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    NME3 NME/NM23 nucleoside diphosphate kinase 3 [ Homo sapiens (human) ]

    Gene ID: 4832, updated on 27-Nov-2024

    Summary

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    Official Symbol
    NME3provided by HGNC
    Official Full Name
    NME/NM23 nucleoside diphosphate kinase 3provided by HGNC
    Primary source
    HGNC:HGNC:7851
    See related
    Ensembl:ENSG00000103024 MIM:601817; AllianceGenome:HGNC:7851
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NDPKC; NDPK-C; NM23H3; DR-nm23; NM23-H3; c371H6.2
    Summary
    Enables nucleoside diphosphate kinase activity. Involved in DNA repair; mitochondrial fusion; and nucleoside triphosphate biosynthetic process. Located in mitochondrial outer membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in prostate (RPKM 24.8), fat (RPKM 18.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NME3 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (1770320..1771543, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (1786150..1787373, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (1820321..1821544, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase 8 interacting protein 3 Neighboring gene MAPK8IP3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10233 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1784965-1785466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1785467-1785966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1789279-1789857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1789858-1790435 Neighboring gene microRNA 3177 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:1800917-1801129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1802173-1802673 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:1810494-1810664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:1814128-1814842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7003 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7005 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7006 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:1824057-1824845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1825681-1826181 Neighboring gene mitochondrial ribosomal protein S34 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7007 Neighboring gene essential meiotic structure-specific endonuclease subunit 2 Neighboring gene splA/ryanodine receptor domain and SOCS box containing 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. 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. Venturelli D, et al. Proc Natl Acad Sci U S A, 1995 Aug 1. PMID 7638209, Free PMC Article
    2. Gene structure, promoter activity, and chromosomal location of the DR-nm23 gene, a related member of the nm23 gene family. Martinez R, et al. Cancer Res, 1997 Mar 15. PMID 9067290
    3. Inhibitory effect of upregulated DR-nm23 expression on invasion and metastasis in colorectal cancer. Qu L, et al. Eur J Cancer Prev, 2013 Nov. PMID 23765094
    4. Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes. Amjadi R, et al. Int J Mol Sci, 2024 Sep 10. PMID 39337255, Free PMC Article
    5. Two separate functions of NME3 critical for cell survival underlie a neurodegenerative disorder. Chen CW, et al. Proc Natl Acad Sci U S A, 2019 Jan 8. PMID 30587587, Free PMC Article

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes.
      Title: Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes.
    2. NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.
      Title: NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.
    3. Genetic defects in peroxisome morphogenesis (Pex11beta, dynamin-like protein 1, and nucleoside diphosphate kinase 3) affect docosahexaenoic acid-phospholipid metabolism.
      Title: Genetic defects in peroxisome morphogenesis (Pex11β, dynamin-like protein 1, and nucleoside diphosphate kinase 3) affect docosahexaenoic acid-phospholipid metabolism.
    4. NME3 Regulates Mitochondria to Reduce ROS-Mediated Genome Instability.
      Title: NME3 Regulates Mitochondria to Reduce ROS-Mediated Genome Instability.
    5. Proinflammatory signaling mediated by innate immunity engagement of flagellin-activated TLR5 in tumor cells results in antitumor effects through NME3 kinase, a positive downstream regulator of flagellin-mediated NFkappaB signaling, enhancing survival for several human cancers.
      Title: Nucleoside Diphosphate Kinase-3 (NME3) Enhances TLR5-Induced NFκB Activation.
    6. Given the critical role of mitochondrial dynamics and energy requirements in neuronal development, the homozygous mutation in NME3 is linked to a fatal mitochondrial neurodegenerative disorder.
      Title: Two separate functions of NME3 critical for cell survival underlie a neurodegenerative disorder.
    7. The ciliopathy-typical manifestations of NME3 depletion in two vertebrate in vivo models, the biochemical association of NME3 with validated NPHPs, and its localization to the basal body reveal a role for NME3 in ciliary function. We conclude that mutations in the NME3 gene may aggravate the ciliopathy phenotypes observed in humans.
      Title: The nucleoside-diphosphate kinase NME3 associates with nephronophthisis proteins and is required for ciliary function during renal development.
    8. Thus Tip60 interacts with RNR and NME3 to provide site-specific synthesis of dNTP for facilitating DNA repair in serum-deprived cells which contain low levels of dNTPs.
      Title: The direct interaction of NME3 with Tip60 in DNA repair.
    9. Down-regulated DR-nm23 expression is associated with invasion and metastasis in colorectal cancer.
      Title: Inhibitory effect of upregulated DR-nm23 expression on invasion and metastasis in colorectal cancer.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0516

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleoside diphosphate kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleoside diphosphate kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in CTP biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in GTP biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in UTP biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in apoptotic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mitochondrial fusion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nucleoside triphosphate biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in ciliary basal body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrial outer membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    nucleoside diphosphate kinase 3
    Names
    NDK 3
    NDP kinase 3
    NDP kinase C
    non-metastatic cells 3, protein expressed in
    nucleoside diphosphate kinase C
    NP_002504.2
    XP_005255389.1
    XP_011520805.1
    XP_011520806.1
    XP_054236378.1
    XP_054236379.1
    XP_054236380.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_002513.3 → NP_002504.2  nucleoside diphosphate kinase 3 precursor

      See identical proteins and their annotated locations for NP_002504.2

      Status: VALIDATED

      Source sequence(s)
      AC012180
      Consensus CDS
      CCDS10443.1
      UniProtKB/Swiss-Prot
      Q13232, Q9BWH4
      UniProtKB/TrEMBL
      Q9NUF9
      Related
      ENSP00000219302.3, ENST00000219302.8
      Conserved Domains (1) summary
      cd04413
      Location:22 → 151
      NDPk_I; Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      1770320..1771543 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255332.5 → XP_005255389.1  nucleoside diphosphate kinase 3 isoform X2

      Conserved Domains (2) summary
      cd04413
      Location:22 → 128
      NDPk_I; Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside ...
      pfam00334
      Location:22 → 128
      NDK; Nucleoside diphosphate kinase

    2. XM_011522503.3 → XP_011520805.1  nucleoside diphosphate kinase 3 isoform X1

      Conserved Domains (2) summary
      cl00335
      Location:22 → 169
      NDPk; Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are ...
      pfam00334
      Location:22 → 157
      NDK; Nucleoside diphosphate kinase

    3. XM_011522504.3 → XP_011520806.1  nucleoside diphosphate kinase 3 isoform X3

      UniProtKB/TrEMBL
      H3BRA8
      Related
      ENSP00000456160.1, ENST00000564628.1
      Conserved Domains (1) summary
      cl00335
      Location:22 → 60
      NDPk; Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      1786150..1787373 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380404.1 → XP_054236379.1  nucleoside diphosphate kinase 3 isoform X2

    2. XM_054380403.1 → XP_054236378.1  nucleoside diphosphate kinase 3 isoform X1

    3. XM_054380405.1 → XP_054236380.1  nucleoside diphosphate kinase 3 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13232.2 GenPept UniProtKB/Swiss-Prot:Q13232

    Gene LinkOut

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