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Q6ZVK8

- NUD18_HUMAN

UniProt

Q6ZVK8 - NUD18_HUMAN

Protein

8-oxo-dGDP phosphatase NUDT18

Gene

NUDT18

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 3 (06 Mar 2013)
      Previous versions | rss
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    Functioni

    Mediates the hydrolyzis of oxidized nucleoside diphosphate derivatives. Hydrolyzes 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing deoxyribo- and ribonucleoside diphosphates to the monophosphates. Hydrolyzes 8-oxo-dGDP and 8-oxo-GDP with the same efficiencies. Hydrolyzes also 8-OH-dADP and 2-OH-dADP. Exhibited no or minimal hydrolyzis activity against 8-oxo-dGTP, 8-oxo-GTP, dGTP, GTP, dGDP and GDP. Probably removes oxidized guanine nucleotides from both the DNA and RNA precursor pools.1 Publication

    Catalytic activityi

    8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate.1 Publication

    Cofactori

    Manganese By similarity. Magnesium.By similarity1 Publication

    Kineticsi

    1. KM=10.7 µM for 8-Oxo-dGDP1 Publication
    2. KM=11.7 µM for 8-Oxo-GDP1 Publication

    Vmax=212 pmol/min/µg enzyme toward 8-Oxo-dGDP (at 30 degrees Celsius)1 Publication

    Vmax=246 pmol/min/µg enzyme toward 8-Oxo-GDP (at 30 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 8.5.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi91 – 911Magnesium or manganeseBy similarity
    Metal bindingi95 – 951Magnesium or manganeseBy similarity

    GO - Molecular functioni

    1. 8-hydroxy-dADP phosphatase activity Source: UniProtKB
    2. 8-oxo-dGDP phosphatase activity Source: UniProtKB
    3. 8-oxo-GDP phosphatase activity Source: UniProtKB
    4. magnesium ion binding Source: UniProtKB
    5. protein binding Source: IntAct

    GO - Biological processi

    1. dADP catabolic process Source: UniProtKB
    2. dGDP catabolic process Source: UniProtKB
    3. GDP catabolic process Source: UniProtKB
    4. nucleobase-containing small molecule catabolic process Source: Reactome
    5. nucleobase-containing small molecule metabolic process Source: Reactome
    6. small molecule metabolic process Source: Reactome

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Nucleotide metabolism

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:ENSG00000173566-MONOMER.
    ReactomeiREACT_150237. Phosphate bond hydrolysis by NUDT proteins.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    8-oxo-dGDP phosphatase NUDT18 (EC:3.6.1.58)
    Alternative name(s):
    2-hydroxy-dADP phosphatase
    7,8-dihydro-8-oxoguanine phosphatase
    MutT homolog 3
    Nucleoside diphosphate-linked moiety X motif 18
    Short name:
    Nudix motif 18
    Gene namesi
    Name:NUDT18
    Synonyms:MTH3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 8

    Organism-specific databases

    HGNCiHGNC:26194. NUDT18.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: Reactome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA142671238.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3233238-oxo-dGDP phosphatase NUDT18PRO_0000324567Add
    BLAST

    Proteomic databases

    MaxQBiQ6ZVK8.
    PaxDbiQ6ZVK8.
    PRIDEiQ6ZVK8.

    PTM databases

    PhosphoSiteiQ6ZVK8.

    Expressioni

    Gene expression databases

    ArrayExpressiQ6ZVK8.
    BgeeiQ6ZVK8.
    CleanExiHS_NUDT18.
    GenevestigatoriQ6ZVK8.

    Organism-specific databases

    HPAiHPA028581.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    APIPQ96GX93EBI-740486,EBI-359248
    DHPSP493663EBI-740486,EBI-741925
    DUTP333163EBI-740486,EBI-353224
    EVI5LQ96CN43EBI-740486,EBI-749523
    HSD17B14Q9BPX13EBI-740486,EBI-742664
    NT5C2P499023EBI-740486,EBI-742084
    PAICSP222343EBI-740486,EBI-712261
    RAB3IL1Q8TBN03EBI-740486,EBI-743796
    RABAC1Q9UI143EBI-740486,EBI-712367

    Protein-protein interaction databases

    BioGridi122961. 34 interactions.
    IntActiQ6ZVK8. 32 interactions.
    MINTiMINT-1436358.
    STRINGi9606.ENSP00000307852.

    Structurei

    Secondary structure

    1
    323
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi43 – 497
    Beta strandi55 – 617
    Helixi65 – 673
    Beta strandi74 – 774
    Helixi84 – 9613
    Beta strandi98 – 11215
    Beta strandi115 – 12713
    Helixi132 – 1343
    Beta strandi136 – 1383
    Beta strandi140 – 1467
    Beta strandi152 – 1554
    Helixi158 – 17215

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3GG6X-ray2.10A26-179[»]
    4HVYX-ray1.46A26-179[»]
    ProteinModelPortaliQ6ZVK8.
    SMRiQ6ZVK8. Positions 36-179.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ6ZVK8.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini37 – 167131Nudix hydrolasePROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi76 – 9722Nudix boxAdd
    BLAST

    Sequence similaritiesi

    Belongs to the Nudix hydrolase family.Curated
    Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG1051.
    HOGENOMiHOG000035136.
    HOVERGENiHBG108203.
    InParanoidiQ6ZVK8.
    KOiK17817.
    OMAiQEAKKEC.
    PhylomeDBiQ6ZVK8.
    TreeFamiTF106355.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR020476. Nudix_hydrolase.
    IPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    PRINTSiPR00502. NUDIXFAMILY.
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q6ZVK8-1) [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

