{"gene":"NME3","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":1995,"finding":"Constitutive overexpression of DR-nm23 (NME3) in 32Dc13 myeloid precursor cells inhibits granulocyte colony-stimulating factor-induced granulocytic differentiation and induces apoptosis, establishing a functional role in myeloid differentiation arrest.","method":"Stable overexpression in 32Dc13 cells with G-CSF stimulation assay and apoptosis measurement (flow cytometry)","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean gain-of-function with defined cellular phenotype, single lab, two readouts (differentiation inhibition + apoptosis)","pmids":["7638209"],"is_preprint":false},{"year":2000,"finding":"Mutations in the catalytic domain and at serine 61 phosphorylation site of DR-nm23 (NME3) impair neural differentiation induction in neuroblastoma cells; wild-type and mutant DR-nm23 localize predominantly to the mitochondrial fraction; wild-type DR-nm23 binds other NM23 family members via co-immunoprecipitation, but mutations in the catalytic, RGD domains or serine 61 disrupt hetero-multimer formation. The anti-apoptotic effect in neuroblastoma does not require intact catalytic activity or serine 61.","method":"Site-directed mutagenesis, subcellular fractionation, co-immunoprecipitation, overexpression assays in neuroblastoma cell lines","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis combined with co-IP and fractionation, single lab, multiple orthogonal methods","pmids":["11042679"],"is_preprint":false},{"year":1997,"finding":"DR-nm23 (NME3) fused to GFP localizes to the cytoplasm when transfected in SAOS-2 cells; the gene maps to chromosome 16q13, consists of six exons, and its promoter is transactivated ~3-fold by AP-2, which binds two specific sites in the 5'-flanking region as shown by EMSA.","method":"GFP fusion + transfection/fluorescence microscopy for localization; EMSA and CAT reporter assays for promoter analysis","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct localization experiment and promoter binding confirmed by EMSA, single lab","pmids":["9067290"],"is_preprint":false},{"year":2012,"finding":"The mouse Nme3 t-allele carries a P89S mutation that reduces NDP kinase enzymatic activity; reduction of Nme3 dosage by gene targeting enhanced t-haplotype transmission ratio distortion, phenocopying distorter function, while transgenic overexpression of the t-allele reduced transmission, identifying Nme3 as a quantitative trait locus distorter acting through RHO signaling to impair sperm motility.","method":"Gene targeting (knockout), transgenic overexpression, biochemical enzymatic activity assay, genetic epistasis analysis in mice","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — enzymatic activity assay, genetic loss-of-function and gain-of-function with clear phenotype, epistasis analysis in vivo","pmids":["22438820"],"is_preprint":false},{"year":2016,"finding":"NME3 directly interacts with Tip60 histone acetyltransferase to form a complex with ribonucleotide reductase (RNR), and this interaction is required for NME3 recruitment to DNA damage sites; disruption of NME3–Tip60 interaction suppresses DNA repair in serum-deprived (quiescent) cells.","method":"Co-immunoprecipitation, site-specific recruitment assay at DNA damage sites, loss-of-function with interaction-disrupting mutants","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP, functional rescue with mutants, single lab with two orthogonal methods","pmids":["26945015"],"is_preprint":false},{"year":2018,"finding":"NME3 is a mitochondrial outer-membrane protein that interacts with MFN1/2; NME3 depletion causes dysfunction in mitochondrial dynamics (slow rate of fusion/fission); catalytic-dead NME3 restores mitochondrial elongation but only wild-type NME3 sustains ATP production and cell viability under glucose starvation, showing two separate functions—oligomerization-dependent mitochondrial fusion and NDP kinase catalytic activity—are both required for metabolic adaptation.","method":"Patient fibroblast studies, exome sequencing, wild-type/catalytic-dead/oligomerization-attenuated NME3 rescue experiments, mitochondrial dynamics live imaging, ATP measurement, cell viability assay, co-immunoprecipitation with MFN1/2","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (co-IP, live imaging, domain-specific mutants, patient cells), rigorous mechanistic dissection in single study","pmids":["30587587"],"is_preprint":false},{"year":2018,"finding":"NME3 acts as a positive regulator of TLR5-induced NFκB signaling mechanistically downstream of MyD88; knockdown reduces and overexpression enhances NFκB activation in response to flagellin stimulation.","method":"siRNA loss-of-function screen, targeted knockdown, overexpression assays, NFκB bioluminescent reporter, epistasis placement downstream of MyD88","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockdown and overexpression confirmed with reporter assay, pathway placement by epistasis, single lab","pmids":["29523766"],"is_preprint":false},{"year":2018,"finding":"NME3 localizes to the basal body and associates with nephronophthisis proteins NEK8, CEP164, and ANKS6 as well as centrosomal protein NEK6; depletion of nme3 in zebrafish and Xenopus causes ciliopathy phenotypes including renal malformations and left-right asymmetry defects.","method":"Co-immunoprecipitation with NPHP proteins, immunolocalization to basal body, morpholino knockdown in zebrafish and Xenopus with phenotypic analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with multiple proteins, direct localization, in vivo loss-of-function in two vertebrate models, single lab","pmids":["30111592"],"is_preprint":false},{"year":2020,"finding":"NME3 localizes to peroxisomes as well as mitochondria; suppression of NME3 or expression of catalytically-inactive NME3 causes peroxisome elongation, and elevated NME3 promotes peroxisome division; NME3 NDP kinase activity is required for peroxisome division (constriction/scission), likely by generating GTP for DLP1, and impaired peroxisome division reduces ethanolamine plasmalogen levels.","method":"siRNA knockdown, patient fibroblasts (initiation-codon mutation), catalytically-inactive NME3 expression, peroxisome morphology quantification, ATAD1-silencing overexpression model, ether-lipid mass measurement","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function, gain-of-function, and catalytic-dead mutant with defined organelle morphology phenotype, single lab","pmids":["33126676"],"is_preprint":false},{"year":2020,"finding":"NME3 knockdown increases mitochondrial fragmentation, which causes mitochondrial oxidative stress-mediated DNA single-strand breaks in nuclear DNA; re-expression of wild-type NME3 or inhibition of mitochondrial fission rescues SSBs and DNA repair, whereas N-terminal-deleted NME3 (defective in mitochondrial membrane binding) has no rescue effect, demonstrating that NME3 maintains genome stability through its mitochondrial fusion function.","method":"siRNA knockdown, wild-type and N-terminal deleted mutant re-expression, mitochondrial morphology imaging, comet assay for