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Protein

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

Gene

DNPH1

Organism
Homo sapiens (Human)
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 annotation2 Publications

Catalytic activityi

A deoxyribonucleoside 5'-monophosphate + H20 = deoxyribose 5-monophosphate + a purine or pyrimidine base.UniRule annotation2 Publications

Kineticsi

kcat is 0.002 sec(-1) with dGMP as substrate. kcat is 0.0025 sec(-1) with dAMP as substrate. kcat is 0.0016 sec(-1) with dIMP as substrate. kcat is 0.2 sec(-1) with dUMP as substrate. kcat is 0.0083 sec(-1) with dCMP as substrate. kcat is 0.025 sec(-1) with dTMP as substrate.1 Publication

Manual assertion based on experiment ini

  1. KM=57 µM for dGMP1 Publication
  2. KM=97 µM for dAMP1 Publication
  3. KM=104 µM for dIMP1 Publication
  4. KM=2500 µM for dCMP1 Publication
  5. KM=7800 µM for dUMP1 Publication
  6. KM=25000 µM for dTMP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei39SubstrateUniRule annotation1
    Binding sitei56Substrate1 Publication1
    Binding sitei104SubstrateUniRule annotation1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    • cell proliferation Source: ProtInc
    • deoxyribonucleoside monophosphate catabolic process Source: UniProtKB
    • epithelial cell differentiation Source: UniProtKB
    • nucleoside metabolic process Source: UniProtKB-HAMAP
    • nucleotide metabolic process Source: UniProtKB-KW
    • positive regulation of cell growth Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Nucleotide metabolism

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000112667-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2'-deoxynucleoside 5'-phosphate N-hydrolase 1UniRule annotation (EC:3.2.2.-UniRule annotation2 Publications)
    Alternative name(s):
    c-Myc-responsive protein RCLUniRule annotation
    Gene namesi
    Name:DNPH1UniRule annotation
    Synonyms:C6orf108, RCLUniRule annotation
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 6

    Organism-specific databases

    HGNCiHGNC:21218. DNPH1.

    Subcellular locationi

    • Cytoplasm UniRule annotation1 Publication
    • Nucleus UniRule annotation

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Organism-specific databases

    OpenTargetsiENSG00000112667.
    PharmGKBiPA134918815.

    Chemistry databases

    ChEMBLiCHEMBL3351218.

    Polymorphism and mutation databases

    BioMutaiDNPH1.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemovedCombined sources
    ChainiPRO_00000972002 – 1742'-deoxynucleoside 5'-phosphate N-hydrolase 1Add BLAST173

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei2N-acetylalanineCombined sources1
    Modified residuei28PhosphoserineCombined sources1
    Modified residuei98PhosphoserineCombined sources1
    Modified residuei123PhosphoserineCombined sources1
    Modified residuei128PhosphoserineCombined sources1
    Modified residuei138PhosphoserineCombined sources1
    Modified residuei169PhosphoserineCombined sources1

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    EPDiO43598.
    MaxQBiO43598.
    PaxDbiO43598.
    PeptideAtlasiO43598.
    PRIDEiO43598.
    TopDownProteomicsiO43598-1. [O43598-1]

    PTM databases

    iPTMnetiO43598.
    PhosphoSitePlusiO43598.

    Expressioni

    Tissue specificityi

    Expressed at low levels in brain, colon, lung, peripheral blood leukocytes, placenta, small intestine, and thymus. Expressed at high levels in heart, kidney, liver, skeletal muscle and spleen. Overexpressed in a significant proportion of breast cancers.1 Publication

    Inductioni

    Expression is induced by ETV1.1 Publication

    Gene expression databases

    BgeeiENSG00000112667.
    CleanExiHS_C6orf108.
    ExpressionAtlasiO43598. baseline and differential.
    GenevisibleiO43598. HS.

    Organism-specific databases

    HPAiHPA029675.
    HPA029676.

    Interactioni

    Subunit structurei

    Monomer and homodimer.UniRule annotation1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself4EBI-748674,EBI-748674
    TERF1P542742EBI-748674,EBI-710997

    Protein-protein interaction databases

    BioGridi115840. 11 interactors.
    IntActiO43598. 4 interactors.
    MINTiMINT-5002237.
    STRINGi9606.ENSP00000230431.

    Chemistry databases

    BindingDBiO43598.

    Structurei

    Secondary structure

    1174
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi22 – 26Combined sources5
    Helixi36 – 46Combined sources11
    Turni47 – 49Combined sources3
    Beta strandi50 – 53Combined sources4
    Helixi55 – 58Combined sources4
    Turni68 – 71Combined sources4
    Helixi73 – 86Combined sources14
    Beta strandi88 – 93Combined sources6
    Helixi99 – 110Combined sources12
    Beta strandi115 – 119Combined sources5
    Helixi121 – 123Combined sources3
    Helixi129 – 134Combined sources6
    Beta strandi137 – 144Combined sources8
    Helixi147 – 149Combined sources3
    Helixi150 – 160Combined sources11

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4P5EX-ray1.35A/B20-162[»]
    ProteinModelPortaliO43598.
    SMRiO43598.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni24 – 30Substrate bindingUniRule annotation1 Publication7
    Regioni128 – 130Substrate binding; shared with homodimeric partnerUniRule annotation3

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG410IVY6. Eukaryota.
    ENOG4111SC2. LUCA.
    GeneTreeiENSGT00390000001216.
    HOGENOMiHOG000015361.
    HOVERGENiHBG079123.
    PhylomeDBiO43598.
    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]

    Sequences (2)i

    Sequence statusi: Complete.

