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    NME1 NME/NM23 nucleoside diphosphate kinase 1 [ Homo sapiens (human) ]

    Gene ID: 4830, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NME1provided by HGNC
    Official Full Name
    NME/NM23 nucleoside diphosphate kinase 1provided by HGNC
    Primary source
    HGNC:HGNC:7849
    See related
    Ensembl:ENSG00000239672 MIM:156490; AllianceGenome:HGNC:7849
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NB; AWD; NBS; GAAD; NDKA; NM23; NDPKA; NDPK-A; NM23-H1
    Summary
    This gene (NME1) was identified because of its reduced mRNA transcript levels in highly metastatic cells. Nucleoside diphosphate kinase (NDK) exists as a hexamer composed of 'A' (encoded by this gene) and 'B' (encoded by NME2) isoforms. Mutations in this gene have been identified in aggressive neuroblastomas. Two transcript variants encoding different isoforms have been found for this gene. Co-transcription of this gene and the neighboring downstream gene (NME2) generates naturally-occurring transcripts (NME1-NME2), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in appendix (RPKM 37.1), brain (RPKM 32.2) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See NME1 in Genome Data Viewer
    Location:
    17q21.33
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (51153559..51162168)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (52020874..52029483)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (49230920..49239529)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904029 Neighboring gene Sharpr-MPRA regulatory region 1122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49029041-49029542 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:49031243-49032442 Neighboring gene sperm associated antigen 9 Neighboring gene Sharpr-MPRA regulatory region 10137 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49175960-49176460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12398 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:49198151-49198965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12400 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:49205455-49205678 Neighboring gene MPRA-validated peak2888 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr17:49219886-49220387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49222416-49222916 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:49230233-49231432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:49232587-49233118 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:49243725-49244333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8725 Neighboring gene NME1-NME2 readthrough Neighboring gene MPRA-validated peak2890 silencer Neighboring gene NME/NM23 nucleoside diphosphate kinase 2 Neighboring gene mbt domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8727 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8728 Neighboring gene UTP18 small subunit processome component

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Dual functions of NME1 in suppression of cell motility and enhancement of genomic stability in melanoma. Kaetzel DM, et al. Naunyn Schmiedebergs Arch Pharmacol, 2015 Feb. PMID 25017017, Free PMC Article
    2. NME1L Negatively Regulates IGF1-Dependent Proliferation of Breast Cancer Cells. You DJ, et al. J Cell Biochem, 2016 Jun. PMID 26565392
    3. nm23-H1 protein expression and gene mutation in 150 patients with non-Hodgkin's lymphomas. Lee JH, et al. J Korean Med Sci, 2006 Aug. PMID 16891807, Free PMC Article
    4. Metastasis suppressor NME1 regulates melanoma cell morphology, self-adhesion and motility via induction of fibronectin expression. Novak M, et al. Exp Dermatol, 2015 Jun. PMID 25808322, Free PMC Article
    5. Regulatory roles for nm23/nucleoside diphosphate kinase-like enzymes in insulin secretion from the pancreatic islet beta cell. Kowluru A, et al. J Bioenerg Biomembr, 2006 Aug. PMID 16957985

    See all (420) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NME1 and DCC variants are associated with susceptibility and tumor characteristics in Mexican patients with colorectal cancer.
      Title: NME1 and DCC variants are associated with susceptibility and tumor characteristics in Mexican patients with colorectal cancer.
    2. NSUN6 Regulates NM23-H1 Expression in an m5C Manner to Affect Epithelial-Mesenchymal Transition in Lung Cancer.
      Title: NSUN6 Regulates NM23-H1 Expression in an m5C Manner to Affect Epithelial-Mesenchymal Transition in Lung Cancer.
    3. A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.
      Title: A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.
    4. Does the Blood-Brain Barrier Integrity Change in Regard to the Onset of Fetal Growth Restriction?
      Title: Does the Blood-Brain Barrier Integrity Change in Regard to the Onset of Fetal Growth Restriction?
    5. Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism.
      Title: Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism.
    6. Metastasis suppressor NME1 in exosomes or liposomes conveys motility and migration inhibition in breast cancer model systems.
      Title: Metastasis suppressor NME1 in exosomes or liposomes conveys motility and migration inhibition in breast cancer model systems.
    7. MicroRNA-139-5p negatively regulates NME1 expression in hepatocellular carcinoma cells.
      Title: MicroRNA-139-5p negatively regulates NME1 expression in hepatocellular carcinoma cells.
    8. Long-chain fatty acyl coenzyme A inhibits NME1/2 and regulates cancer metastasis.
      Title: Long-chain fatty acyl coenzyme A inhibits NME1/2 and regulates cancer metastasis.
    9. Metastasis-suppressor NME1 controls the invasive switch of breast cancer by regulating MT1-MMP surface clearance.
      Title: Metastasis-suppressor NME1 controls the invasive switch of breast cancer by regulating MT1-MMP surface clearance.
    10. The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor.
      Title: The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor.
    Submit: New GeneRIF Correction See all GeneRIFs (259)

    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    SiRNA-mediated knockdown of one of the components of the SET complex, NM23-H1, inhibits HIV-1 infection with significantly reduced levels of integrated HIV-1 DNA and viral production in HeLa-CD4 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    reverse transcriptase gag-pol HIV-1 RT forms a complex with NDPKA in vitro PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5' exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA nuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GTP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 
    enables ribosomal small subunit 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 metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lactation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of cell population proliferation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of apoptotic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 
    located_in nucleus HDA PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in ruffle membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    nucleoside diphosphate kinase A
    Names
    NDP kinase A
    epididymis secretory sperm binding protein
    granzyme A-activated DNase
    metastasis inhibition factor nm23
    non-metastatic cells 1, protein (NM23A) expressed in
    tumor metastatic process-associated protein
    NP_000260.1
    NP_937818.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_021169.1 RefSeqGene

      Range
      5001..13610
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000269.3 → NP_000260.1  nucleoside diphosphate kinase A isoform b

      See identical proteins and their annotated locations for NP_000260.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1. The resulting isoform (b) has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AC005839, AF487339, BE727815, BF965472, BG715560, BI666785, BM479520, BU600979
      Consensus CDS
      CCDS11579.1
      UniProtKB/Swiss-Prot
      P15531, Q6FGK3, Q86XQ2, Q9UDJ6
      UniProtKB/TrEMBL
      A0A384MTW7
      Related
      ENSP00000376892.3, ENST00000393196.8
      Conserved Domains (1) summary
      PTZ00093
      Location:5 → 151
      PTZ00093; nucleoside diphosphate kinase, cytosolic; Provisional

    2. NM_198175.1 → NP_937818.1  nucleoside diphosphate kinase A isoform a

      See identical proteins and their annotated locations for NP_937818.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AF487339, AL360191, BE727815, BF965472, BG531372, BG715560, BG757842, BI666785, BM479520
      Consensus CDS
      CCDS11578.1
      UniProtKB/Swiss-Prot
      P15531
      Related
      ENSP00000337060.3, ENST00000336097.7
      Conserved Domains (2) summary
      PTZ00093
      Location:30 → 176
      PTZ00093; nucleoside diphosphate kinase, cytosolic; Provisional
      pfam00334
      Location:30 → 164
      NDK; Nucleoside diphosphate kinase

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      51153559..51162168
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      52020874..52029483
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P15531.1 GenPept UniProtKB/Swiss-Prot:P15531

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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