SSBs, ROS measurement, inhibitor of fission (Mdivi-1)","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain-specific mutant rescue, two orthogonal readouts (SSBs + ROS), single lab","pmids":["32708927"],"is_preprint":false},{"year":2023,"finding":"NME3 binds directly to phosphatidic acid (PA) via its N-terminal amphipathic helix and is enriched at the contact interface of closely positioned mitochondria in a PLD6-dependent manner; PA binding and hexamerization are both required for NME3 mitochondrial tethering activity; nutrient starvation enhances NME3 enrichment at mitochondrial contact interfaces, and NME3 tethering promotes selective fusion between PLD6-remodeled mitochondria.","method":"Lipid-binding assay (PA-liposome pulldown), live-cell imaging/super-resolution microscopy of NME3 at contact interfaces, domain mutant analysis (amphipathic helix deletion, hexamerization mutant), PLD6 depletion epistasis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct biochemical lipid binding assay, structural domain mutagenesis, live-cell imaging, genetic epistasis with PLD6, multiple orthogonal methods in single study","pmids":["37584589"],"is_preprint":false},{"year":2024,"finding":"NME3 acts as a gatekeeper for DRP1-dependent mitophagy in hypoxia: hypoxia-induced PA on mitochondria is required for NME3–DRP1 interaction; active site phosphohistidine of NME3 (not NDPK catalytic turnover per se) protects DRP1 from MUL1-mediated ubiquitination and proteasomal degradation, allowing sufficient active DRP1 to execute mitophagy. Knock-in mice disrupting NME3 histidine phosphorylation are vulnerable to ischemia/reperfusion injury and show cerebellar defects.","method":"Knock-in mouse model (active-site histidine mutation), co-immunoprecipitation of NME3 with DRP1, ubiquitination assay, MUL1 overexpression epistasis, ubiquitin-resistant DRP1 mutant rescue, hypoxia-induced mitophagy assay, PA-binding domain mutant analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vivo knock-in model, biochemical reconstitution of ubiquitination protection, multiple domain mutants and epistasis experiments, replicated in cell and mouse systems","pmids":["38480688"],"is_preprint":false},{"year":2024,"finding":"NME3 is recruited to the mitochondrial outer membrane under redox stress (mitochondrial glutathione depletion); in the absence of NME3, mitophagy is impaired, leading to accumulation of dysfunctional mitochondria, increased mitochondrial ROS, mtDNA lesions, and a senescence-associated secretory phenotype.","method":"Genome-wide CRISPR/Cas9 screen with mitochondria-penetrating glutathione-depleting probe (mtCDNB), NME3 knockout validation, mitophagy assay, ROS measurement, mtDNA damage quantification, SASP assessment","journal":"ACS chemical biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide CRISPR screen followed by KO validation with multiple phenotypic readouts, single lab","pmids":["39133631"],"is_preprint":false},{"year":2026,"finding":"NME3 interacts with PLD6/MitoPLD on the outer mitochondrial membrane of depolarized mitochondria to generate phosphatidic acid (PA) from cardiolipin; this NME3-regulated PA signal is essential for repositioning MFN2 near PINK1 for phosphorylation of ubiquitin conjugates on MFN2, enabling p-S65-Ub-dependent PRKN/parkin amplification. NME3 deficiency causes mitochondria-ER tethering that prevents MFN2 access to PINK1, impairing PRKN activation for mitophagy.","method":"Co-immunoprecipitation, proximity ligation assay (FRET/PLA), NME3 KO cells, PLD6 interaction assays, phospho-ubiquitin and PRKN binding measurements, mitochondria-ER tethering quantification, ubiquitin-resistant MFN2 mutants","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple co-IP and PLA experiments, KO cell mechanistic analysis, domain mutants, single lab with several orthogonal methods","pmids":["41640016"],"is_preprint":false},{"year":2026,"finding":"NME3 interacts with NAA10 (N-α-acetyltransferase 10), and this interaction modulates odontogenic differentiation of human dental pulp stem cells; NAA10 knockdown rescues differentiation deficits from NME3 silencing, while NAA10 overexpression attenuates NME3-driven differentiation; NME3 facilitates nuclear translocation of RUNX2, a key transcription factor in odontogenesis.","method":"Mass spectrometry identification of interactor, co-localization, siRNA knockdown of NME3 and NAA10, overexpression, RUNX2 nuclear translocation assay (immunofluorescence), mineralization assay","journal":"FASEB journal","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-localization and genetic epistasis (knockdown rescue) without biochemical reconstitution of interaction; single lab, single study","pmids":["42165278"],"is_preprint":false}],"current_model":"NME3 (DR-nm23/NM23-H3/NDPKC) is an NDP kinase localized to the mitochondrial outer membrane (and peroxisomes) that serves two separable functions: (1) an oligomerization-dependent mitochondrial tethering/fusion role mediated by direct binding of its N-terminal amphipathic helix to phosphatidic acid generated by PLD6, and (2) an NDP kinase catalytic function (requiring active-site histidine phosphorylation) that protects DRP1 from MUL1-mediated ubiquitination to enable hypoxia-induced mitophagy and supports ATP production; NME3 also cooperates with PLD6 to generate PA on depolarized mitochondria, facilitating Mito-ER untethering and PINK1-PRKN/parkin-dependent mitophagy, while additional roles include direct interaction with Tip60–RNR for site-specific dNTP synthesis at DNA damage sites, association with nephronophthisis proteins at the basal body for ciliary function, positive regulation of TLR5-NFκB signaling downstream of MyD88, and NDP kinase-dependent GTP supply for peroxisome division."},"narrative":{"mechanistic_narrative":"NME3 is a nucleoside diphosphate (NDP) kinase that anchors to the mitochondrial outer membrane and executes two genetically separable activities—an oligomerization-dependent membrane-tethering function and a catalytic NDP kinase function—that together govern mitochondrial dynamics, mitophagy, and metabolic adaptation [PMID:30587587]. Mitochondrial targeting and tethering depend on an N-terminal amphipathic helix that binds directly to phosphatidic acid (PA) generated by PLD6 at mitochondrial contact interfaces; PA binding together with hexamerization drives selective fusion of PLD6-remodeled mitochondria, a process enhanced by nutrient starvation [PMID:37584589]. NME3 interacts with the fusion machinery MFN1/2, and while catalytic-dead NME3 can restore mitochondrial elongation, only catalytically active NME3 sustains ATP production and viability under glucose starvation [PMID:30587587]. Through its membrane-binding fusion activity, NME3 also preserves nuclear genome stability, since its loss fragments mitochondria, elevates ROS, and produces nuclear DNA single-strand breaks [PMID:32708927]. In mitophagy, NME3 cooperates with PLD6 to produce PA on depolarized mitochondria that repositions MFN2 near PINK1 to amplify PRKN/parkin activation [PMID:41640016], and hypoxia-induced PA enables an NME3–DRP1 interaction in which the NME3 