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

Gene ID: 4832, updated on 14-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
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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 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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