Affinage

CNNM3

Metal transporter CNNM3 · UniProt Q8NE01

Length
707 aa
Mass
76.1 kDa
Annotated
2026-06-09
26 papers in source corpus 13 papers cited in narrative 13 extracted findings
Cross-family judge faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CNNM3 is a CBS-pair/CNBH domain magnesium-transport regulator that couples cellular Mg2+ homeostasis to oncogenic signaling and divalent cation entry (PMID:24632616, PMID:34928937). Its defining interaction is a direct, high-affinity heterodimer with PRL phosphatases (PRL-2, PRL-3) formed through a loop unique to the CNNM3 CBS-pair domain, in which residue D426 is essential — the D426A mutant fails to bind PRL-2, loses its effect on membrane current, and abrogates cancer cell proliferation and xenograft tumor growth, establishing the PRL·CNNM3 complex as pro-oncogenic (PMID:24632616, PMID:26969161, PMID:32733084). The crystal structure of the PRL2–CNNM3 CBS complex shows that PRL binds via its catalytic-site cysteine, and endogenous phosphocysteine formation during the phosphatase catalytic cycle blocks this interaction, providing a regulatory switch over Mg2+ efflux (PMID:27856537, PMID:37220097). CNNM3 selectively binds the TRPM7 channel to stimulate divalent cation entry, and this CNNM3–TRPM7 axis is reciprocally tuned: the GTP-binding protein ARL15 binds the CBS domain, promotes CNNM3 complex N-glycosylation, drives CNNM3–TRPM7 complex formation, and suppresses TRPM7, while PRL-1/2 counteract ARL15 to relieve TRPM7 inhibition in a Mg2+-dependent manner, with co-targeting of TRPM7 and PRL altering mitochondrial function (PMID:34928937, PMID:34089346, PMID:36972446). Structurally, the CNNM3 CNBH domain mediates constitutive homodimerization rather than cyclic-nucleotide binding, and CNNM3 exists exclusively as a dimer, correlating with its lack of intrinsic Mg2+ efflux activity relative to active family members such as CNNM4 (PMID:30341174). Functional ortholog studies place CNNM-mediated Mg2+ efflux upstream of AMPK-TORC1 signaling in gonadogenesis (PMID:27564576).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2014 High

    Established that CNNM3 is not a phosphatase substrate but a binding partner of PRL-2, defining a heterodimer that controls cellular magnesium and drives transformation.

    Evidence Co-IP, PRL-2 knockdown with Mg2+ influx measurement, xenograft assays with a CNNM3 binding mutant, and PRL-2 KO mouse serum Mg2+

    PMID:24632616

    Open questions at the time
    • Did not define the atomic interaction interface
    • Direction of Mg2+ flux (influx vs efflux) regulated by CNNM3 not yet resolved
  2. 2014 Medium

    Demonstrated by heterologous expression that Cnnm3 itself mediates Mg2+ efflux and localizes to the lateral membrane of transport epithelia, framing it as an ion transporter.

    Evidence In situ hybridization, immunohistochemistry, and Xenopus oocyte expression with Mg2+ content/free Mg2+ measurements (fish ortholog)

    PMID:24965791

    Open questions at the time
    • Efflux activity shown for fish ortholog, not directly human CNNM3
    • Transport mechanism and selectivity not defined
  3. 2016 High

    Resolved the structural basis of the PRL–CNNM3 interaction and identified phosphocysteine formation as the regulatory switch that gates complex formation and Mg2+ efflux.

    Evidence X-ray crystallography of the PRL2–CNNM3 CBS complex, phosphocysteine detection, mutagenesis, and cellular Mg2+ efflux assay

    PMID:27856537

    Open questions at the time
    • Physiological trigger of phosphocysteine cycling in vivo not established
    • Stoichiometry of the assembled complex on the membrane unclear
  4. 2016 High

    Pinpointed CNNM3 residue D426 as the critical determinant of PRL-2 binding and showed binding is required for CNNM3-dependent membrane current and tumor growth.