active-site phosphohistidine protects DRP1 from MUL1-mediated ubiquitination, allowing DRP1-dependent mitophagy; knock-in mice lacking this histidine phosphorylation are vulnerable to ischemia/reperfusion injury [PMID:38480688]. Beyond mitochondria, NME3 localizes to peroxisomes where its NDP kinase activity supports division [PMID:33126676], associates with Tip60–ribonucleotide reductase for recruitment to DNA damage sites in quiescent cells [PMID:26945015], localizes to the basal body with nephronophthisis proteins to support ciliary function [PMID:30111592], and positively regulates TLR5–NFκB signaling downstream of MyD88 [PMID:29523766].","teleology":[{"year":1995,"claim":"Established the first cellular phenotype for NME3 by showing it arrests myeloid differentiation, framing it as a regulator of cell-fate decisions before any molecular mechanism was known.","evidence":"Stable overexpression in 32Dc13 myeloid precursors with G-CSF stimulation and apoptosis readouts","pmids":["7638209"],"confidence":"Medium","gaps":["No molecular activity linked to the differentiation arrest","Overexpression phenotype not tied to endogenous function"]},{"year":1997,"claim":"Mapped the gene and its AP-2-driven promoter and reported a cytoplasmic GFP localization, an early and partial view of where the protein acts.","evidence":"GFP fusion microscopy in SAOS-2 cells, EMSA and CAT reporter promoter analysis","pmids":["9067290"],"confidence":"Medium","gaps":["Cytoplasmic localization later refined to mitochondrial/peroxisomal compartments","GFP fusion may mislocalize the membrane-anchored protein"]},{"year":2000,"claim":"Began separating catalytic from non-catalytic roles by showing catalytic and serine-61 mutants impair differentiation and disrupt NM23 hetero-multimer formation, while the anti-apoptotic effect was catalysis-independent.","evidence":"Site-directed mutagenesis, subcellular fractionation, and co-IP in neuroblastoma cells","pmids":["11042679"],"confidence":"Medium","gaps":["Mechanism of the catalysis-independent anti-apoptotic effect unresolved","Functional consequence of hetero-multimerization not defined"]},{"year":2012,"claim":"Provided in vivo genetic evidence that NDP kinase activity matters for organismal phenotype, identifying mouse Nme3 as a t-haplotype distorter acting through RHO signaling on sperm motility.","evidence":"Knockout, transgenic overexpression, enzymatic assay, and genetic epistasis in mice","pmids":["22438820"],"confidence":"High","gaps":["RHO signaling link is genetic, not biochemically reconstituted","Relevance to mammalian somatic NME3 function unclear"]},{"year":2016,"claim":"Connected NME3 to localized dNTP supply by showing it complexes with Tip60 and RNR and is recruited to DNA damage sites to support repair in quiescent cells.","evidence":"Reciprocal co-IP, site-specific recruitment assay, interaction-disrupting mutants","pmids":["26945015"],"confidence":"Medium","gaps":["Direct demonstration of local dNTP synthesis at lesions not shown","Structural basis of Tip60 interaction unknown"]},{"year":2018,"claim":"Defined NME3 as a mitochondrial outer-membrane protein with two separable functions—oligomerization-dependent fusion and NDP kinase catalysis—both required for metabolic adaptation, anchoring the modern model.","evidence":"Patient fibroblasts, domain-specific rescue mutants, live imaging, ATP and viability assays, MFN1/2 co-IP","pmids":["30587587"],"confidence":"High","gaps":["Molecular basis of MFN1/2 interaction not structurally defined","How catalysis sustains ATP under starvation not fully resolved"]},{"year":2018,"claim":"Extended NME3 function beyond mitochondria into innate immune signaling, placing it as a positive regulator of TLR5–NFκB downstream of MyD88.","evidence":"siRNA screen, knockdown/overexpression, NFκB reporter, epistasis placement","pmids":["29523766"],"confidence":"Medium","gaps":["Direct molecular target in the TLR5 pathway not identified","Whether NDP kinase activity is required is unknown"]},{"year":2018,"claim":"Implicated NME3 in ciliary biology by localizing it to the basal body with nephronophthisis proteins and showing knockdown causes ciliopathy phenotypes in two vertebrate models.","evidence":"Co-IP with NEK8/CEP164/ANKS6/NEK6, immunolocalization, morpholino knockdown in zebrafish and Xenopus","pmids":["30111592"],"confidence":"Medium","gaps":["Molecular role at the basal body undefined","Direct vs indirect nature of NPHP-protein associations unclear"]},{"year":2020,"claim":"Showed NME3 also functions at peroxisomes, where its NDP kinase activity drives division, likely by supplying GTP for DLP1, linking it to ether-lipid homeostasis.","evidence":"siRNA knockdown, catalytically-inactive mutant, patient fibroblasts, peroxisome morphology and ether-lipid measurement","pmids":["33126676"],"confidence":"Medium","gaps":["Direct GTP supply to DLP1 inferred, not demonstrated biochemically","How NME3 partitions between mitochondria and peroxisomes unknown"]},{"year":2020,"claim":"Causally linked NME3's mitochondrial fusion function to nuclear genome stability, showing fragmentation upon loss drives ROS-mediated nuclear DNA single-strand breaks.","evidence":"Knockdown, wild-type vs N-terminal-deletion rescue, comet assay, ROS measurement, fission inhibitor (Mdivi-1)","pmids":["32708927"],"confidence":"Medium","gaps":["Mechanistic chain from ROS to specific SSB lesions not detailed","Relationship to the Tip60–RNR repair role unclear"]},{"year":2023,"claim":"Provided the biochemical mechanism of mitochondrial tethering—direct PA binding via the N-terminal amphipathic helix plus hexamerization—and showed PLD6-dependent enrichment at contact interfaces drives selective fusion.","evidence":"PA-liposome pulldown, super-resolution live imaging, amphipathic-helix and hexamerization mutants, PLD6 depletion epistasis","pmids":["37584589"],"confidence":"High","gaps":["Structural basis of PA-bound hexamer not solved","How tethering selects specific mitochondria not fully defined"]},{"year":2024,"claim":"Defined NME3 as a gatekeeper for DRP1-dependent mitophagy, showing its phosphohistidine protects DRP1 from MUL1 ubiquitination, with in vivo relevance to ischemia/reperfusion injury.","evidence":"Active-site histidine knock-in mice, NME3–DRP1 co-IP, ubiquitination assays, MUL1 epistasis, ubiquitin-resistant DRP1 rescue, hypoxia mitophagy assay","pmids":["38480688"],"confidence":"High","gaps":["How phosphohistidine biochemically blocks ubiquitination unresolved","Whether this protection is direct on DRP1 or via an intermediary unknown"]},{"year":2024,"claim":"Showed NME3 is recruited under redox stress and is required for mitophagy that clears damaged mitochondria, preventing ROS accumulation, mtDNA lesions, and senescence.","evidence":"Genome-wide CRISPR screen with glutathione-depleting probe, KO validation, mitophagy/ROS/mtDNA/SASP readouts","pmids":["39133631"],"confidence":"Medium","gaps":["Recruitment trigger under redox stress not molecularly defined","Relation to PA/PLD6 recruitment pathway not integrated"]},{"year":2026,"claim":"Integrated NME3 into PINK1-PRKN mitophagy, showing it