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Protein

5'(3')-deoxyribonucleotidase, cytosolic type

Gene

NT5C

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

Functioni

Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.

Cofactori

Mg2+1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei10NucleophileCurated1
Metal bindingi10Magnesium1
Active sitei12Proton donorCurated1
Metal bindingi12Magnesium; via carbonyl oxygen1
Binding sitei18Substrate1
Binding sitei44Substrate1
Binding sitei65SubstrateBy similarity1
Binding sitei99SubstrateCurated1
Binding sitei134SubstrateCurated1
Metal bindingi145Magnesium1

GO - Molecular functioni

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

GO - Biological processi

  • dephosphorylation Source: UniProtKB
  • purine nucleotide catabolic process Source: Reactome
  • pyrimidine deoxyribonucleotide catabolic process Source: UniProtKB
  • 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.
R-HSA-74259. Purine catabolism.
SABIO-RKQ8TCD5.

Names & Taxonomyi

Protein namesi
Recommended name:
5'(3')-deoxyribonucleotidase, cytosolic type (EC:3.1.3.-)
Alternative name(s):
Cytosolic 5',3'-pyrimidine nucleotidase
Deoxy-5'-nucleotidase 1
Short name:
dNT-1
Gene namesi
Name:NT5C
Synonyms:DNT1, UMPH2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:17144. NT5C.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: Reactome
  • extracellular exosome Source: UniProtKB
  • mitochondrion Source: Ensembl
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi30833.
OpenTargetsiENSG00000125458.
PharmGKBiPA31798.

Chemistry databases

DrugBankiDB00709. Lamivudine.

Polymorphism and mutation databases

BioMutaiNT5C.
DMDMi38258193.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001643711 – 2015'(3')-deoxyribonucleotidase, cytosolic typeAdd BLAST201

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei182PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8TCD5.
PaxDbiQ8TCD5.
PeptideAtlasiQ8TCD5.
PRIDEiQ8TCD5.

2D gel databases

OGPiQ8TCD5.

PTM databases

DEPODiQ8TCD5.
iPTMnetiQ8TCD5.
PhosphoSitePlusiQ8TCD5.

Expressioni

Tissue specificityi

Detected in skeletal muscle, heart and pancreas.1 Publication

Gene expression databases

BgeeiENSG00000125458.
CleanExiHS_NT5C.
ExpressionAtlasiQ8TCD5. baseline and differential.
GenevisibleiQ8TCD5. HS.

Organism-specific databases

HPAiHPA021581.
HPA023632.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi119049. 7 interactors.
IntActiQ8TCD5. 1 interactor.
STRINGi9606.ENSP00000245552.

Structurei

Secondary structure

1201
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 9Combined sources5
Turni13 – 15Combined sources3
Helixi18 – 29Combined sources12
Helixi38 – 40Combined sources3
Helixi46 – 53Combined sources8
Helixi57 – 65Combined sources9
Turni68 – 73Combined sources6
Helixi80 – 89Combined sources10
Beta strandi93 – 99Combined sources7
Turni106 – 108Combined sources3
Helixi109 – 120Combined sources12
Helixi122 – 125Combined sources4
Beta strandi128 – 130Combined sources3
Helixi134 – 136Combined sources3
Beta strandi140 – 147Combined sources8
Beta strandi157 – 163Combined sources7
Helixi166 – 168Combined sources3
Beta strandi177 – 180Combined sources4
Helixi187 – 192Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2I7DX-ray1.20A/B3-195[»]
4L57X-ray1.08A/B1-195[»]
4YIHX-ray1.82A/B1-195[»]
ProteinModelPortaliQ8TCD5.
SMRiQ8TCD5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8TCD5.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG410IHG0. Eukaryota.
ENOG410XQYS. LUCA.
GeneTreeiENSGT00390000011596.
HOGENOMiHOG000236944.
HOVERGENiHBG045599.
KOiK01081.
OMAiFTCCHNR.
OrthoDBiEOG091G0L73.
PhylomeDBiQ8TCD5.
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.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8TCD5-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MARSVRVLVD MDGVLADFEA GLLRGFRRRF PEEPHVPLEQ RRGFLAREQY
60 70 80 90 100
RALRPDLADK VASVYEAPGF FLDLEPIPGA LDAVREMNDL PDTQVFICTS
110 120 130 140 150
PLLKYHHCVG EKYRWVEQHL GPQFVERIIL TRDKTVVLGD LLIDDKDTVR
160 170 180 190 200
GQEETPSWEH ILFTCCHNRH LVLPPTRRRL LSWSDNWREI LDSKRGAAQR

E
Length:201
Mass (Da):23,383
Last modified:October 31, 2003 - v2
Checksum:iC4C289BBDEC0FA89
GO
Isoform 2 (identifier: Q8TCD5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     93-100: Missing.
     113-125: YRWVEQHLGPQFV → VWLPRPYSARGAA
     126-201: Missing.