    Evidence Site-directed mutagenesis, co-IP, whole-cell voltage clamping, proliferation/anchorage-independent growth, and orthotopic xenograft breast cancer model

    PMID:26969161

    Open questions at the time
    • Molecular identity of the CNNM3-influenced surface current not defined
    • Whether D426A affects intrinsic transport vs partner recruitment not separated
  5. 2016 Medium

    Placed CNNM-mediated Mg2+ efflux upstream of AMPK-TORC1 signaling in a developmental (gonadogenesis) context via genetic epistasis.

    Evidence C. elegans double/triple mutant epistasis (cnnm-1; cnnm-3; aak-2), genome-wide RNAi, and Mg2+ supplementation rescue

    PMID:27564576

    Open questions at the time
    • Conservation of the CNNM–AMPK–TORC1 axis in mammals not demonstrated
    • Redundancy between cnnm-1 and cnnm-3 leaves CNNM3-specific role unclear
  6. 2018 High

    Showed the CNNM3 CNBH domain mediates dimerization rather than cyclic-nucleotide binding, linking CNNM3's exclusive dimeric state to its lack of intrinsic Mg2+ efflux activity.

    Evidence X-ray crystallography of CNNM3 CNBH domain, analytical ultracentrifugation, mutagenesis, and Mg2+ efflux assay

    PMID:30341174

    Open questions at the time
    • Mechanistic explanation for why dimer-locking abolishes efflux not established
    • Whether dimerization state is dynamically regulated in cells unknown
  7. 2020 Medium

    Confirmed by reconstitution that CNNM3 CBS domain binds PRL2 directly with measurable affinity and that loop-derived peptides can block the interaction, validating it as a druggable interface.

    Evidence FRET-based binding assay with purified recombinant proteins and competitive peptide inhibition

    PMID:32733084

    Open questions at the time
    • Single-lab in vitro affinity not yet linked to cellular potency of peptides
    • Effect of phosphocysteine state on measured Kd not tested here
  8. 2021 High

    Identified CNNM3 as a selective binding partner and positive cofactor of the TRPM7 channel, redefining part of its function as channel regulation rather than autonomous transport.

    Evidence Co-IP, CNNM3/4 knockout in HEK-293, 25Mg2+/divalent uptake, NS8593 inhibition, whole-cell electrophysiology, and surface biotinylation

    PMID:34928937

    Open questions at the time
    • Molecular mechanism by which CNNM3 stimulates TRPM7 conductance not defined
    • Relationship between TRPM7-dependent entry and CNNM3 intrinsic efflux unresolved
  9. 2021 Medium

    Identified ARL15 as a CBS-domain partner that promotes CNNM3 N-glycosylation and acts as a negative regulator of CNNM-mediated Mg2+ transport.

    Evidence Co-IP, co-localization, 25Mg2+ uptake with ARL15 overexpression/knockdown, and in silico modeling in kidney cancer cells

    PMID:34089346

    Open questions at the time
    • GTPase-dependence of ARL15 regulation not established
    • Whether glycosylation directly causes transport suppression not proven
  10. 2023 Medium

    Integrated ARL15 and PRL into a reciprocal regulatory circuit over CNNM3–TRPM7, linking Mg2+ status to channel activity and mitochondrial/metabolic stress sensitivity.

    Evidence Genetically encoded intracellular Mg2+ reporter, co-IP, CNNM3 and PRL-1/2 perturbation, and mitochondrial function assays

    PMID:36972446

    Open questions at the time
    • Quantitative thresholds of Mg2+ that switch the circuit not defined
    • Single-lab study; in vivo relevance of the metabolic-stress phenotype untested
  11. 2023 Medium

    Mapped the PRL-3 active site as directly involved in CNNM3 CBS binding using nanobody competition, reinforcing that catalytic-site engagement underlies the interaction.

