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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
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Genomic context

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See NT5M in Genome Data Viewer
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

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