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O35820

- DNPH1_RAT

UniProt

O35820 - DNPH1_RAT

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
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    • History
      Entry version 81 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      Previous versions | rss
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    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

    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-SubCell
    2. nucleus Source: UniProtKB

    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[»]
    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

    MAASGEQAPC SVYFCGSIRG GREDQALYAR IVSRLRRYGK VLTEHVADAE    50
    LEPLGEEAAG GDQFIHEQDL NWLQQADVVV AEVTQPSLGV GYELGRAVAL 100
    GKPILCLFRP QSGRVLSAMI RGAADGSRFQ VWDYAEGEVE TMLDRYFEAY 150
    LPQKTASSSH PSA 163
    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 [» ]
    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 1, 2014
    This is version 81 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