Note: No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Show »
Length:117
Mass (Da):13,299
Checksum:i014A63DE1B5347F6
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04810268P → L.1 PublicationCorresponds to variant rs11541956dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00871093 – 100Missing in isoform 2. 1 Publication8
Alternative sequenceiVSP_008711113 – 125YRWVE…GPQFV → VWLPRPYSARGAA in isoform 2. 1 PublicationAdd BLAST13
Alternative sequenceiVSP_008712126 – 201Missing in isoform 2. 1 PublicationAdd BLAST76

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF154829 mRNA. Translation: AAF36534.2.
AK000419 mRNA. Translation: BAA91151.1.
AC022211 Genomic DNA. No translation available.
BC008183 mRNA. Translation: AAH08183.1.
BC017454 mRNA. Translation: AAH17454.1.
BC022334 mRNA. Translation: AAH22334.1.
BK000192 Genomic DNA. Translation: DAA00070.1.
CCDSiCCDS11715.1. [Q8TCD5-1]
RefSeqiNP_001239306.1. NM_001252377.1.
NP_055410.1. NM_014595.2. [Q8TCD5-1]
UniGeneiHs.67201.

Genome annotation databases

EnsembliENST00000245552; ENSP00000245552; ENSG00000125458. [Q8TCD5-1]
ENST00000580758; ENSP00000462123; ENSG00000125458. [Q8TCD5-2]
GeneIDi30833.
KEGGihsa:30833.
UCSCiuc060jte.1. human. [Q8TCD5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF154829 mRNA. Translation: AAF36534.2.
AK000419 mRNA. Translation: BAA91151.1.
AC022211 Genomic DNA. No translation available.
BC008183 mRNA. Translation: AAH08183.1.
BC017454 mRNA. Translation: AAH17454.1.
BC022334 mRNA. Translation: AAH22334.1.
BK000192 Genomic DNA. Translation: DAA00070.1.
CCDSiCCDS11715.1. [Q8TCD5-1]
RefSeqiNP_001239306.1. NM_001252377.1.
NP_055410.1. NM_014595.2. [Q8TCD5-1]
UniGeneiHs.67201.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2I7DX-ray1.20A/B3-195[»]
4L57X-ray1.08A/B1-195[»]
4YIHX-ray1.82A/B1-195[»]
ProteinModelPortaliQ8TCD5.
SMRiQ8TCD5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119049. 7 interactors.
IntActiQ8TCD5. 1 interactor.
STRINGi9606.ENSP00000245552.

Chemistry databases

DrugBankiDB00709. Lamivudine.

PTM databases

DEPODiQ8TCD5.
iPTMnetiQ8TCD5.
PhosphoSitePlusiQ8TCD5.

Polymorphism and mutation databases

BioMutaiNT5C.
DMDMi38258193.

2D gel databases

OGPiQ8TCD5.

Proteomic databases

EPDiQ8TCD5.
PaxDbiQ8TCD5.
PeptideAtlasiQ8TCD5.
PRIDEiQ8TCD5.

Protocols and materials databases

DNASUi30833.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000245552; ENSP00000245552; ENSG00000125458. [Q8TCD5-1]
ENST00000580758; ENSP00000462123; ENSG00000125458. [Q8TCD5-2]
GeneIDi30833.
KEGGihsa:30833.
UCSCiuc060jte.1. human. [Q8TCD5-1]

Organism-specific databases

CTDi30833.
DisGeNETi30833.
GeneCardsiNT5C.
HGNCiHGNC:17144. NT5C.
HPAiHPA021581.
HPA023632.
MIMi191720. gene.
neXtProtiNX_Q8TCD5.
OpenTargetsiENSG00000125458.
PharmGKBiPA31798.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IHG0. Eukaryota.
ENOG410XQYS. LUCA.
GeneTreeiENSGT00390000011596.
HOGENOMiHOG000236944.
HOVERGENiHBG045599.
KOiK01081.
OMAiFTCCHNR.
OrthoDBiEOG091G0L73.
PhylomeDBiQ8TCD5.
TreeFamiTF331117.

Enzyme and pathway databases

ReactomeiR-HSA-73621. Pyrimidine catabolism.
R-HSA-74259. Purine catabolism.
SABIO-RKQ8TCD5.

Miscellaneous databases

EvolutionaryTraceiQ8TCD5.
GeneWikiiNT5C.
GenomeRNAii30833.
PROiQ8TCD5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000125458.
CleanExiHS_NT5C.
ExpressionAtlasiQ8TCD5. baseline and differential.
GenevisibleiQ8TCD5. 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 nameiNT5C_HUMAN
AccessioniPrimary (citable) accession number: Q8TCD5
Secondary accession number(s): Q96HS6, Q9NP82
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2003
Last sequence update: October 31, 2003
Last modified: November 2, 2016
This is version 135 of the entry and version 2 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.