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Protein

2'-deoxynucleoside 5'-phosphate N-hydrolase 1

Gene

Dnph1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine bases are preferred to those containing pyrimidine bases.UniRule annotation4 Publications

Catalytic activityi

A deoxyribonucleoside 5'-monophosphate + H20 = deoxyribose 5-monophosphate + a purine or pyrimidine base.UniRule annotation4 Publications

Enzyme regulationi

Inhibited by zinc ions. Competitive inhibition of dGMP hydrolysis by GMP and 6-methylthio-GMP.1 Publication

Kineticsi

  1. KM=48 µM for dGMP1 Publication
  2. KM=250 µM for dAMP1 Publication
  3. KM=450 µM for dIMP1 Publication
  4. KM=4 mM for dCMP1 Publication
  5. KM=15.6 mM for dUMP1 Publication
  1. Vmax=0.09 µmol/min/mg enzyme toward dGMP1 Publication

pH dependencei

Optimum pH is 6.0 with dGMP or dCMP as substrate.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei28Substrate1 Publication1
Binding sitei45Substrate2 Publications1
Binding sitei93Substrate5 Publications1

GO - Molecular functioni

  • deoxyribonucleoside 5'-monophosphate N-glycosidase activity Source: UniProtKB
  • nucleoside deoxyribosyltransferase activity Source: InterPro
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Nucleotide metabolism

Names & Taxonomyi

Protein namesi
Recommended name:
2'-deoxynucleoside 5'-phosphate N-hydrolase 1UniRule annotation (EC:3.2.2.-UniRule annotation4 Publications)
Alternative name(s):
Deoxyribonucleoside 5'-monophosphate N-glycosidase
c-Myc-responsive protein RclUniRule annotation
Gene namesi
Name:Dnph1
Synonyms:Rcl
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 9

Organism-specific databases

RGDi620382. Dnph1.

Subcellular locationi

  • Cytoplasm UniRule annotation
  • Nucleus UniRule annotation1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • extracellular exosome Source: Ensembl
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi13Y → A: 100-fold decrease binding affinity for GMP as substrate. 1 Publication1
Mutagenesisi93E → A: 100-fold increase in Km and 170-fold decrease in catalytic efficiency for dGMP as substrate. 2 Publications1

Chemistry databases

ChEMBLiCHEMBL3329079.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedUniRule annotationBy similarity1 Publication
ChainiPRO_00000972022 – 1632'-deoxynucleoside 5'-phosphate N-hydrolase 1Add BLAST162

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei17PhosphoserineBy similarity1
Modified residuei87PhosphoserineBy similarity1
Modified residuei112PhosphoserineBy similarity1
Modified residuei117PhosphoserineCombined sources1
Modified residuei127PhosphoserineBy similarity1
Modified residuei158PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiO35820.
PRIDEiO35820.

PTM databases

iPTMnetiO35820.
PhosphoSitePlusiO35820.

Expressioni

Tissue specificityi

Highly expressed in heart, kidney, liver and spleen. Weakly expressed in lung and skeletal muscle.1 Publication

Inductioni

Up-regulated in response to c-Myc and by partial hepatectomy.1 Publication

Gene expression databases

BgeeiENSRNOG00000018397.
GenevisibleiO35820. RN.

Interactioni

Subunit structurei

Monomer and homodimer.UniRule annotation4 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000024815.

Chemistry databases

BindingDBiO35820.

Structurei

Secondary structure

1163
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 15Combined sources5
Beta strandi22 – 24Combined sources3
Helixi25 – 35Combined sources11
Turni36 – 38Combined sources3
Beta strandi39 – 41Combined sources3
Helixi44 – 46Combined sources3
Beta strandi50 – 52Combined sources3
Helixi59 – 61Combined sources3
Helixi62 – 75Combined sources14
Beta strandi77 – 82Combined sources6
Helixi88 – 100Combined sources13
Beta strandi104 – 108Combined sources5
Helixi110 – 112Combined sources3
Helixi118 – 121Combined sources4
Turni126 – 128Combined sources3
Beta strandi129 – 133Combined sources5
Helixi136 – 138Combined sources3
Helixi139 – 150Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KHZNMR-A/B1-163[»]
2KLHNMR-A/B11-151[»]
4FYHX-ray2.44A/B/C/D11-151[»]
4FYIX-ray1.96A/B/C/D11-151[»]
4FYKX-ray1.79A/B/C/D11-151[»]
4KXLX-ray1.69A/B/C/D11-151[»]
4KXMX-ray2.24A/B/C/D11-151[»]
4KXNX-ray1.90A/B/C/D11-151[»]
4P5DX-ray2.11A/C11-151[»]
ProteinModelPortaliO35820.
SMRiO35820.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO35820.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni13 – 19Substrate binding5 Publications7
Regioni117 – 119Substrate binding; shared with homodimeric partner5 Publications3

