAP1 in a kinase-independent manner, preventing NRF2 ubiquitination and degradation, thereby promoting NRF2-dependent transcription and suppressing ferroptosis in hepatocellular carcinoma cells. Co-immunoprecipitation (PIP5K1A–KEAP1 interaction), ubiquitination assays, kinase-dead mutant analysis, siRNA knockdown with lipid peroxidation and ferroptosis readouts, pharmacological inhibition (ISA-2011B) Advanced science Medium 40405713
2024 PIP5K1A functions upstream of the Akt/GSK-3β pathway to regulate CDK2 and cyclin D1 expression and cell cycle progression in colorectal cancer; rupatadine inhibits PIP5K1A kinase activity (confirmed by kinase activity assay and bio-layer interferometry) and suppresses CRC proliferation in vitro and in vivo. Kinase activity assay, bio-layer interferometry, western blot, cell proliferation assays, in vivo xenograft Biomedicine & pharmacotherapy Medium 38838507
2026 DCLK1 interacts with PIP5K1A and inhibits its threonine phosphorylation, thereby facilitating PIP5K1A membrane localization and downstream PI3K-AKT signaling activation in pancreatic cancer under high matrix stiffness conditions. Co-immunoprecipitation, phosphorylation analysis, subcellular fractionation of PIP5K1A localization, in vitro and in vivo tumor models with DCLK1 knockdown/overexpression Experimental hematology & oncology Medium 41692802
2026 In porcine embryos, PIP5K1A residue Q169 mediates interaction with RhoA; the PIPB motif anchors PIP5K1A to the plasma membrane; the activation loop drives catalytic activity and is required for proper RhoA membrane localization. PIP5K1A-enriched membrane clusters serve as hubs for RhoA recruitment during cytokinesis. PIP5K1A also sustains PLC-IP3-Ca2+ signaling for vesicle fusion and cytoskeletal remodeling. Structure-function mutagenesis (Q169, PIPB motif, activation loop), live imaging of membrane localization, maternal depletion and overexpression in porcine embryos, co-localization with RhoA International journal of biological sciences Medium 42212321
2025 PIP5K1A (referred to as PIP5KA in the paper) produces a dedicated PI(4,5)P2 pool at the plasma membrane in collaboration with the scaffolding protein EFR3A, which is required for sorting AT1R angiotensin II receptors into an AP2-positive compartment for rapid GPCR re-sensitization without receptor internalization. Genetic perturbation of PIP5K1A and EFR3A, PI(4,5)P2 reporter assays, GPCR re-sensitization assays, AP2 co-localization imaging bioRxiv (preprint)preprint Medium bio_10.1101_2025.03.28.645988

Source papers

Stage 0 corpus · 22 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2018 Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability. Nature communications 73 30194290
2019 Circular RNA PIP5K1A promotes colon cancer development through inhibiting miR-1273a. World journal of gastroenterology 71 31558874
2021 CLIC1 recruits PIP5K1A/C to induce cell-matrix adhesions for tumor metastasis. The Journal of clinical investigation 59 33079727
2021 CircRNA PIP5K1A promotes the progression of glioma through upregulation of the TCF12/PI3K/AKT pathway by sponging miR-515-5p. Cancer cell international 48 33413401
2021 Exosomal circ_PIP5K1A regulates the progression of non-small cell lung cancer and cisplatin sensitivity by miR-101/ABCC1 axis. Molecular and cellular biochemistry 47 33570734
2015 Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled. Nature communications 46 26365782
2014 Amplification of Chromosome 1q Genes Encoding the Phosphoinositide Signalling Enzymes PI4KB, AKT3, PIP5K1A and PI3KC2B in Breast Cancer. Journal of Cancer 32 25368680
2021 Circ_PIP5K1A regulates cisplatin resistance and malignant progression in non-small cell lung cancer cells and xenograft murine model via depending on miR-493-5p/ROCK1 axis. Respiratory research 27 34537072
2019 Membrane Recognition and Binding by the Phosphatidylinositol Phosphate Kinase PIP5K1A: A Multiscale Simulation Study. Structure (London, England : 1993) 18 31204251
2017 Regulation of HGF-induced hepatocyte proliferation by the small GTPase Arf6 through the PIP2-producing enzyme PIP5K1A. Scientific reports 18 28842595
2022 Knockdown of circ-PIP5K1A overcomes resistance to cisplatin in ovarian cancer by miR-942-5p/NFIB axis. Anti-cancer drugs 17 36730637
2022 Circular RNA PIP5K1A act as microRNA-552-3p sponge to regulates inflammation, oxidative damage in glucolipotoxicity-induced pancreatic INS-1 β-cells via Janus kinase 1. Bioengineered 15 35184688
2022 The role of PIP5K1A in cancer development and progression. Medical oncology (Northwood, London, England) 13 35852640
2023 Circular RNA PIP5K1A Promotes Glucose and Lipid Metabolism Disorders and Inflammation in Type 2 Diabetes Mellitus. Molecular biotechnology 11 37966664
2021 Circular RNA PIP5K1A (circPIP5K1A) accelerates endometriosis progression by regulating the miR-153-3p/Thymosin Beta-4 X-Linked (TMSB4X) pathway. Bioengineered 9 34546850
2025 PIP5K1A Suppresses Ferroptosis and Induces Sorafenib Resistance by Stabilizing NRF2 in Hepatocellular Carcinoma. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 8 40405713
2024 Rupatadine inhibits colorectal cancer cell proliferation through the PIP5K1A/Akt/CDK2 pathway. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 5 38838507
2025 Extrachromosomal DNA (ecDNA) drives hepatocellular carcinoma malignancy through high-copy amplification of chromosome 1q21-derived PIP5K1A oncogene. Cancer letters 3 40865673
2023 Lipid kinase PIP5K1A regulates let-7 microRNA biogenesis through interacting with nuclear export protein XPO5. Nucleic acids research 3 37655623
2026 Matrix stiffness induces Ca2+-DCLK1-PIP5K1A mechanotransduction as a context-specific amplifier in pancreatic cancer progression and chemotherapy resistance. Experimental hematology & oncology 0 41692802
2026 PIP5K1A-PIP2-RhoA Signaling Orchestrates Membrane Remodeling during Early Porcine Embryo Development. International journal of biological sciences 0 42212321
2025 Functional analysis of the PIP5K1A gene in Liaoning Cashmere goats: an investigation based on bioinformatics, tissue localization, and biological functions. Cellular and molecular biology (Noisy-le-Grand, France) 0 39799498

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