cooperates with PLD6 to generate PA from cardiolipin that repositions MFN2 near PINK1 to amplify parkin activation.","evidence":"Co-IP, PLA/FRET, KO cells, phospho-ubiquitin and PRKN binding assays, mito-ER tethering quantification, ubiquitin-resistant MFN2 mutants","pmids":["41640016"],"confidence":"Medium","gaps":["Direct demonstration that NME3 stimulates PLD6 catalysis on cardiolipin lacking","Quantitative contribution relative to DRP1 pathway unclear"]},{"year":2026,"claim":"Reported a new NME3 interactor, NAA10, modulating odontogenic differentiation via RUNX2 nuclear translocation, hinting at a developmental signaling role.","evidence":"Mass spectrometry, co-localization, knockdown rescue, overexpression, RUNX2 translocation and mineralization assays","pmids":["42165278"],"confidence":"Low","gaps":["Interaction not biochemically reconstituted (co-localization plus epistasis only)","Mechanism linking NME3 to RUNX2 trafficking undefined","Single lab, single study"]},{"year":null,"claim":"How NME3 coordinates its multiple compartment-specific roles—mitochondrial fusion, mitophagy, peroxisome division, DNA repair, ciliary function, and immune signaling—through shared catalytic and membrane-binding modules remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying structural model of catalytic vs membrane-tethering states","Mechanism controlling partitioning among organelles unknown","Physiological hierarchy of the parallel mitophagy pathways undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[3,5,8,11]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[10]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[11]}],"localization":[{"term_id":"GO:0005777","term_label":"peroxisome","supporting_discovery_ids":[8]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[11,12,13]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[5,8,10]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[4,9]}],"complexes":["NME3-Tip60-RNR complex","basal body NPHP module (NEK8/CEP164/ANKS6)"],"partners":["MFN1","MFN2","PLD6","DRP1","TIP60","NEK8","NAA10","MUL1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13232","full_name":"Nucleoside diphosphate kinase C","aliases":["DR-nm23","Nucleoside diphosphate kinase 3","NDK3","nm23-H3"],"length_aa":169,"mass_kda":19.0,"function":"Catalyzes the transfer of a gamma-phosphoryl group from a nucleoside triphosphate, mainly ATP, to a nucleoside diphosphate via a ping-pong mechanism involving a phosphohistidine intermediate, therefore contributing to the nucleoside triphosphate homeostasis (PubMed:11277919, PubMed:30587587, PubMed:39337255). In vitro, can also use other phosphate donors such as UTP and GTP (PubMed:30587587, PubMed:39337255). Independently of its nucleoside diphosphate kinase activity, involved in mitochondrial membrane tethering, a prerequisite for fusion through direct membrane-binding and hexamerization (PubMed:30587587, PubMed:37584589). Involved in DNA repair of both single- and double-stranded breaks by associating with the ribonucleotide reductase (RNR) complex via interaction with the histone acetyltransferase KAT5, facilitating recruitment to DNA damage sites independently of its kinase activity (PubMed:26945015). Inhibits granulocyte differentiation (PubMed:7638209). May be required for ciliary function during renal development (By similarity)","subcellular_location":"Mitochondrion outer membrane; Cytoplasm; Cytoplasm, cytoskeleton, cilium basal body","url":"https://www.uniprot.org/uniprotkb/Q13232/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NME3","classification":"Not Classified","n_dependent_lines":12,"n_total_lines":1208,"dependency_fraction":0.009933774834437087},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NME3","total_profiled":1310},"omim":[{"mim_id":"601818","title":"NME/NM23 NUCLEOSIDE DIPHOSPHATE KINASE 4; NME4","url":"https://www.omim.org/entry/601818"},{"mim_id":"601817","title":"NME/NM23 NUCLEOSIDE DIPHOSPHATE KINASE 3; NME3","url":"https://www.omim.org/entry/601817"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NME3"},"hgnc":{"alias_symbol":["DR-nm23","NM23-H3","NDPKC"],"prev_symbol":[]},"alphafold":{"accession":"Q13232","domains":[{"cath_id":"3.30.70.141","chopping":"18-169","consensus_level":"medium","plddt":97.0089,"start":18,"end":169}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13232","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13232-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13232-F1-predicted_aligned_error_v6.png","plddt_mean":92.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NME3","jax_strain_url":"https://www.jax.org/strain/search?query=NME3"},"sequence":{"accession":"Q13232","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13232.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13232/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13232"}},"corpus_meta":[{"pmid":"7638209","id":"PMC_7638209","title":"Overexpression of DR-nm23, a protein encoded by a member of the nm23 gene family, inhibits granulocyte differentiation and induces apoptosis in 32Dc13 myeloid cells.","date":"1995","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/7638209","citation_count":148,"is_preprint":false},{"pmid":"30587587","id":"PMC_30587587","title":"Two separate functions of NME3 critical for cell survival underlie a neurodegenerative disorder.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30587587","citation_count":42,"is_preprint":false},{"pmid":"11042679","id":"PMC_11042679","title":"Neuroblastoma specific effects of DR-nm23 and its mutant forms on differentiation and apoptosis.","date":"2000","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/11042679","citation_count":39,"is_preprint":false},{"pmid":"9067290","id":"PMC_9067290","title":"Gene structure, promoter activity, and chromosomal location of the DR-nm23 gene, a related member of the nm23 gene family.","date":"1997","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/9067290","citation_count":39,"is_preprint":false},{"pmid":"22438820","id":"PMC_22438820","title":"The nucleoside diphosphate kinase gene Nme3 acts as quantitative trait locus promoting non-Mendelian inheritance.","date":"2012","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22438820","citation_count":36,"is_preprint":false},{"pmid":"29523766","id":"PMC_29523766","title":"Nucleoside Diphosphate Kinase-3 (NME3) Enhances TLR5-Induced NFκB Activation.","date":"2018","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/29523766","citation_count":20,"is_preprint":false},{"pmid":"37584589","id":"PMC_37584589","title":"NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.","date":"2023","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/37584589","citation_count":19,"is_preprint":false},{"pmid":"26945015","id":"PMC_26945015","title":"The direct interaction of NME3 with Tip60 in DNA repair.","date":"2016","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/26945015","citation_count":17,"is_preprint":false},{"pmid":"11464913","id":"PMC_11464913","title":"DR-nm23 expression affects neuroblastoma cell differentiation, integrin expression, and adhesion characteristics.","date":"2001","source":"Medical and pediatric oncology","url":"https://pubmed.ncbi.nlm.nih.gov/11464913","citation_count":17,"is_preprint":false},{"pmid":"38480688","id":"PMC_38480688","title":"NME3 is a gatekeeper for DRP1-dependent mitophagy in hypoxia.