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

Gene ID: 4830, updated on 13-Apr-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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Location:
17q21.33
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (51153559..51162168)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (52020874..52029483)
105.20220307 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: 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. A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1. Tossounian MA, et al. Int J Mol Sci, 2023 May 27. PMID 37298313, Free PMC Article
  2. Metastasis suppressor NME1 in exosomes or liposomes conveys motility and migration inhibition in breast cancer model systems. Khan I, et al. Clin Exp Metastasis, 2022 Oct. PMID 35939247, Free PMC Article
  3. The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor. Cho JH, et al. Int J Mol Sci, 2021 Nov 11. PMID 34830075, Free PMC Article
  4. The multiple regulation of metastasis suppressor NM23-H1 in cancer. Yu L, et al. Life Sci, 2021 Mar 1. PMID 33421524
  5. Metastasis Suppressor NME1 Modulates Choice of Double-Strand Break Repair Pathways in Melanoma Cells by Enhancing Alternative NHEJ while Inhibiting NHEJ and HR. Puts G, et al. Int J Mol Sci, 2020 Aug 17. PMID 32824412, Free PMC Article

See all (399) 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)

Genotypes

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 phosphorylation 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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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_2023_10

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.

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