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O35820

- DNPH1_RAT

UniProt

O35820 - DNPH1_RAT

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Protein

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

Gene

Dnph1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - 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.1 PublicationUniRule annotation

Catalytic activityi

A deoxyribonucleoside 5'-monophosphate + H20 = deoxyribose 5-monophosphate + a purine or pyrimidine base.1 PublicationUniRule annotation

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

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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei28 – 281Substrate
Binding sitei93 – 931Substrate

GO - Molecular functioni

  1. deoxyribonucleoside 5'-monophosphate N-glycosidase activity Source: UniProtKB
  2. nucleoside deoxyribosyltransferase activity Source: InterPro
  3. protein homodimerization activity Source: UniProtKB

GO - Biological processi

  1. deoxyribonucleoside monophosphate catabolic process Source: UniProtKB
  2. nucleoside metabolic process Source: UniProtKB-HAMAP
  3. nucleotide metabolic process Source: UniProtKB-KW
  4. positive regulation of cell growth Source: UniProtKB
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 annotation)
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
ProteomesiUP000002494: Chromosome 9

Organism-specific databases

RGDi620382. Dnph1.

Subcellular locationi

Cytoplasm UniRule annotation. Nucleus 1 PublicationUniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
  2. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi13 – 131Y → A: 100-fold decrease binding affinity for GMP as substrate. 1 Publication
Mutagenesisi93 – 931E → A: 100-fold increase in Km and 170-fold decrease in catalytic efficiency for dGMP as substrate. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 PublicationUniRule annotation
Chaini2 – 1631622'-deoxynucleoside 5'-phosphate N-hydrolase 1PRO_0000097202Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei17 – 171PhosphoserineBy similarity
Modified residuei158 – 1581PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiO35820.

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

GenevestigatoriO35820.

Interactioni

Subunit structurei

Monomer and homodimer.2 PublicationsUniRule annotation

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000024815.

Structurei

Secondary structure

1
163
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 155
Beta strandi22 – 243
Helixi25 – 3511
Turni36 – 383
Beta strandi39 – 413
Helixi44 – 463
Beta strandi50 – 523
Helixi59 – 613
Helixi62 – 7514
Beta strandi77 – 826
Helixi88 – 10013
Beta strandi104 – 1085
Helixi110 – 1123
Helixi118 – 1214
Turni126 – 1283
Beta strandi129 – 1335
Helixi136 – 1383
Helixi139 – 15012

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO35820.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni13 – 197Substrate binding
Regioni117 – 1193Substrate binding; shared with homodimeric partner

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiNOG08389.
GeneTreeiENSGT00390000001216.
HOGENOMiHOG000015361.
HOVERGENiHBG079123.
InParanoidiO35820.
OMAiVYFCGSI.
OrthoDBiEOG7CNZHC.
PhylomeDBiO35820.
TreeFamiTF329719.

Family and domain databases

Gene3Di3.40.50.1810. 1 hit.
HAMAPiMF_03036. Nuc_phosphate_hydrolase.
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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
U82591 mRNA. Translation: AAB95314.1 .
RefSeqi NP_598209.1. NM_133525.1.
UniGenei Rn.6997.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2KHZ NMR - A/B 1-163 [» ]
2KLH NMR - A/B 11-151 [» ]
4FYH X-ray 2.44 A/B/C/D 11-151 [» ]
4FYI X-ray 1.96 A/B/C/D 11-151 [» ]
4FYK X-ray 1.79 A/B/C/D 11-151 [» ]
4KXL X-ray 1.69 A/B/C/D 11-151 [» ]
4KXM X-ray 2.24 A/B/C/D 11-151 [» ]
4KXN X-ray 1.90 A/B/C/D 11-151 [» ]
4P5D X-ray 2.11 A/C 11-151 [» ]
ProteinModelPortali O35820.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 10116.ENSRNOP00000024815.

Proteomic databases

PRIDEi O35820.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSRNOT00000024815 ; ENSRNOP00000024815 ; ENSRNOG00000018397 .
GeneIDi 171047.
KEGGi rno:171047.
UCSCi RGD:620382. rat.

Organism-specific databases

CTDi 10591.
RGDi 620382. Dnph1.

Phylogenomic databases

eggNOGi NOG08389.
GeneTreei ENSGT00390000001216.
HOGENOMi HOG000015361.
HOVERGENi HBG079123.
InParanoidi O35820.
OMAi VYFCGSI.
OrthoDBi EOG7CNZHC.
PhylomeDBi O35820.
TreeFami TF329719.

Miscellaneous databases

EvolutionaryTracei O35820.
NextBioi 621577.
PROi O35820.

Gene expression databases

Genevestigatori O35820.

Family and domain databases

Gene3Di 3.40.50.1810. 1 hit.
HAMAPi MF_03036. Nuc_phosphate_hydrolase.
InterProi IPR028607. DNPH1.
IPR007710. Nucleoside_deoxyribTrfase.
[Graphical view ]
Pfami PF05014. Nuc_deoxyrib_tr. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Identification of putative c-Myc-responsive genes: characterization of rcl, a novel growth-related gene."
    Lewis B.C., Shim H., Li Q., Wu C.S., Lee L.A., Maity A., Dang C.V.
    Mol. Cell. Biol. 17:4967-4978(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION.
    Tissue: Liver.
  2. "The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase."
    Ghiorghi Y.K., Zeller K.I., Dang C.V., Kaminski P.A.
    J. Biol. Chem. 282:8150-8156(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, HOMODIMERIZATION, CLEAVAGE OF INITIATOR METHIONINE, MUTAGENESIS OF GLU-93.
  3. "Solution structure of RCL, a novel 2'-deoxyribonucleoside 5'-monophosphate N-glycosidase."
    Doddapaneni K., Mahler B., Pavlovicz R., Haushalter A., Yuan C., Wu Z.
    J. Mol. Biol. 394:423-434(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR IN COMPLEX WITH GMP, MUTAGENESIS OF TYR-13 AND GLU-93.
  4. "Structural characterization of the mammalian deoxynucleotide N-hydrolase Rcl and its stabilizing interactions with two inhibitors."
    Yang Y., Padilla A., Zhang C., Labesse G., Kaminski P.A.
    J. Mol. Biol. 394:435-447(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR IN COMPLEX WITH GMP.

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: October 29, 2014
This is version 82 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

External Data

Dasty 3