    Evidence HDX-MS interface mapping and co-IP with nanobody competition

    PMID:37220097

    Open questions at the time
    • Functional consequence of nanobody-mediated disruption on Mg2+ transport not shown
    • Selectivity of nanobodies across PRL isoforms not characterized

Open questions

Synthesis pass · forward-looking unresolved questions
  • How CNNM3's distinct activities — TRPM7-dependent divalent entry, the lack of intrinsic efflux tied to constitutive dimerization, and PRL/ARL15 regulation — are integrated to set net cellular Mg2+ and drive oncogenic outcomes in vivo remains unresolved.
  • No structural model of the full-length CNNM3–TRPM7 or CNNM3–ARL15 complex
  • Mechanism converting Mg2+ status into AMPK/mitochondrial signaling in mammalian cells undefined
  • Subcellular localization of human CNNM3 inconsistent across reports

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 3 GO:0005215 transporter activity 2 GO:0140313 molecular sequestering activity 2
Localization
GO:0005886 plasma membrane 2
Pathway
R-HSA-162582 Signal Transduction 2 R-HSA-382551 Transport of small molecules 2
Partners
ARL15PRL-2PRL-3PTP4A1TRPM7
Complex memberships
CNNM3 homodimerCNNM3-PRL2 heterodimerCNNM3-TRPM7 complex

