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Protein

5'(3')-deoxyribonucleotidase, mitochondrial

Gene

NT5M

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.1 Publication

Cofactori

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei41 – 411Nucleophile
Metal bindingi41 – 411Magnesium1 Publication
Active sitei43 – 431Proton donorCurated
Metal bindingi43 – 431Magnesium; via carbonyl oxygen1 Publication
Binding sitei43 – 431Substrate
Binding sitei49 – 491Substrate
Binding sitei75 – 751Substrate
Binding sitei76 – 761Substrate
Binding sitei77 – 771Substrate; via amide nitrogen
Binding sitei96 – 961Substrate
Binding sitei130 – 1301Substrate
Binding sitei165 – 1651Substrate
Metal bindingi176 – 1761Magnesium1 Publication

GO - Molecular functioni

  • 5'-nucleotidase activity Source: Reactome
  • metal ion binding Source: UniProtKB-KW
  • nucleotidase activity Source: ProtInc
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  • DNA replication Source: ProtInc
  • dUMP catabolic process Source: Ensembl
  • pyrimidine deoxyribonucleotide catabolic process Source: ProtInc
  • pyrimidine nucleoside catabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-73621. Pyrimidine catabolism.
SABIO-RKQ9NPB1.

Names & Taxonomyi

Protein namesi
Recommended name:
5'(3')-deoxyribonucleotidase, mitochondrial (EC:3.1.3.-)
Short name:
5',3'-nucleotidase, mitochondrial
Alternative name(s):
Deoxy-5'-nucleotidase 2
Short name:
dNT-2
Gene namesi
Name:NT5M
Synonyms:DNT2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:15769. NT5M.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial matrix Source: Reactome
  • mitochondrion Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA31805.

Polymorphism and mutation databases

BioMutaiNT5M.
DMDMi38258255.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3131MitochondrionSequence analysisAdd
BLAST
Chaini32 – 2281975'(3')-deoxyribonucleotidase, mitochondrialPRO_0000000011Add
BLAST

Proteomic databases

PaxDbiQ9NPB1.
PeptideAtlasiQ9NPB1.
PRIDEiQ9NPB1.

PTM databases

DEPODiQ9NPB1.
iPTMnetiQ9NPB1.
PhosphoSiteiQ9NPB1.

Expressioni

Tissue specificityi

Highly expressed in heart, brain and skeletal muscle. Detected at very low levels in kidney and pancreas.1 Publication

Gene expression databases

BgeeiQ9NPB1.
CleanExiHS_NT5M.
ExpressionAtlasiQ9NPB1. baseline and differential.
GenevisibleiQ9NPB1. HS.

Organism-specific databases

HPAiHPA043777.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi121277. 1 interaction.
STRINGi9606.ENSP00000373674.

Structurei

Secondary structure

1
228
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi36 – 405Combined sources
Turni44 – 463Combined sources
Helixi49 – 6012Combined sources
Helixi69 – 713Combined sources
Helixi77 – 848Combined sources
Helixi88 – 969Combined sources
Turni99 – 1046Combined sources
Helixi111 – 12010Combined sources
Beta strandi124 – 1307Combined sources
Turni136 – 1383Combined sources
Helixi139 – 15113Combined sources
Helixi153 – 1586Combined sources
Beta strandi159 – 1613Combined sources
Helixi165 – 1673Combined sources
Beta strandi171 – 1766Combined sources
Beta strandi188 – 1947Combined sources
Turni197 – 2015Combined sources
Beta strandi209 – 2113Combined sources
Helixi218 – 2236Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MH9X-ray1.80A32-228[»]
1Q91X-ray1.60A32-228[»]
1Q92X-ray1.40A32-228[»]
1Z4IX-ray1.98A32-228[»]
1Z4JX-ray1.80A32-228[»]
1Z4KX-ray1.75A32-228[»]
1Z4LX-ray1.80A32-228[»]
1Z4MX-ray1.70A32-228[»]
1Z4PX-ray2.00X32-228[»]
1Z4QX-ray2.05A32-228[»]
2JAUX-ray1.80A32-228[»]
2JAWX-ray1.95A32-228[»]
4L6AX-ray1.40A32-228[»]
4L6CX-ray1.80A32-228[»]
4MUMX-ray1.27A32-227[»]
4MWOX-ray1.67A32-227[»]
4NFLX-ray1.38A32-227[»]
4YIKX-ray1.48A32-227[»]
ProteinModelPortaliQ9NPB1.
SMRiQ9NPB1. Positions 33-227.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NPB1.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IHG0. Eukaryota.
ENOG410XQYS. LUCA.
GeneTreeiENSGT00390000011596.
HOGENOMiHOG000236944.
HOVERGENiHBG045599.
KOiK01081.
OrthoDBiEOG7CRTQX.
PhylomeDBiQ9NPB1.
TreeFamiTF331117.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR010708. 5'(3')-deoxyribonucleotidase.
IPR023214. HAD-like_dom.
[Graphical view]
PfamiPF06941. NT5C. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9NPB1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIRLGGWCAR RLCSAAVPAG RRGAAGGLGL AGGRALRVLV DMDGVLADFE
60 70 80 90 100
GGFLRKFRAR FPDQPFIALE DRRGFWVSEQ YGRLRPGLSE KAISIWESKN
110 120 130 140 150
FFFELEPLPG AVEAVKEMAS LQNTDVFICT SPIKMFKYCP YEKYAWVEKY
160 170 180 190 200
FGPDFLEQIV LTRDKTVVSA DLLIDDRPDI TGAEPTPSWE HVLFTACHNQ
210 220
HLQLQPPRRR LHSWADDWKA ILDSKRPC
Length:228
Mass (Da):25,862
Last modified:October 1, 2000 - v1
Checksum:i9AE6F57B16977F0F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ277557 Genomic DNA. Translation: CAB99251.1.
AF210652 mRNA. Translation: AAF87076.1.
BC035838 mRNA. Translation: AAH35838.1.
CCDSiCCDS32581.1.
RefSeqiNP_064586.1. NM_020201.3.
UniGeneiHs.513977.

