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Aliases for NUDT3 Gene

Aliases for NUDT3 Gene

  • Nudix Hydrolase 3 2 3 5
  • Nudix (Nucleoside Diphosphate Linked Moiety X)-Type Motif 3 2 3
  • Diadenosine 5,5-P1,P6-Hexaphosphate Hydrolase 1 3 4
  • Nucleoside Diphosphate-Linked Moiety X Motif 3 3 4
  • Nudix Motif 3 3 4
  • DIPP-1 3 4
  • DIPP1 3 4
  • DIPP 3 4
  • Diphosphoinositol Polyphosphate Phosphohydrolase 1 3
  • EC 3.6.1.52 4
  • EC 3.6.1.- 4

External Ids for NUDT3 Gene

Previous GeneCards Identifiers for NUDT3 Gene

  • GC06M034258
  • GC06M034302
  • GC06M034363
  • GC06M033978
  • GC06M034388
  • GC06M034894
  • GC06M035232
  • GC06M035727
  • GC06M034550
  • GC06M035568
  • GC06M036281
  • GC06M036655
  • GC06M037008

Summaries for NUDT3 Gene

Entrez Gene Summary for NUDT3 Gene

  • NUDT3 belongs to the MutT, or Nudix, protein family. Nudix proteins act as homeostatic checkpoints at important stages in nucleoside phosphate metabolic pathways, guarding against elevated levels of potentially dangerous intermediates, like 8-oxo-dGTP, which promotes AT-to-CG transversions (Safrany et al., 1998 [PubMed 9822604]).[supplied by OMIM, Feb 2011]

GeneCards Summary for NUDT3 Gene

NUDT3 (Nudix Hydrolase 3) is a Protein Coding gene. Among its related pathways are Inositol phosphate metabolism (REACTOME) and Metabolism. GO annotations related to this gene include hydrolase activity and diphosphoinositol-polyphosphate diphosphatase activity. An important paralog of this gene is NUDT4.

UniProtKB/Swiss-Prot for NUDT3 Gene

  • Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate) and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate), suggesting that it may play a role in signal transduction. InsP6 (inositol hexakisphophate) is not a substrate. Acts as a negative regulator of the ERK1/2 pathway. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5-phosphoribose 1-diphosphate.

Gene Wiki entry for NUDT3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NUDT3 Gene

Genomics for NUDT3 Gene

Regulatory Elements for NUDT3 Gene

Enhancers for NUDT3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G033423 1.8 FANTOM5 ENCODE dbSUPER 10.1 +966.7 966716 3.9 HDGF PKNOX1 CREB3L1 ARNT AGO1 ARID4B SIN3A YBX1 DMAP1 FEZF1 DAXX WDR46 BRD2 VPS52 LEMD2 RXRB ZBTB9 KIFC1 RPL35AP4 SYNGAP1
GH06G033837 1.7 Ensembl ENCODE dbSUPER 10.1 +552.8 552780 4.2 HDGF PKNOX1 FOXA2 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B LEMD2 RING1 RXRB VPS52 WDR46 SYNGAP1 BRD2 IP6K3 DAXX ITPR3
GH06G033430 1.5 FANTOM5 ENCODE dbSUPER 10.1 +960.3 960261 4.5 HDGF ATF1 FOXA2 ARID4B SIN3A ZNF48 GLIS2 ELK1 ZNF143 FOS RING1 HCG25 DAXX ZBTB9 SYNGAP1 LEMD2 VPS52 SMIM29 PHF1 KIFC1
GH06G034390 1.4 ENCODE dbSUPER 10.8 +0.5 544 3.6 MLX CREB3L1 AGO1 ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF263 RPS10 ENSG00000272374 LEMD2 ITPR3 NUDT3 SYNGAP1 PIR34626
GH06G034314 1.5 Ensembl ENCODE dbSUPER 9.8 +74.7 74724 6.5 HDGF PKNOX1 ARNT ZNF766 CBX5 ZNF207 KLF13 TBX21 ZNF592 MEF2D RPS10 NUDT3 PIR34626
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NUDT3 on UCSC Golden Path with GeneCards custom track