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38480688","citation_count":16,"is_preprint":false},{"pmid":"33126676","id":"PMC_33126676","title":"Mammalian Homologue NME3 of DYNAMO1 Regulates Peroxisome Division.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33126676","citation_count":16,"is_preprint":false},{"pmid":"32708927","id":"PMC_32708927","title":"NME3 Regulates Mitochondria to Reduce ROS-Mediated Genome Instability.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32708927","citation_count":14,"is_preprint":false},{"pmid":"30111592","id":"PMC_30111592","title":"The nucleoside-diphosphate kinase NME3 associates with nephronophthisis proteins and is required for ciliary function during renal development.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30111592","citation_count":12,"is_preprint":false},{"pmid":"23765094","id":"PMC_23765094","title":"Inhibitory effect of upregulated DR-nm23 expression on invasion and metastasis in colorectal cancer.","date":"2013","source":"European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP)","url":"https://pubmed.ncbi.nlm.nih.gov/23765094","citation_count":12,"is_preprint":false},{"pmid":"11670444","id":"PMC_11670444","title":"Reactions of H(3)Al.NMe(3) with E(SiMe(3))(3) (E = P, As). Structural Characterization of the Trimer [H(2)AlP(SiMe(3))(2)](3) and Base-Stabilized Adduct [H(2)AlAs(SiMe(3))(2)].NMe(3) and Their Thermal Decomposition toward Nanocrystalline AlP and AlAs, Respectively.","date":"1998","source":"Inorganic chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11670444","citation_count":9,"is_preprint":false},{"pmid":"39133631","id":"PMC_39133631","title":"Mitochondrial Probe for Glutathione Depletion Reveals NME3 Essentiality for Mitochondrial Redox Response.","date":"2024","source":"ACS chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/39133631","citation_count":3,"is_preprint":false},{"pmid":"23484687","id":"PMC_23484687","title":"[Expressing trend of NME3 protein in acute myeloid leukemia HL-60 cells and patients' bone marrow].","date":"2013","source":"Zhongguo shi yan xue ye xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/23484687","citation_count":1,"is_preprint":false},{"pmid":"42165278","id":"PMC_42165278","title":"NME3 Interacts With NAA10 to Promote RUNX2 Nuclear Translocation and Odontogenic Differentiation in Human Dental Pulp Stem Cells.","date":"2026","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/42165278","citation_count":0,"is_preprint":false},{"pmid":"41640016","id":"PMC_41640016","title":"PRKN activation for mitophagy requires an NME3-regulated phosphatidic acid signal that separates mitochondria from endoplasmic reticulum tethering.","date":"2026","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/41640016","citation_count":0,"is_preprint":false},{"pmid":"41803653","id":"PMC_41803653","title":"Targeting NME3 to Restore Mitochondrial Fission-Fusion Balance Defines a Novel Disease-Modifying Strategy for Parkinson's Disease.","date":"2026","source":"CNS neuroscience & therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/41803653","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12516,"output_tokens":4390,"usd":0.051699,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12330,"output_tokens":4956,"usd":0.092775,"stage2_stop_reason":"end_turn"},"total_usd":0.144474,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1995,\n      \"finding\": \"Constitutive overexpression of DR-nm23 (NME3) in 32Dc13 myeloid precursor cells inhibits granulocyte colony-stimulating factor-induced granulocytic differentiation and induces apoptosis, establishing a functional role in myeloid differentiation arrest.\",\n      \"method\": \"Stable overexpression in 32Dc13 cells with G-CSF stimulation assay and apoptosis measurement (flow cytometry)\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean gain-of-function with defined cellular phenotype, single lab, two readouts (differentiation inhibition + apoptosis)\",\n      \"pmids\": [\"7638209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Mutations in the catalytic domain and at serine 61 phosphorylation site of DR-nm23 (NME3) impair neural differentiation induction in neuroblastoma cells; wild-type and mutant DR-nm23 localize predominantly to the mitochondrial fraction; wild-type DR-nm23 binds other NM23 family members via co-immunoprecipitation, but mutations in the catalytic, RGD domains or serine 61 disrupt hetero-multimer formation. The anti-apoptotic effect in neuroblastoma does not require intact catalytic activity or serine 61.\",\n      \"method\": \"Site-directed mutagenesis, subcellular fractionation, co-immunoprecipitation, overexpression assays in neuroblastoma cell lines\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis combined with co-IP and fractionation, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"11042679\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"DR-nm23 (NME3) fused to GFP localizes to the cytoplasm when transfected in SAOS-2 cells; the gene maps to chromosome 16q13, consists of six exons, and its promoter is transactivated ~3-fold by AP-2, which binds two specific sites in the 5'-flanking region as shown by EMSA.\",\n      \"method\": \"GFP fusion + transfection/fluorescence microscopy for localization; EMSA and CAT reporter assays for promoter analysis\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct localization experiment and promoter binding confirmed by EMSA, single lab\",\n      \"pmids\": [\"9067290\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The mouse Nme3 t-allele carries a P89S mutation that reduces NDP kinase enzymatic activity; reduction of Nme3 dosage by gene targeting enhanced t-haplotype transmission ratio distortion, phenocopying distorter function, while transgenic overexpression of the t-allele reduced transmission, identifying Nme3 as a quantitative trait locus distorter acting through RHO signaling to impair sperm motility.\",\n      \"method\": \"Gene targeting (knockout), transgenic overexpression, biochemical enzymatic activity assay, genetic epistasis analysis in mice\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — enzymatic activity assay, genetic loss-of-function and gain-of-function with clear phenotype, epistasis analysis in vivo\",\n      \"pmids\": [\"22438820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"NME3 directly interacts with Tip60 histone acetyltransferase to form a complex with ribonucleotide reductase (RNR), and this interaction is required for NME3 recruitment to DNA damage sites; disruption of NME3–Tip60 interaction suppresses DNA repair in serum-deprived (quiescent) cells.