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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

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 – 281Substrate1 Publication
Binding sitei45 – 451Substrate2 Publications
Binding sitei93 – 931Substrate5 Publications

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 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
ProteomesiUP000002494 Componenti: Chromosome 9

Organism-specific databases

RGDi620382. Dnph1.

Subcellular locationi

Cytoplasm UniRule annotation. Nucleus UniRule annotation1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  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 – 11RemovedUniRule annotation1 Publication
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 residuei87 – 871PhosphoserineBy similarity
Modified residuei117 – 1171PhosphoserineBy similarity
Modified residuei127 – 1271PhosphoserineBy 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.UniRule annotation4 Publications

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 – 155Combined sources
Beta strandi22 – 243Combined sources
Helixi25 – 3511Combined sources
Turni36 – 383Combined sources
Beta strandi39 – 413Combined sources
Helixi44 – 463Combined sources
Beta strandi50 – 523Combined sources
Helixi59 – 613Combined sources
Helixi62 – 7514Combined sources
Beta strandi77 – 826Combined sources
Helixi88 – 10013Combined sources
Beta strandi104 – 1085Combined sources
Helixi110 – 1123Combined sources
Helixi118 – 1214Combined sources
Turni126 – 1283Combined sources
Beta strandi129 – 1335Combined sources
Helixi136 – 1383Combined sources
Helixi139 – 15012Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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 binding5 Publications
Regioni117 – 1193Substrate binding; shared with homodimeric partner5 Publications

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:
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
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...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000024815.

Chemistry

BindingDBiO35820.

Proteomic databases

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

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

Miscellaneous databases

EvolutionaryTraceiO35820.
NextBioi621577.
PROiO35820.

Gene expression databases

GenevestigatoriO35820.

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]
ProtoNetiSearch...

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(1996) [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(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, HOMODIMERIZATION, SUBUNIT, 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(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR IN COMPLEX WITH GMP, MUTAGENESIS OF TYR-13 AND GLU-93, SUBUNIT.
  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(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 11-151 IN COMPLEX WITH THE SUBSTRATE GMP, SUBUNIT, CATALYTIC ACTIVITY, FUNCTION.
  5. "Structure of the oncoprotein Rcl bound to three nucleotide analogues."
    Padilla A., Amiable C., Pochet S., Kaminski P.A., Labesse G.
    Acta Crystallogr. D 69:247-255(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) OF 11-151 IN COMPLEX WITH SUBSTRATE ANALOGS.
  6. "N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1."
    Amiable C., Pochet S., Padilla A., Labesse G., Kaminski P.A.
    PLoS ONE 8:E80755-E80755(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 11-151 IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY.
  7. "6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities."
    Amiable C., Paoletti J., Haouz A., Padilla A., Labesse G., Kaminski P.A., Pochet S.
    Eur. J. Med. Chem. 85C:418-437(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.11 ANGSTROMS) OF 11-151 IN COMPLEX WITH THE SUBSTRATE ANALOG 6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-9H-PURINE, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT.

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: March 4, 2015
This is version 85 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

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 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.