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2014 PRL-2 forms a functional heterodimer with CNNM3, interacting through a loop unique to the CBS pair domains of CNNM3. CNNM3 is not a phosphorylated substrate of PRL-2. The PRL-2/CNNM3 interaction regulates intracellular magnesium levels, and PRL-2 knockdown reduces cellular magnesium influx. A CNNM3 mutant that does not associate with PRL-2 loses transforming activity in xenograft tumor assays, confirming that the PRL-2/CNNM3 complex is pro-oncogenic. Co-immunoprecipitation, PRL-2 knockdown with Mg2+ influx measurement, xenograft tumor assays with CNNM3 binding mutant, PRL-2 knockout mouse serum Mg2+ measurements Oncogene High 24632616
2016 The crystal structure of the complex between PRL2 and the CBS-pair domain of CNNM3 reveals the molecular basis for their interaction. PRL catalytic-site cysteine is endogenously phosphorylated (phosphocysteine) during the catalytic cycle; phosphocysteine formation blocks PRL binding to CNNM Mg2+ transporters. Mutations that block the PRL-CNNM interaction prevent regulation of Mg2+ efflux in cultured cells. X-ray crystallography of PRL2-CNNM3 CBS domain complex, phosphocysteine detection, site-directed mutagenesis, cellular Mg2+ efflux assay EMBO reports High 27856537
2016 Residue D426 on the CBS-domain loop of CNNM3 is critical for PRL-2 binding; the D426A point mutation completely disrupts PRL-2·CNNM3 complex formation. Whole-cell voltage clamping showed that wild-type CNNM3 expression influences surface current, whereas the D426A binding mutant does not, indicating PRL-2 binding is required for CNNM3 activity. The D426A mutant decreases cancer cell proliferation under Mg2+-deprived conditions and reduces tumor growth in orthotopic xenograft models. Site-directed mutagenesis, co-immunoprecipitation, whole-cell voltage clamping (patch clamp), proliferation assays, anchorage-independent growth, orthotopic xenograft breast cancer model The Journal of biological chemistry High 26969161
2018 The crystal structures of the CNBH domains of CNNM2 and CNNM3 (at 2.6 and 1.9 Å resolution) reveal that these domains mediate dimerization rather than binding cyclic nucleotides. CNNM3's CNBH domain exists exclusively as a dimer and CNNM3 lacks Mg2+ efflux activity, whereas active family members (e.g., CNNM4) show both monomer and dimer forms. Mutational analysis confirmed that the CNBH domain is required for Mg2+ efflux activity of CNNM4. X-ray crystallography (CNNM3 CNBH at 1.9 Å), analytical ultracentrifugation, site-directed mutagenesis, Mg2+ efflux assay The Journal of biological chemistry High 30341174
2021 CNNM3 (and CNNM4) selectively bind to the TRPM7 channel, and co-expression stimulates divalent cation entry. Knockout of CNNM3 and CNNM4 in HEK-293 cells significantly reduces TRPM7-mediated divalent cation entry without affecting TRPM7 expression or surface levels. Whole-cell electrophysiology confirmed that CNNM3/4 knockout impairs both heterologously expressed and native TRPM7 channel function. PRL overexpression stimulates TRPM7-dependent divalent cation entry in a CNNM-dependent manner. Co-immunoprecipitation, CNNM3/4 knockout (HEK-293), 25Mg2+/divalent cation uptake assays, TRPM7 inhibitor (NS8593), whole-cell electrophysiology, surface biotinylation PLoS biology High 34928937
2021 ARL15, a small GTP-binding protein, interacts with CNNM proteins (including CNNM3) at their CBS domains and promotes complex N-glycosylation of CNNM3. Overexpression of ARL15 promotes complex N-glycosylation of CNNM3, and ARL15 knockdown increases 25Mg2+ uptake in kidney cancer cell lines, establishing ARL15 as a negative regulator of CNNM-mediated Mg2+ transport. Co-immunoprecipitation, immunocytochemistry (co-localization), 25Mg2+ stable isotope uptake assay, ARL15 overexpression/knockdown, in silico modeling Cellular and molecular life sciences : CMLS Medium 34089346
2023 ARL15 increases CNNM3/TRPM7 protein complex formation to reduce TRPM7 activity, whereas PRL-2 overexpression counteracts ARL15 binding to CNNM3 and enhances TRPM7 function. CNNM3 overexpression reduces TRPM7-induced cell signaling. Lowering cellular Mg2+ reduces CNNM3-TRPM7 interaction in a PRL-dependent manner, and PRL-1/2 knockdown restores this complex. TRPM7 and PRL-1/2 co-targeting alters mitochondrial function and sensitizes cells to metabolic stress. Genetically encoded intracellular Mg2+ reporter, co-immunoprecipitation, CNNM3 overexpression/knockdown, PRL-1/2 knockdown, mitochondrial function assays Proceedings of the National Academy of Sciences of the United States of America Medium 36972446
2014 Fish Cnnm3 localizes to the lateral membrane of proximal tubule cells in the marine teleost kidney. Expression of Cnnm3 in Xenopus laevis oocytes significantly decreased whole cellular Mg2+ content and free intracellular Mg2+ activity, indicating Cnnm3 mediates Mg2+ efflux. In situ hybridization, immunohistochemistry, Xenopus oocyte expression with Mg2+ content and free Mg2+ activity measurements American journal of physiology. Regulatory, integrative and comparative physiology Medium 24965791
2003 Human CNNM3 (ACDP3) protein localizes predominantly to the nucleus of permeabilized HeLa cells as determined by immunofluorescence staining. The protein's conserved domain shows structural homology to cyclin molecules. Immunofluorescence staining of permeabilized HeLa cells Gene Low 12657465
2004 Mouse Acdp3 (Cnnm3) protein shows strong amino acid homology to the bacterial CorC protein involved in magnesium and cobalt efflux, and the mouse Acdp1 protein localizes predominantly to the plasma membrane in hippocampal neurons (as determined by immunostaining), suggesting the family functions in ion transport. Sequence homology analysis, immunostaining of hippocampal neurons BMC genomics Low 14723793
2020 FRET-based binding assay using purified proteins confirmed direct binding between the CBS domain of human CNNM3 and human PRL2, with a measurable Kd. Peptides derived from the CNNM3 CBS domain loop region (PRL-binding sequences) inhibited CNNM3-PRL2 interaction in vitro. FRET-based binding assay with purified recombinant proteins, competitive inhibition with unlabeled proteins and synthetic peptides Scientific reports Medium 32733084
2016 In C. elegans, cnnm-1 and cnnm-3 double mutant worms show excessive Mg2+ accumulation and sterility due to gonadogenesis defects. Genetic epistasis identified that AMPK (aak-2) acts downstream: aak-2 mutation suppressed the gonadal elongation defect of cnnm-1; cnnm-3 mutants, placing CNNM-mediated Mg2+ efflux upstream of AMPK-TORC1 signaling in gonadogenesis. C. elegans double mutant analysis, genome-wide RNAi screen, triple mutant epistasis (cnnm-1; cnnm-3; aak-2), Mg2+ supplementation rescue PLoS genetics Medium 27564576
2023 Nanobodies targeting PRL-3 bind partially within its active site (identified by HDX-MS) and reduce PRL-3 interaction with the CBS domain of CNNM3 as shown by co-immunoprecipitation, confirming that the PRL-3 active site is directly involved in CNNM3 CBS domain binding. Hydrogen-deuterium exchange mass spectrometry (HDX-MS), co-immunoprecipitation with nanobody competition PloS one Medium 37220097