\",\n      \"method\": \"Co-immunoprecipitation, site-specific recruitment assay at DNA damage sites, loss-of-function with interaction-disrupting mutants\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP, functional rescue with mutants, single lab with two orthogonal methods\",\n      \"pmids\": [\"26945015\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NME3 is a mitochondrial outer-membrane protein that interacts with MFN1/2; NME3 depletion causes dysfunction in mitochondrial dynamics (slow rate of fusion/fission); catalytic-dead NME3 restores mitochondrial elongation but only wild-type NME3 sustains ATP production and cell viability under glucose starvation, showing two separate functions—oligomerization-dependent mitochondrial fusion and NDP kinase catalytic activity—are both required for metabolic adaptation.\",\n      \"method\": \"Patient fibroblast studies, exome sequencing, wild-type/catalytic-dead/oligomerization-attenuated NME3 rescue experiments, mitochondrial dynamics live imaging, ATP measurement, cell viability assay, co-immunoprecipitation with MFN1/2\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (co-IP, live imaging, domain-specific mutants, patient cells), rigorous mechanistic dissection in single study\",\n      \"pmids\": [\"30587587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NME3 acts as a positive regulator of TLR5-induced NFκB signaling mechanistically downstream of MyD88; knockdown reduces and overexpression enhances NFκB activation in response to flagellin stimulation.\",\n      \"method\": \"siRNA loss-of-function screen, targeted knockdown, overexpression assays, NFκB bioluminescent reporter, epistasis placement downstream of MyD88\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockdown and overexpression confirmed with reporter assay, pathway placement by epistasis, single lab\",\n      \"pmids\": [\"29523766\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NME3 localizes to the basal body and associates with nephronophthisis proteins NEK8, CEP164, and ANKS6 as well as centrosomal protein NEK6; depletion of nme3 in zebrafish and Xenopus causes ciliopathy phenotypes including renal malformations and left-right asymmetry defects.\",\n      \"method\": \"Co-immunoprecipitation with NPHP proteins, immunolocalization to basal body, morpholino knockdown in zebrafish and Xenopus with phenotypic analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with multiple proteins, direct localization, in vivo loss-of-function in two vertebrate models, single lab\",\n      \"pmids\": [\"30111592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NME3 localizes to peroxisomes as well as mitochondria; suppression of NME3 or expression of catalytically-inactive NME3 causes peroxisome elongation, and elevated NME3 promotes peroxisome division; NME3 NDP kinase activity is required for peroxisome division (constriction/scission), likely by generating GTP for DLP1, and impaired peroxisome division reduces ethanolamine plasmalogen levels.\",\n      \"method\": \"siRNA knockdown, patient fibroblasts (initiation-codon mutation), catalytically-inactive NME3 expression, peroxisome morphology quantification, ATAD1-silencing overexpression model, ether-lipid mass measurement\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function, gain-of-function, and catalytic-dead mutant with defined organelle morphology phenotype, single lab\",\n      \"pmids\": [\"33126676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NME3 knockdown increases mitochondrial fragmentation, which causes mitochondrial oxidative stress-mediated DNA single-strand breaks in nuclear DNA; re-expression of wild-type NME3 or inhibition of mitochondrial fission rescues SSBs and DNA repair, whereas N-terminal-deleted NME3 (defective in mitochondrial membrane binding) has no rescue effect, demonstrating that NME3 maintains genome stability through its mitochondrial fusion function.\",\n      \"method\": \"siRNA knockdown, wild-type and N-terminal deleted mutant re-expression, mitochondrial morphology imaging, comet assay for SSBs, ROS measurement, inhibitor of fission (Mdivi-1)\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain-specific mutant rescue, two orthogonal readouts (SSBs + ROS), single lab\",\n      \"pmids\": [\"32708927\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NME3 binds directly to phosphatidic acid (PA) via its N-terminal amphipathic helix and is enriched at the contact interface of closely positioned mitochondria in a PLD6-dependent manner; PA binding and hexamerization are both required for NME3 mitochondrial tethering activity; nutrient starvation enhances NME3 enrichment at mitochondrial contact interfaces, and NME3 tethering promotes selective fusion between PLD6-remodeled mitochondria.\",\n      \"method\": \"Lipid-binding assay (PA-liposome pulldown), live-cell imaging/super-resolution microscopy of NME3 at contact interfaces, domain mutant analysis (amphipathic helix deletion, hexamerization mutant), PLD6 depletion epistasis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct biochemical lipid binding assay, structural domain mutagenesis, live-cell imaging, genetic epistasis with PLD6, multiple orthogonal methods in single study\",\n      \"pmids\": [\"37584589\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NME3 acts as a gatekeeper for DRP1-dependent mitophagy in hypoxia: hypoxia-induced PA on mitochondria is required for NME3–DRP1 interaction; active site phosphohistidine of NME3 (not NDPK catalytic turnover per se) protects DRP1 from MUL1-mediated ubiquitination and proteasomal degradation, allowing sufficient active DRP1 to execute mitophagy. Knock-in mice disrupting NME3 histidine phosphorylation are vulnerable to ischemia/reperfusion injury and show cerebellar defects.\",\n      \"method\": \"Knock-in mouse model (active-site histidine mutation), co-immunoprecipitation of NME3 with DRP1, ubiquitination assay, MUL1 overexpression epistasis, ubiquitin-resistant DRP1 mutant rescue, hypoxia-induced mitophagy assay, PA-binding domain mutant analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vivo knock-in model, biochemical reconstitution of ubiquitination protection, multiple domain mutants and epistasis experiments, replicated in cell and mouse systems\",\n      \"pmids\": [\"38480688\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NME3 is recruited to the mitochondrial outer membrane under redox stress (mitochondrial glutathione depletion); in the absence of NME3, mitophagy is impaired, leading to accumulation of dysfunctional mitochondria, increased mitochondrial ROS, mtDNA lesions, and a senescence-associated secretory phenotype.\",\n      \"method\": \"Genome-wide CRISPR/Cas9 screen with mitochondria-penetrating glutathione-depleting probe (mtCDNB), NME3 knockout validation, mitophagy assay, ROS measurement, mtDNA damage quantification, SASP assessment\",\n      \"journal\": \"ACS chemical biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide CRISPR screen followed by KO validation with multiple phenotypic readouts, single lab\",\n      \"pmids\": [\"39133631\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NME3 interacts with PLD6/MitoPLD on the outer mitochondrial membrane of depolarized mitochondria to generate phosphatidic acid (PA) from cardiolipin; this NME3-regulated PA signal is essential for repositioning MFN2 near PINK1 for phosphorylation of ubiquitin conjugates on MFN2, enabling p-S65-Ub-dependent PRKN/parkin amplification. NME3 deficiency causes mitochondria-ER tethering that prevents MFN2 access to PINK1, impairing PRKN activation for mitophagy.