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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)DescriptionActionsGraphical viewLength
Active sitei41Nucleophile1
Metal bindingi41Magnesium1 Publication1
Active sitei43Proton donorCurated1
Metal bindingi43Magnesium; via carbonyl oxygen1 Publication1
Binding sitei43Substrate1
Binding sitei49Substrate1
Binding sitei75Substrate1
Binding sitei76Substrate1
Binding sitei77Substrate; via amide nitrogen1
Binding sitei96Substrate1
Binding sitei130Substrate1
Binding sitei165Substrate1
Metal bindingi176Magnesium1 Publication1

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

DisGeNETi56953.
OpenTargetsiENSG00000205309.
PharmGKBiPA31805.

Polymorphism and mutation databases

BioMutaiNT5M.
DMDMi38258255.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 31MitochondrionSequence analysisAdd BLAST31
ChainiPRO_000000001132 – 2285'(3')-deoxyribonucleotidase, mitochondrialAdd BLAST197

Proteomic databases

PaxDbiQ9NPB1.
PeptideAtlasiQ9NPB1.
PRIDEiQ9NPB1.

PTM databases

DEPODiQ9NPB1.
iPTMnetiQ9NPB1.
PhosphoSitePlusiQ9NPB1.

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

BgeeiENSG00000205309.
CleanExiHS_NT5M.
ExpressionAtlasiQ9NPB1. baseline and differential.
GenevisibleiQ9NPB1. HS.

Organism-specific databases

HPAiHPA043777.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi121277. 1 interactor.
STRINGi9606.ENSP00000373674.

Structurei

Secondary structure

1228
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi36 – 40Combined sources5
Turni44 – 46Combined sources3
Helixi49 – 60Combined sources12
Helixi69 – 71Combined sources3
Helixi77 – 84Combined sources8
Helixi88 – 96Combined sources9
Turni99 – 104Combined sources6
Helixi111 – 120Combined sources10
Beta strandi124 – 130Combined sources7
Turni136 – 138Combined sources3
Helixi139 – 151Combined sources13
Helixi153 – 158Combined sources6
Beta strandi159 – 161Combined sources3
Helixi165 – 167Combined sources3
Beta strandi171 – 176Combined sources6
Beta strandi188 – 194Combined sources7
Turni197 – 201Combined sources5
Beta strandi209 – 211Combined sources3
Helixi218 – 223Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NPB1.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IHG0. Eukaryota.
ENOG410XQYS. LUCA.
GeneTreeiENSGT00390000011596.
HOGENOMiHOG000236944.
HOVERGENiHBG045599.
KOiK01081.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121277. 1 interactor.
STRINGi9606.ENSP00000373674.

PTM databases

DEPODiQ9NPB1.
iPTMnetiQ9NPB1.
PhosphoSitePlusiQ9NPB1.

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.
DisGeNETi56953.
GeneCardsiNT5M.
HGNCiHGNC:15769. NT5M.
HPAiHPA043777.
MIMi605292. gene.
neXtProtiNX_Q9NPB1.
OpenTargetsiENSG00000205309.
PharmGKBiPA31805.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiQ9NPB1.
GenomeRNAii56953.
PROiQ9NPB1.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000205309.
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...

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: November 2, 2016
This is version 128 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.