Promoters for NUDT3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195948 580 2601 MLX CREB3L1 AGO1 ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 ZNF263

Genomic Location for NUDT3 Gene

Chromosome:
6
Start:
34,279,679 bp from pter
End:
34,392,680 bp from pter
Size:
113,002 bases
Orientation:
Minus strand

Genomic View for NUDT3 Gene

Genes around NUDT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NUDT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NUDT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NUDT3 Gene

Proteins for NUDT3 Gene

  • Protein details for NUDT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95989-NUDT3_HUMAN
    Recommended name:
    Diphosphoinositol polyphosphate phosphohydrolase 1
    Protein Accession:
    O95989
    Secondary Accessions:
    • B2R8N4

    Protein attributes for NUDT3 Gene

    Size:
    172 amino acids
    Molecular mass:
    19471 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for NUDT3 Gene

neXtProt entry for NUDT3 Gene

Post-translational modifications for NUDT3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NUDT3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NUDT3 Gene

Domains & Families for NUDT3 Gene

Gene Families for NUDT3 Gene

Protein Domains for NUDT3 Gene

Suggested Antigen Peptide Sequences for NUDT3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O95989

UniProtKB/Swiss-Prot:

NUDT3_HUMAN :
  • Belongs to the Nudix hydrolase family. DIPP subfamily.
Family:
  • Belongs to the Nudix hydrolase family. DIPP subfamily.
genes like me logo Genes that share domains with NUDT3: view

Function for NUDT3 Gene

Molecular function for NUDT3 Gene

GENATLAS Biochemistry:
nudix (nucleoside diphosphate linked moiety X)-type motif 3,hydrolase,most predominantly expressed in brain,heart,pancreas,liver,putative mouse cleaning gene whose functions is to cleanse the cell of potentially deleterious endogenous metabolites and to modulate the accumulation of intermediates in biochemical pathways
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=5.9 uM for Ap6A {ECO:0000269 PubMed:10419486, ECO:0000269 PubMed:12370170, ECO:0000269 PubMed:9822604}; KM=7.7 uM for Ap5A {ECO:0000269 PubMed:10419486, ECO:0000269 PubMed:12370170, ECO:0000269 PubMed:9822604}; KM=38 mM for 5-phosphoribose 1-diphosphate {ECO:0000269 PubMed:10419486, ECO:0000269 PubMed:12370170, ECO:0000269 PubMed:9822604}; KM=4.2 nM for PP-InsP5 {ECO:0000269 PubMed:10419486, ECO:0000269 PubMed:12370170, ECO:0000269 PubMed:9822604}; pH dependence: Optimum pH is 7-7.5. {ECO:0000269 PubMed:10419486, ECO:0000269 PubMed:12370170, ECO:0000269 PubMed:9822604};
UniProtKB/Swiss-Prot CatalyticActivity:
Diphospho-myo-inositol polyphosphate + H(2)O = myo-inositol polyphosphate + phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by fluoride and InsP6.
UniProtKB/Swiss-Prot Function:
Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate) and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate), suggesting that it may play a role in signal transduction. InsP6 (inositol hexakisphophate) is not a substrate. Acts as a negative regulator of the ERK1/2 pathway. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5-phosphoribose 1-diphosphate.

Enzyme Numbers (IUBMB) for NUDT3 Gene

Gene Ontology (GO) - Molecular Function for NUDT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IDA 19585659
GO:0000298 endopolyphosphatase activity IBA --
GO:0008486 diphosphoinositol-polyphosphate diphosphatase activity IDA,TAS 10585413
GO:0016787 hydrolase activity IEA --
GO:0034431 bis(5-adenosyl)-hexaphosphatase activity IBA --
genes like me logo Genes that share ontologies with NUDT3: view
genes like me logo Genes that share phenotypes with NUDT3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for NUDT3

CRISPR Products

miRNA for NUDT3 Gene

miRTarBase miRNAs that target NUDT3

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NUDT3 Gene

Localization for NUDT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NUDT3 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NUDT3 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 4