\",\n      \"method\": \"Co-immunoprecipitation, proximity ligation assay (FRET/PLA), NME3 KO cells, PLD6 interaction assays, phospho-ubiquitin and PRKN binding measurements, mitochondria-ER tethering quantification, ubiquitin-resistant MFN2 mutants\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple co-IP and PLA experiments, KO cell mechanistic analysis, domain mutants, single lab with several orthogonal methods\",\n      \"pmids\": [\"41640016\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NME3 interacts with NAA10 (N-α-acetyltransferase 10), and this interaction modulates odontogenic differentiation of human dental pulp stem cells; NAA10 knockdown rescues differentiation deficits from NME3 silencing, while NAA10 overexpression attenuates NME3-driven differentiation; NME3 facilitates nuclear translocation of RUNX2, a key transcription factor in odontogenesis.\",\n      \"method\": \"Mass spectrometry identification of interactor, co-localization, siRNA knockdown of NME3 and NAA10, overexpression, RUNX2 nuclear translocation assay (immunofluorescence), mineralization assay\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-localization and genetic epistasis (knockdown rescue) without biochemical reconstitution of interaction; single lab, single study\",\n      \"pmids\": [\"42165278\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NME3 (DR-nm23/NM23-H3/NDPKC) is an NDP kinase localized to the mitochondrial outer membrane (and peroxisomes) that serves two separable functions: (1) an oligomerization-dependent mitochondrial tethering/fusion role mediated by direct binding of its N-terminal amphipathic helix to phosphatidic acid generated by PLD6, and (2) an NDP kinase catalytic function (requiring active-site histidine phosphorylation) that protects DRP1 from MUL1-mediated ubiquitination to enable hypoxia-induced mitophagy and supports ATP production; NME3 also cooperates with PLD6 to generate PA on depolarized mitochondria, facilitating Mito-ER untethering and PINK1-PRKN/parkin-dependent mitophagy, while additional roles include direct interaction with Tip60–RNR for site-specific dNTP synthesis at DNA damage sites, association with nephronophthisis proteins at the basal body for ciliary function, positive regulation of TLR5-NFκB signaling downstream of MyD88, and NDP kinase-dependent GTP supply for peroxisome division.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NME3 is a nucleoside diphosphate (NDP) kinase that anchors to the mitochondrial outer membrane and executes two genetically separable activities—an oligomerization-dependent membrane-tethering function and a catalytic NDP kinase function—that together govern mitochondrial dynamics, mitophagy, and metabolic adaptation [#5]. Mitochondrial targeting and tethering depend on an N-terminal amphipathic helix that binds directly to phosphatidic acid (PA) generated by PLD6 at mitochondrial contact interfaces; PA binding together with hexamerization drives selective fusion of PLD6-remodeled mitochondria, a process enhanced by nutrient starvation [#10]. NME3 interacts with the fusion machinery MFN1/2, and while catalytic-dead NME3 can restore mitochondrial elongation, only catalytically active NME3 sustains ATP production and viability under glucose starvation [#5]. Through its membrane-binding fusion activity, NME3 also preserves nuclear genome stability, since its loss fragments mitochondria, elevates ROS, and produces nuclear DNA single-strand breaks [#9]. In mitophagy, NME3 cooperates with PLD6 to produce PA on depolarized mitochondria that repositions MFN2 near PINK1 to amplify PRKN/parkin activation [#13], and hypoxia-induced PA enables an NME3–DRP1 interaction in which the NME3 active-site phosphohistidine protects DRP1 from MUL1-mediated ubiquitination, allowing DRP1-dependent mitophagy; knock-in mice lacking this histidine phosphorylation are vulnerable to ischemia/reperfusion injury [#11]. Beyond mitochondria, NME3 localizes to peroxisomes where its NDP kinase activity supports division [#8], associates with Tip60–ribonucleotide reductase for recruitment to DNA damage sites in quiescent cells [#4], localizes to the basal body with nephronophthisis proteins to support ciliary function [#7], and positively regulates TLR5–NF\\u03baB signaling downstream of MyD88 [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Established the first cellular phenotype for NME3 by showing it arrests myeloid differentiation, framing it as a regulator of cell-fate decisions before any molecular mechanism was known.\",\n      \"evidence\": \"Stable overexpression in 32Dc13 myeloid precursors with G-CSF stimulation and apoptosis readouts\",\n      \"pmids\": [\"7638209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular activity linked to the differentiation arrest\", \"Overexpression phenotype not tied to endogenous function\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Mapped the gene and its AP-2-driven promoter and reported a cytoplasmic GFP localization, an early and partial view of where the protein acts.\",\n      \"evidence\": \"GFP fusion microscopy in SAOS-2 cells, EMSA and CAT reporter promoter analysis\",\n      \"pmids\": [\"9067290\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cytoplasmic localization later refined to mitochondrial/peroxisomal compartments\", \"GFP fusion may mislocalize the membrane-anchored protein\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Began separating catalytic from non-catalytic roles by showing catalytic and serine-61 mutants impair differentiation and disrupt NM23 hetero-multimer formation, while the anti-apoptotic effect was catalysis-independent.\",\n      \"evidence\": \"Site-directed mutagenesis, subcellular fractionation, and co-IP in neuroblastoma cells\",\n      \"pmids\": [\"11042679\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of the catalysis-independent anti-apoptotic effect unresolved\", \"Functional consequence of hetero-multimerization not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Provided in vivo genetic evidence that NDP kinase activity matters for organismal phenotype, identifying mouse Nme3 as a t-haplotype distorter acting through RHO signaling on sperm motility.\",\n      \"evidence\": \"Knockout, transgenic overexpression, enzymatic assay, and genetic epistasis in mice\",\n      \"pmids\": [\"22438820\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"RHO signaling link is genetic, not biochemically reconstituted\", \"Relevance to mammalian somatic NME3 function unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Connected NME3 to localized dNTP supply by showing it complexes with Tip60 and RNR and is recruited to DNA damage sites to support repair in quiescent cells.