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    NT5M 5',3'-nucleotidase, mitochondrial [ Homo sapiens (human) ]

    Gene ID: 56953, updated on 5-Mar-2024

    Summary

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    Official Symbol
    NT5Mprovided by HGNC
    Official Full Name
    5',3'-nucleotidase, mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:15769
    See related
    Ensembl:ENSG00000205309 MIM:605292; AllianceGenome:HGNC:15769
    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
    mdN; dNT2; dNT-2
    Summary
    This gene encodes a 5' nucleotidase that localizes to the mitochondrial matrix. This enzyme dephosphorylates the 5'- and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 2.8), bone marrow (RPKM 2.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17p11.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (17303373..17347663)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17249440..17292730)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17206687..17250977)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17154504-17154606 Neighboring gene actin gamma 1 pseudogene 24 Neighboring gene COP9 signalosome subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11795 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17204068-17204643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17229781-17230281 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17254745-17255324 Neighboring gene Sharpr-MPRA regulatory region 4579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17258250-17258750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17258751-17259251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17291286-17291786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11799 Neighboring gene ribosomal protein L13 pseudogene 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17306668-17307222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17307223-17307775 Neighboring gene Sharpr-MPRA regulatory region 14253 Neighboring gene NFE2L2 motif-containing MPRA enhancer 126 Neighboring gene ligand of numb-protein X 1, E3 ubiquitin protein ligase pseudogene

    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. Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase. Pachl P, et al. J Enzyme Inhib Med Chem, 2015 Feb. PMID 24506201
    2. Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase. Walldén K, et al. Structure, 2005 Jul. PMID 16004879
    3. Crystal structure of a human mitochondrial deoxyribonucleotidase. Rinaldo-Matthis A, et al. Nat Struct Biol, 2002 Oct. PMID 12352955
    4. Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects. Gallinaro L, et al. J Biol Chem, 2002 Sep 20. PMID 12124385
    5. A deoxyribonucleotidase in mitochondria: involvement in regulation of dNTP pools and possible link to genetic disease. Rampazzo C, et al. Proc Natl Acad Sci U S A, 2000 Jul 18. PMID 10899995, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. An alternative splice variant of the mdN gene containing an 18-nucleotide insertion encoding 6 amino acids (GKWPAT) at the 3'-end of the penultimate exon 4 has been characterized.
      Title: Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    3. substrate specificity analysis of the human mitochondrial deoxyribonucleotidase
      Title: Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase.
    4. Overproduction in cultured cells and functional aspects
      Title: Human mitochondrial 5'-deoxyribonucleotidase. Overproduction in cultured cells and functional aspects.
    5. structures of dNT-2 in complex with bound phosphate and beryllium trifluoride plus thymidine as model for a phosphoenzyme-product complex
      Title: Crystal structure of a human mitochondrial deoxyribonucleotidase.
    Submit: New GeneRIF Correction

    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

    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 5'-nucleotidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotidase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA replication TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in dUMP catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in pyrimidine deoxyribonucleotide catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    5'(3')-deoxyribonucleotidase, mitochondrial
    Names
    5' nucleotidase, mitochondrial
    5(3)-deoxyribonucleotidase
    deoxy-5'-nucleotidase 2
    mitochondrial 5' nucleotidase
    NP_064586.1
    XP_005256788.1
    XP_005256789.1
    XP_011522264.1
    XP_011522266.1
    XP_011522268.1
    XP_011522269.1
    XP_047292375.1
    XP_047292376.1
    XP_047292377.1
    XP_047292378.1
    XP_054172673.1
    XP_054172674.1
    XP_054172675.1
    XP_054172676.1
    XP_054172677.1
    XP_054172678.1
    XP_054172679.1
    XP_054172680.1
    XP_054172681.1
    XP_054172682.1

    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_020201.4 → NP_064586.1  5'(3')-deoxyribonucleotidase, mitochondrial precursor

      See identical proteins and their annotated locations for NP_064586.1

      Status: REVIEWED

      Source sequence(s)
      AF210652, AL526346, BC035838
      Consensus CDS
      CCDS32581.1
      UniProtKB/Swiss-Prot
      Q9NPB1
      Related
      ENSP00000373674.4, ENST00000389022.9
      Conserved Domains (2) summary
      pfam00702
      Location:38 → 168
      Hydrolase; haloacid dehalogenase-like hydrolase
      cl21460
      Location:38 → 225
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    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
      17303373..17347663
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436421.1 → XP_047292377.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X6

    2. XM_047436419.1 → XP_047292375.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X1

    3. XM_011523967.3 → XP_011522269.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X2

      Conserved Domains (2) summary
      pfam00702
      Location:38 → 131
      Hydrolase; haloacid dehalogenase-like hydrolase
      cl21460
      Location:38 → 262
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    4. XM_047436422.1 → XP_047292378.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X7

    5. XM_047436420.1 → XP_047292376.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X3

    6. XM_005256731.4 → XP_005256788.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X4

      Conserved Domains (2) summary
      pfam00702
      Location:38 → 168
      Hydrolase; haloacid dehalogenase-like hydrolase
      cl21460
      Location:38 → 250
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    7. XM_005256732.4 → XP_005256789.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X5

      See identical proteins and their annotated locations for XP_005256789.1

      UniProtKB/TrEMBL
      A6NCJ5, Q2I378
      Related
      ENSP00000481269.1, ENST00000616989.1
      Conserved Domains (2) summary
      pfam00702
      Location:38 → 168
      Hydrolase; haloacid dehalogenase-like hydrolase
      cl21460
      Location:38 → 231
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    8. XM_011523966.2 → XP_011522268.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X10

      Conserved Domains (2) summary
      pfam00702
      Location:38 → 131
      Hydrolase; haloacid dehalogenase-like hydrolase
      cl21460
      Location:38 → 120
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    9. XM_011523962.3 → XP_011522264.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X8

      Conserved Domains (2) summary
      pfam00702
      Location:38 → 131
      Hydrolase; haloacid dehalogenase-like hydrolase
      cl21460
      Location:38 → 120
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    10. XM_011523964.2 → XP_011522266.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X9

      See identical proteins and their annotated locations for XP_011522266.1

      Conserved Domains (1) summary
      cl21460
      Location:51 → 145
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      17249440..17292730
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316703.1 → XP_054172678.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X6

    2. XM_054316698.1 → XP_054172673.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X1

    3. XM_054316699.1 → XP_054172674.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X2

    4. XM_054316704.1 → XP_054172679.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X7

    5. XM_054316700.1 → XP_054172675.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X3

    6. XM_054316701.1 → XP_054172676.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X4

    7. XM_054316702.1 → XP_054172677.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X5

      UniProtKB/TrEMBL
      A6NCJ5, Q2I378

    8. XM_054316707.1 → XP_054172682.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X10

    9. XM_054316705.1 → XP_054172680.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X8

    10. XM_054316706.1 → XP_054172681.1  5'(3')-deoxyribonucleotidase, mitochondrial isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NPB1.1 GenPept UniProtKB/Swiss-Prot:Q9NPB1

    Gene LinkOut

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

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