Gene Ontology (GO) - Cellular Components for NUDT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IEA,IBA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with NUDT3: view

Pathways & Interactions for NUDT3 Gene

genes like me logo Genes that share pathways with NUDT3: view

Pathways by source for NUDT3 Gene

Gene Ontology (GO) - Biological Process for NUDT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007267 cell-cell signaling TAS 10419486
GO:0015961 diadenosine polyphosphate catabolic process TAS 10419486
GO:0043647 inositol phosphate metabolic process TAS --
GO:0071544 diphosphoinositol polyphosphate catabolic process IDA 10585413
GO:1901907 diadenosine pentaphosphate catabolic process IBA --
genes like me logo Genes that share ontologies with NUDT3: view

No data available for SIGNOR curated interactions for NUDT3 Gene

Drugs & Compounds for NUDT3 Gene

(3) Drugs for NUDT3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Magnesium Nutra 0

(8) Additional Compounds for NUDT3 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-Diphosphoinositol pentakisphosphate
  • 1,2,3,4,6-Pentakis-O-phosphono-1D-myo-inositol 5-(trihydrogen diphosphate)
  • 1D-Myo-inositol 5-diphosphate pentakisphosphate
  • 5-Diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate
  • 5-Diphospho-1D-myo-inositol pentakisphosphate
  • 5-PP-InsP5
Diadenosine hexaphosphate
  • Adenosine 5'-(heptahydrogen hexaphosphate) P->5'-ester with adenosine
  • Adenosine 5'-(heptahydrogen hexaphosphate)5'-5'-ester with adenosine
  • Adenosine 5'-hexaphosphate 5'-ester with adenosine
  • Adenosine-(5')-hexaphospho-(5')-adenosine
  • Ap(6)A
56983-23-4
Myo-inositol hexakisphosphate
  • 1D-Myo-Inositol 1,2,3,4,5,6-hexakisphosphate
  • 1D-Myo-inositol hexakisphosphate
  • D-Myo-Inositol 1,2,3,4,5,6-hexakisphosphate
  • Inositol 1,2,3,4,5,6-hexakisphosphate
  • Myo-Inositol 1,2,3,4,5,6-hexakisphosphate
83-86-3
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2
genes like me logo Genes that share compounds with NUDT3: view

Transcripts for NUDT3 Gene

mRNA/cDNA for NUDT3 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(1683) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NUDT3 Gene

Nudix (nucleoside diphosphate linked moiety X)-type motif 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NUDT3 Gene

No ASD Table

Relevant External Links for NUDT3 Gene

GeneLoc Exon Structure for
NUDT3
ECgene alternative splicing isoforms for
NUDT3

Expression for NUDT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NUDT3 Gene

Protein differential expression in normal tissues from HIPED for NUDT3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (11.6) and Fetal Brain (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NUDT3 Gene



Protein tissue co-expression partners for NUDT3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NUDT3 Gene:

NUDT3

SOURCE GeneReport for Unigene cluster for NUDT3 Gene:

Hs.188882

mRNA Expression by UniProt/SwissProt for NUDT3 Gene:

O95989-NUDT3_HUMAN
Tissue specificity: Widely expressed. Expressed at higher level in brain, heart, pancreas and liver. Also expressed in placenta, lung and kidney.

Evidence on tissue expression from TISSUES for NUDT3 Gene

  • Nervous system(4.8)
  • Lung(3.1)
genes like me logo Genes that share expression patterns with NUDT3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NUDT3 Gene

Orthologs for NUDT3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NUDT3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPS10 35
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NUDT3 34 35
  • 95.74 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NUDT3 35
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NUDT3 35
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NUDT3 34 35
  • 91.86 (n)
mouse
(Mus musculus)
Mammalia Nudt3 34 16 35
  • 91.07 (n)
rat
(Rattus norvegicus)
Mammalia Nudt3 34
  • 88.89 (n)
chicken
(Gallus gallus)
Aves NUDT3 34 35
  • 85.8 (n)
lizard
(Anolis carolinensis)
Reptilia NUDT3 35
  • 91 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii nudt3a 35
  • 84 (a)
OneToMany
nudt3b 34 35
  • 76.22 (n)
zgc55746 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7396 34
fruit fly
(Drosophila melanogaster)
Insecta CG6391 36
  • 57 (a)
Aps 34 35
  • 56.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009901 34
  • 55.41 (n)
worm
(Caenorhabditis elegans)
Secernentea Y92H12BL.5 34 35
  • 49.48 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8787 35
  • 38 (a)
OneToMany
Species where no ortholog for NUDT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for NUDT3 Gene