Sequence similaritiesi

Belongs to the 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family.UniRule annotation

Phylogenomic databases

eggNOGiENOG410IVY6. Eukaryota.
ENOG4111SC2. LUCA.
GeneTreeiENSGT00390000001216.
HOGENOMiHOG000015361.
HOVERGENiHBG079123.
InParanoidiO35820.
OMAiRAVDMKK.
OrthoDBiEOG091G0WTP.
PhylomeDBiO35820.
TreeFamiTF329719.

Family and domain databases

Gene3Di3.40.50.1810. 1 hit.
HAMAPiMF_03036. Nuc_phosphate_hydrolase. 1 hit.
InterProiIPR028607. DNPH1.
IPR007710. Nucleoside_deoxyribTrfase.
[Graphical view]
PfamiPF05014. Nuc_deoxyrib_tr. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O35820-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAASGEQAPC SVYFCGSIRG GREDQALYAR IVSRLRRYGK VLTEHVADAE
60 70 80 90 100
LEPLGEEAAG GDQFIHEQDL NWLQQADVVV AEVTQPSLGV GYELGRAVAL
110 120 130 140 150
GKPILCLFRP QSGRVLSAMI RGAADGSRFQ VWDYAEGEVE TMLDRYFEAY
160
LPQKTASSSH PSA
Length:163
Mass (Da):17,781
Last modified:January 1, 1998 - v1
Checksum:iC670D4213F96D883
GO

Mass spectrometryi

Molecular mass is 17649.54±0.92 Da from positions 2 - 163. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82591 mRNA. Translation: AAB95314.1.
RefSeqiNP_598209.1. NM_133525.1.
UniGeneiRn.6997.

Genome annotation databases

EnsembliENSRNOT00000024815; ENSRNOP00000024815; ENSRNOG00000018397.
GeneIDi171047.
KEGGirno:171047.
UCSCiRGD:620382. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82591 mRNA. Translation: AAB95314.1.
RefSeqiNP_598209.1. NM_133525.1.
UniGeneiRn.6997.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KHZNMR-A/B1-163[»]
2KLHNMR-A/B11-151[»]
4FYHX-ray2.44A/B/C/D11-151[»]
4FYIX-ray1.96A/B/C/D11-151[»]
4FYKX-ray1.79A/B/C/D11-151[»]
4KXLX-ray1.69A/B/C/D11-151[»]
4KXMX-ray2.24A/B/C/D11-151[»]
4KXNX-ray1.90A/B/C/D11-151[»]
4P5DX-ray2.11A/C11-151[»]
ProteinModelPortaliO35820.
SMRiO35820.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000024815.

Chemistry databases

BindingDBiO35820.
ChEMBLiCHEMBL3329079.

PTM databases

iPTMnetiO35820.
PhosphoSitePlusiO35820.

Proteomic databases

PaxDbiO35820.
PRIDEiO35820.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000024815; ENSRNOP00000024815; ENSRNOG00000018397.
GeneIDi171047.
KEGGirno:171047.
UCSCiRGD:620382. rat.

Organism-specific databases

CTDi10591.
RGDi620382. Dnph1.

Phylogenomic databases

eggNOGiENOG410IVY6. Eukaryota.
ENOG4111SC2. LUCA.
GeneTreeiENSGT00390000001216.
HOGENOMiHOG000015361.
HOVERGENiHBG079123.
InParanoidiO35820.
OMAiRAVDMKK.
OrthoDBiEOG091G0WTP.
PhylomeDBiO35820.
TreeFamiTF329719.

Miscellaneous databases

EvolutionaryTraceiO35820.
PROiO35820.

Gene expression databases

BgeeiENSRNOG00000018397.
GenevisibleiO35820. RN.

Family and domain databases

Gene3Di3.40.50.1810. 1 hit.
HAMAPiMF_03036. Nuc_phosphate_hydrolase. 1 hit.
InterProiIPR028607. DNPH1.
IPR007710. Nucleoside_deoxyribTrfase.
[Graphical view]
PfamiPF05014. Nuc_deoxyrib_tr. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDNPH1_RAT
AccessioniPrimary (citable) accession number: O35820
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.