\",\n      \"evidence\": \"Reciprocal co-IP, site-specific recruitment assay, interaction-disrupting mutants\",\n      \"pmids\": [\"26945015\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct demonstration of local dNTP synthesis at lesions not shown\", \"Structural basis of Tip60 interaction unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined NME3 as a mitochondrial outer-membrane protein with two separable functions—oligomerization-dependent fusion and NDP kinase catalysis—both required for metabolic adaptation, anchoring the modern model.\",\n      \"evidence\": \"Patient fibroblasts, domain-specific rescue mutants, live imaging, ATP and viability assays, MFN1/2 co-IP\",\n      \"pmids\": [\"30587587\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of MFN1/2 interaction not structurally defined\", \"How catalysis sustains ATP under starvation not fully resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended NME3 function beyond mitochondria into innate immune signaling, placing it as a positive regulator of TLR5–NF\\u03baB downstream of MyD88.\",\n      \"evidence\": \"siRNA screen, knockdown/overexpression, NF\\u03baB reporter, epistasis placement\",\n      \"pmids\": [\"29523766\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular target in the TLR5 pathway not identified\", \"Whether NDP kinase activity is required is unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Implicated NME3 in ciliary biology by localizing it to the basal body with nephronophthisis proteins and showing knockdown causes ciliopathy phenotypes in two vertebrate models.\",\n      \"evidence\": \"Co-IP with NEK8/CEP164/ANKS6/NEK6, immunolocalization, morpholino knockdown in zebrafish and Xenopus\",\n      \"pmids\": [\"30111592\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular role at the basal body undefined\", \"Direct vs indirect nature of NPHP-protein associations unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed NME3 also functions at peroxisomes, where its NDP kinase activity drives division, likely by supplying GTP for DLP1, linking it to ether-lipid homeostasis.\",\n      \"evidence\": \"siRNA knockdown, catalytically-inactive mutant, patient fibroblasts, peroxisome morphology and ether-lipid measurement\",\n      \"pmids\": [\"33126676\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct GTP supply to DLP1 inferred, not demonstrated biochemically\", \"How NME3 partitions between mitochondria and peroxisomes unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Causally linked NME3's mitochondrial fusion function to nuclear genome stability, showing fragmentation upon loss drives ROS-mediated nuclear DNA single-strand breaks.\",\n      \"evidence\": \"Knockdown, wild-type vs N-terminal-deletion rescue, comet assay, ROS measurement, fission inhibitor (Mdivi-1)\",\n      \"pmids\": [\"32708927\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic chain from ROS to specific SSB lesions not detailed\", \"Relationship to the Tip60–RNR repair role unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided the biochemical mechanism of mitochondrial tethering—direct PA binding via the N-terminal amphipathic helix plus hexamerization—and showed PLD6-dependent enrichment at contact interfaces drives selective fusion.\",\n      \"evidence\": \"PA-liposome pulldown, super-resolution live imaging, amphipathic-helix and hexamerization mutants, PLD6 depletion epistasis\",\n      \"pmids\": [\"37584589\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of PA-bound hexamer not solved\", \"How tethering selects specific mitochondria not fully defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined NME3 as a gatekeeper for DRP1-dependent mitophagy, showing its phosphohistidine protects DRP1 from MUL1 ubiquitination, with in vivo relevance to ischemia/reperfusion injury.\",\n      \"evidence\": \"Active-site histidine knock-in mice, NME3–DRP1 co-IP, ubiquitination assays, MUL1 epistasis, ubiquitin-resistant DRP1 rescue, hypoxia mitophagy assay\",\n      \"pmids\": [\"38480688\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How phosphohistidine biochemically blocks ubiquitination unresolved\", \"Whether this protection is direct on DRP1 or via an intermediary unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed NME3 is recruited under redox stress and is required for mitophagy that clears damaged mitochondria, preventing ROS accumulation, mtDNA lesions, and senescence.\",\n      \"evidence\": \"Genome-wide CRISPR screen with glutathione-depleting probe, KO validation, mitophagy/ROS/mtDNA/SASP readouts\",\n      \"pmids\": [\"39133631\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Recruitment trigger under redox stress not molecularly defined\", \"Relation to PA/PLD6 recruitment pathway not integrated\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Integrated NME3 into PINK1-PRKN mitophagy, showing it cooperates with PLD6 to generate PA from cardiolipin that repositions MFN2 near PINK1 to amplify parkin activation.\",\n      \"evidence\": \"Co-IP, PLA/FRET, KO cells, phospho-ubiquitin and PRKN binding assays, mito-ER tethering quantification, ubiquitin-resistant MFN2 mutants\",\n      \"pmids\": [\"41640016\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct demonstration that NME3 stimulates PLD6 catalysis on cardiolipin lacking\", \"Quantitative contribution relative to DRP1 pathway unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Reported a new NME3 interactor, NAA10, modulating odontogenic differentiation via RUNX2 nuclear translocation, hinting at a developmental signaling role.\",\n      \"evidence\": \"Mass spectrometry, co-localization, knockdown rescue, overexpression, RUNX2 translocation and mineralization assays\",\n      \"pmids\": [\"42165278\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Interaction not biochemically reconstituted (co-localization plus epistasis only)\", \"Mechanism linking NME3 to RUNX2 trafficking undefined\", \"Single lab, single study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NME3 coordinates its multiple compartment-specific roles—mitochondrial fusion, mitophagy, peroxisome division, DNA repair, ciliary function, and immune signaling—through shared catalytic and membrane-binding modules remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying structural model of catalytic vs membrane-tethering states\", \"Mechanism controlling partitioning among organelles unknown\", \"Physiological hierarchy of the parallel mitophagy pathways undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [3, 5, 8, 11]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005741\", \"supporting_discovery_ids\": [5, 10, 12]},\n      {\"term_id\": \"GO:0005777\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [11, 12, 13]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [5, 8, 10]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [4, 9]}\n    ],\n    \"complexes\": [\n      \"NME3-Tip60-RNR complex\",\n      \"basal body NPHP module (NEK8/CEP164/ANKS6)\"\n    ],\n    \"partners\": [\n      \"MFN1\",\n      \"MFN2\",\n      \"PLD6\",\n      \"DRP1\",\n      \"Tip60\",\n      \"NEK8\",\n      \"NAA10\",\n      \"MUL1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}