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 The protein tyrosine phosphatase PRL-2 interacts with the magnesium transporter CNNM3 to promote oncogenesis. Oncogene 100 24632616
2003 Molecular cloning and characterization of a novel gene family of four ancient conserved domain proteins (ACDP). Gene 91 12657465
2021 Ion Transporters and Osmoregulation in the Kidney of Teleost Fishes as a Function of Salinity. Frontiers in physiology 76 33967835
2016 Phosphocysteine in the PRL-CNNM pathway mediates magnesium homeostasis. EMBO reports 68 27856537
2016 Inhibition of PRL-2·CNNM3 Protein Complex Formation Decreases Breast Cancer Proliferation and Tumor Growth. The Journal of biological chemistry 47 26969161
2004 Molecular cloning and characterization of the mouse Acdp gene family. BMC genomics 45 14723793
2021 CNNM proteins selectively bind to the TRPM7 channel to stimulate divalent cation entry into cells. PLoS biology 35 34928937
2018 The cyclic nucleotide-binding homology domain of the integral membrane protein CNNM mediates dimerization and is required for Mg2+ efflux activity. The Journal of biological chemistry 34 30341174
2019 Overexpression of circular RNA hsa_circ_0001038 promotes cervical cancer cell progression by acting as a ceRNA for miR-337-3p to regulate cyclin-M3 and metastasis-associated in colon cancer 1 expression. Gene 32 31809842
2021 ARL15 modulates magnesium homeostasis through N-glycosylation of CNNMs. Cellular and molecular life sciences : CMLS 25 34089346
2015 Molecular Profiling of a Rare Rosette-Forming Glioneuronal Tumor Arising in the Spinal Cord. PloS one 24 26371886
2023 PRL-1/2 phosphatases control TRPM7 magnesium-dependent function to regulate cellular bioenergetics. Proceedings of the National Academy of Sciences of the United States of America 20 36972446
2018 PDK2 induces cisplatin-resistance in lung adenocarcinoma via transcriptional regulation of CNNM3. Journal of drug targeting 19 30457021
2016 Mg2+ Extrusion from Intestinal Epithelia by CNNM Proteins Is Essential for Gonadogenesis via AMPK-TORC1 Signaling in Caenorhabditis elegans. PLoS genetics 19 27564576
2014 Identification and lateral membrane localization of cyclin M3, likely to be involved in renal Mg2+ handling in seawater fish. American journal of physiology. Regulatory, integrative and comparative physiology 15 24965791
2013 Identification of Target Genes Involved in the Antiproliferative Effect of Enzyme-Modified Ginseng Extract in HepG2 Hepatocarcinoma Cell. Evidence-based complementary and alternative medicine : eCAM 15 24174975
2018 Molecular expression of Mg2+ regulator TRPM7 and CNNM4 in rat odontoblasts. Archives of oral biology 14 30278312
2020 A FRET-based screening method to detect potential inhibitors of the binding of CNNM3 to PRL2. Scientific reports 8 32733084
2024 Construction of a cuproptosis‑related lncRNA signature to predict biochemical recurrence of prostate cancer. Oncology letters 7 39268161
2023 Development and characterization of nanobodies that specifically target the oncogenic Phosphatase of Regenerating Liver-3 (PRL-3) and impact its interaction with a known binding partner, CNNM3. PloS one 6 37220097
2023 Temporal Tracking of Insulin Action on the Cell Surface of Proteins at a Resolution of Ten Seconds. Analytical chemistry 4 37272674
2021 Magnesium transport in the aglomerular kidney of the Gulf toadfish (Opsanus beta). Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology 4 34302186
2025 Lnc-CNNM3-DT as a protective factor in cervical cancer: regulation of LIAS expression and intracellular copper levels. Frontiers in oncology 3 40265013
2025 A distal convoluted tubule-specific isoform of murine SLC41A3 extrudes magnesium. Acta physiologica (Oxford, England) 2 39931759
2024 Intestinal Mg2+ accumulation induced by cnnm mutations decreases the body size by suppressing TORC2 signaling in Caenorhabditis elegans. Developmental biology 2 38373693
2025 The reticulocyte restriction: invasion ligand RBP1a of Plasmodium vivax targets human TfR1, prohibitin-2, and basigin. Frontiers in cellular and infection microbiology 0 41078366

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