ENSEMBL:
Gene Tree for NUDT3 (if available)
TreeFam:
Gene Tree for NUDT3 (if available)

Paralogs for NUDT3 Gene

Paralogs for NUDT3 Gene

(4) SIMAP similar genes for NUDT3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with NUDT3: view

Variants for NUDT3 Gene

Sequence variations from dbSNP and Humsavar for NUDT3 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000010018 -- 34,329,049(+) CTGGT(A/G)ACAAT intron-variant
rs1000045434 -- 34,388,209(+) ATTCT(A/G)TGATG intron-variant
rs1000059920 -- 34,368,519(+) AAAAC(A/G/T)TAGTA intron-variant
rs1000096375 -- 34,341,028(+) AATCA(A/G)TCTTA intron-variant
rs1000097815 -- 34,294,657(+) GGAGG(C/T)GGAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NUDT3 Gene

Variant ID Type Subtype PubMed ID
dgv10618n54 CNV loss 21841781
dgv10619n54 CNV loss 21841781
dgv10620n54 CNV loss 21841781
dgv10621n54 CNV loss 21841781
dgv10622n54 CNV loss 21841781
dgv10623n54 CNV loss 21841781
dgv1115e199 CNV deletion 23128226
esv2674771 CNV deletion 23128226
esv2731907 CNV deletion 23290073
esv29044 CNV loss 19812545
esv33496 CNV loss 17666407
esv3425871 CNV insertion 20981092
esv3567619 CNV deletion 23714750
esv3608655 CNV loss 21293372
esv3608656 CNV loss 21293372
esv3608657 CNV loss 21293372
nsv1034978 CNV gain 25217958
nsv473801 CNV novel sequence insertion 20440878
nsv5253 CNV insertion 18451855
nsv602863 CNV loss 21841781
nsv602886 CNV loss 21841781

Variation tolerance for NUDT3 Gene

Residual Variation Intolerance Score: 46.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.67; 14.27% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NUDT3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NUDT3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NUDT3 Gene

Disorders for NUDT3 Gene

Relevant External Links for NUDT3

Genetic Association Database (GAD)
NUDT3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NUDT3

No disorders were found for NUDT3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NUDT3 Gene

Publications for NUDT3 Gene

  1. A novel context for the 'MutT' module, a guardian of cell integrity, in a diphosphoinositol polyphosphate phosphohydrolase. (PMID: 9822604) Safrany S.T. … Shears S.B. (EMBO J. 1998) 2 3 4 22 64
  2. Nudix hydrolases that degrade dinucleoside and diphosphoinositol polyphosphates also have 5-phosphoribosyl 1-pyrophosphate (PRPP) pyrophosphatase activity that generates the glycolytic activator ribose 1,5-bisphosphate. (PMID: 12370170) Fisher D.I. … Cartwright J.L. (J. Biol. Chem. 2002) 3 4 22 64
  3. The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the human diphosphoinositol polyphosphate phosphohydrolase. Overlapping substrate specificities in a MutT-type protein. (PMID: 10419486) Safrany S.T. … Shears S.B. (J. Biol. Chem. 1999) 3 4 22 64
  4. Identification of 15 loci influencing height in a Korean population. (PMID: 19893584) Kim J.J. … Lee J.K. (J. Hum. Genet. 2010) 3 46 64
  5. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. (PMID: 20935630) Speliotes E.K. … Loos R.J. (Nat. Genet. 2010) 3 46 64

Products for NUDT3 Gene

Sources for NUDT3 Gene

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