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

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

    Isoform 1 (identifier: O43598-1) [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
    MAAAMVPGRS ESWERGEPGR PALYFCGSIR GGREDRTLYE RIVSRLRRFG
    60 70 80 90 100
    TVLTEHVAAA ELGARGEEAA GGDRLIHEQD LEWLQQADVV VAEVTQPSLG
    110 120 130 140 150
    VGYELGRAVA FNKRILCLFR PQSGRVLSAM IRGAADGSRF QVWDYEEGEV
    160 170
    EALLDRYFEA DPPGQVAASP DPTT
    Length:174
    Mass (Da):19,108
    Last modified:June 1, 1998 - v1
    Checksum:iC148641A60F383A3
    GO
    Isoform 2 (identifier: O43598-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         126-148: VLSAMIRGAADGSRFQVWDYEEG → GEHPKPPSWLSMDPALSSFPGGL
         149-174: Missing.

    Show »
    Length:148
    Mass (Da):16,187
    Checksum:i561FF979CA656F63
    GO

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_040509126 – 148VLSAM…DYEEG → GEHPKPPSWLSMDPALSSFP GGL in isoform 2. 1 PublicationAdd BLAST23
    Alternative sequenceiVSP_040510149 – 174Missing in isoform 2. 1 PublicationAdd BLAST26

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF040105 mRNA. Translation: AAB96766.1.
    EU585603 mRNA. Translation: ACB87500.1.
    AL133375 Genomic DNA. Translation: CAI20205.1.
    CH471081 Genomic DNA. Translation: EAX04166.1.
    BC011683 mRNA. Translation: AAH11683.1.
    BQ052226 mRNA. No translation available.
    CCDSiCCDS43465.1. [O43598-2]
    CCDS4891.1. [O43598-1]
    RefSeqiNP_006434.1. NM_006443.2. [O43598-1]
    NP_954653.1. NM_199184.1. [O43598-2]
    UniGeneiHs.109752.

    Genome annotation databases

    EnsembliENST00000230431; ENSP00000230431; ENSG00000112667. [O43598-1]
    ENST00000393987; ENSP00000377556; ENSG00000112667. [O43598-2]
    GeneIDi10591.
    KEGGihsa:10591.
    UCSCiuc003ouo.4. human. [O43598-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF040105 mRNA. Translation: AAB96766.1.
    EU585603 mRNA. Translation: ACB87500.1.
    AL133375 Genomic DNA. Translation: CAI20205.1.
    CH471081 Genomic DNA. Translation: EAX04166.1.
    BC011683 mRNA. Translation: AAH11683.1.
    BQ052226 mRNA. No translation available.
    CCDSiCCDS43465.1. [O43598-2]
    CCDS4891.1. [O43598-1]
    RefSeqiNP_006434.1. NM_006443.2. [O43598-1]
    NP_954653.1. NM_199184.1. [O43598-2]
    UniGeneiHs.109752.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4P5EX-ray1.35A/B20-162[»]
    ProteinModelPortaliO43598.
    SMRiO43598.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi115840. 11 interactors.
    IntActiO43598. 4 interactors.
    MINTiMINT-5002237.
    STRINGi9606.ENSP00000230431.

    Chemistry databases

    BindingDBiO43598.
    ChEMBLiCHEMBL3351218.

    PTM databases

    iPTMnetiO43598.
    PhosphoSitePlusiO43598.

    Polymorphism and mutation databases

    BioMutaiDNPH1.

    Proteomic databases

    EPDiO43598.
    MaxQBiO43598.
    PaxDbiO43598.
    PeptideAtlasiO43598.
    PRIDEiO43598.
    TopDownProteomicsiO43598-1. [O43598-1]

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000230431; ENSP00000230431; ENSG00000112667. [O43598-1]
    ENST00000393987; ENSP00000377556; ENSG00000112667. [O43598-2]
    GeneIDi10591.
    KEGGihsa:10591.
    UCSCiuc003ouo.4. human. [O43598-1]

    Organism-specific databases

    CTDi10591.
    GeneCardsiDNPH1.
    HGNCiHGNC:21218. DNPH1.
    HPAiHPA029675.
    HPA029676.
    neXtProtiNX_O43598.
    OpenTargetsiENSG00000112667.
    PharmGKBiPA134918815.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiENOG410IVY6. Eukaryota.
    ENOG4111SC2. LUCA.
    GeneTreeiENSGT00390000001216.
    HOGENOMiHOG000015361.
    HOVERGENiHBG079123.
    PhylomeDBiO43598.
    TreeFamiTF329719.

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000112667-MONOMER.

    Miscellaneous databases

    GenomeRNAii10591.
    PROiO43598.

    Gene expression databases

    BgeeiENSG00000112667.
    CleanExiHS_C6orf108.
    ExpressionAtlasiO43598. baseline and differential.
    GenevisibleiO43598. HS.

    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_HUMAN
    AccessioniPrimary (citable) accession number: O43598
    Secondary accession number(s): B2LUJ9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 10, 2005
    Last sequence update: June 1, 1998
    Last modified: November 30, 2016
    This is version 129 of the entry and version 1 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, Reference proteome

    Documents

    1. Human chromosome 6
      Human chromosome 6: entries, gene names and cross-references to MIM
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.