Genome annotation databases

EnsembliENST00000389022; ENSP00000373674; ENSG00000205309.
GeneIDi56953.
KEGGihsa:56953.
UCSCiuc002grf.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ277557 Genomic DNA. Translation: CAB99251.1.
AF210652 mRNA. Translation: AAF87076.1.
BC035838 mRNA. Translation: AAH35838.1.
CCDSiCCDS32581.1.
RefSeqiNP_064586.1. NM_020201.3.
UniGeneiHs.513977.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MH9X-ray1.80A32-228[»]
1Q91X-ray1.60A32-228[»]
1Q92X-ray1.40A32-228[»]
1Z4IX-ray1.98A32-228[»]
1Z4JX-ray1.80A32-228[»]
1Z4KX-ray1.75A32-228[»]
1Z4LX-ray1.80A32-228[»]
1Z4MX-ray1.70A32-228[»]
1Z4PX-ray2.00X32-228[»]
1Z4QX-ray2.05A32-228[»]
2JAUX-ray1.80A32-228[»]
2JAWX-ray1.95A32-228[»]
4L6AX-ray1.40A32-228[»]
4L6CX-ray1.80A32-228[»]
4MUMX-ray1.27A32-227[»]
4MWOX-ray1.67A32-227[»]
4NFLX-ray1.38A32-227[»]
4YIKX-ray1.48A32-227[»]
ProteinModelPortaliQ9NPB1.
SMRiQ9NPB1. Positions 33-227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121277. 1 interaction.
STRINGi9606.ENSP00000373674.

PTM databases

DEPODiQ9NPB1.
iPTMnetiQ9NPB1.
PhosphoSiteiQ9NPB1.

Polymorphism and mutation databases

BioMutaiNT5M.
DMDMi38258255.

Proteomic databases

PaxDbiQ9NPB1.
PeptideAtlasiQ9NPB1.
PRIDEiQ9NPB1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000389022; ENSP00000373674; ENSG00000205309.
GeneIDi56953.
KEGGihsa:56953.
UCSCiuc002grf.4. human.

Organism-specific databases

CTDi56953.
GeneCardsiNT5M.
HGNCiHGNC:15769. NT5M.
HPAiHPA043777.
MIMi605292. gene.
neXtProtiNX_Q9NPB1.
PharmGKBiPA31805.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IHG0. Eukaryota.
ENOG410XQYS. LUCA.
GeneTreeiENSGT00390000011596.
HOGENOMiHOG000236944.
HOVERGENiHBG045599.
KOiK01081.
OrthoDBiEOG7CRTQX.
PhylomeDBiQ9NPB1.
TreeFamiTF331117.

Enzyme and pathway databases

ReactomeiR-HSA-73621. Pyrimidine catabolism.
SABIO-RKQ9NPB1.

Miscellaneous databases

EvolutionaryTraceiQ9NPB1.
GenomeRNAii56953.
PROiQ9NPB1.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NPB1.
CleanExiHS_NT5M.
ExpressionAtlasiQ9NPB1. baseline and differential.
GenevisibleiQ9NPB1. HS.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR010708. 5'(3')-deoxyribonucleotidase.
IPR023214. HAD-like_dom.
[Graphical view]
PfamiPF06941. NT5C. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A deoxyribonucleotidase in mitochondria: involvement in regulation of dNTP pools and possible link to genetic disease."
    Rampazzo C., Gallinaro L., Milanesi E., Frigimelica E., Reichard P., Bianchi V.
    Proc. Natl. Acad. Sci. U.S.A. 97:8239-8244(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
    Tissue: Muscle.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Hippocampus.
  3. "Crystal structure of a human mitochondrial deoxyribonucleotidase."
    Rinaldo-Matthis A., Rampazzo C., Reichard P., Bianchi V., Nordlund P.
    Nat. Struct. Biol. 9:779-787(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 34-227 IN COMPLEX WITH MAGNESIUM AND A SUBSTRATE ANALOG.

Entry informationi

Entry nameiNT5M_HUMAN
AccessioniPrimary (citable) accession number: Q9NPB1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2003
Last sequence update: October 1, 2000
Last modified: July 6, 2016
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.