    MASEGLAGAL ASVLAGQGSS VHSCDSAPAG EPPAPVRLRK NVCYVVLAVF    50
    LSEQDEVLLI QEAKRECRGS WYLPAGRMEP GETIVEALQR EVKEEAGLHC 100
    EPETLLSVEE RGPSWVRFVF LARPTGGILK TSKEADAESL QAAWYPRTSL 150
    PTPLRAHDIL HLVELAAQYR QQARHPLILP QELPCDLVCQ RLVATFTSAQ 200
    TVWVLVGTVG MPHLPVTACG LDPMEQRGGM KMAVLRLLQE CLTLHHLVVE 250
    IKGLLGLQHL GRDHSDGICL NVLVTVAFRS PGIQDEPPKV RGENFSWWKV 300
    MEEDLQSQLL QRLQGSSVVP VNR 323
    Length:323
    Mass (Da):35,501
    Last modified:March 6, 2013 - v3
    Checksum:i8162BA4BDEC4374D
    GO
    Isoform 2 (identifier: Q6ZVK8-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-100: Missing.
         101-125: EPETLLSVEERGPSWVRFVFLARPT → MSVDSARAALLSTQTLPAPSPTSPP

    Note: No experimental confirmation available.

    Show »
    Length:223
    Mass (Da):24,463
    Checksum:iED9DD93D505E8709
    GO

    Sequence cautioni

    The sequence BAC85853.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti177 – 1771L → P in BAB15376. (PubMed:14702039)Curated
    Sequence conflicti224 – 2241M → V in BAB15376. (PubMed:14702039)Curated
    Sequence conflicti224 – 2241M → V in BAC85853. (PubMed:14702039)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 100100Missing in isoform 2. 1 PublicationVSP_032276Add
    BLAST
    Alternative sequencei101 – 12525EPETL…LARPT → MSVDSARAALLSTQTLPAPS PTSPP in isoform 2. 1 PublicationVSP_032277Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK026147 mRNA. Translation: BAB15376.1.
    AK124446 mRNA. Translation: BAC85853.1. Different initiation.
    BC016902 mRNA. Translation: AAH16902.1.
    RefSeqiNP_079091.3. NM_024815.3. [Q6ZVK8-1]
    UniGeneiHs.527101.
    Hs.745387.

    Genome annotation databases

    GeneIDi79873.
    KEGGihsa:79873.
    UCSCiuc003xaq.1. human. [Q6ZVK8-1]

    Polymorphism databases

    DMDMi460018323.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK026147 mRNA. Translation: BAB15376.1 .
    AK124446 mRNA. Translation: BAC85853.1 . Different initiation.
    BC016902 mRNA. Translation: AAH16902.1 .
    RefSeqi NP_079091.3. NM_024815.3. [Q6ZVK8-1 ]
    UniGenei Hs.527101.
    Hs.745387.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3GG6 X-ray 2.10 A 26-179 [» ]
    4HVY X-ray 1.46 A 26-179 [» ]
    ProteinModelPortali Q6ZVK8.
    SMRi Q6ZVK8. Positions 36-179.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 122961. 34 interactions.
    IntActi Q6ZVK8. 32 interactions.
    MINTi MINT-1436358.
    STRINGi 9606.ENSP00000307852.

    PTM databases

    PhosphoSitei Q6ZVK8.

    Polymorphism databases

    DMDMi 460018323.

    Proteomic databases

    MaxQBi Q6ZVK8.
    PaxDbi Q6ZVK8.
    PRIDEi Q6ZVK8.

    Protocols and materials databases

    DNASUi 79873.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 79873.
    KEGGi hsa:79873.
    UCSCi uc003xaq.1. human. [Q6ZVK8-1 ]

    Organism-specific databases

    CTDi 79873.
    GeneCardsi GC08M022021.
    HGNCi HGNC:26194. NUDT18.
    HPAi HPA028581.
    MIMi 615791. gene.
    neXtProti NX_Q6ZVK8.
    PharmGKBi PA142671238.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1051.
    HOGENOMi HOG000035136.
    HOVERGENi HBG108203.
    InParanoidi Q6ZVK8.
    KOi K17817.
    OMAi QEAKKEC.
    PhylomeDBi Q6ZVK8.
    TreeFami TF106355.

    Enzyme and pathway databases

    BioCyci MetaCyc:ENSG00000173566-MONOMER.
    Reactomei REACT_150237. Phosphate bond hydrolysis by NUDT proteins.

    Miscellaneous databases

    EvolutionaryTracei Q6ZVK8.
    GenomeRNAii 79873.
    NextBioi 69645.
    PROi Q6ZVK8.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q6ZVK8.
    Bgeei Q6ZVK8.
    CleanExi HS_NUDT18.
    Genevestigatori Q6ZVK8.

    Family and domain databases

    Gene3Di 3.90.79.10. 1 hit.
    InterProi IPR020476. Nudix_hydrolase.
    IPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view ]
    Pfami PF00293. NUDIX. 1 hit.
    [Graphical view ]
    PRINTSi PR00502. NUDIXFAMILY.
    SUPFAMi SSF55811. SSF55811. 1 hit.
    PROSITEi PS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Tissue: Cerebellum.
    2. "DNA sequence and analysis of human chromosome 8."
      Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M., Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S., Asakawa T.
      , Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A., Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III, Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K., Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P., Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H., Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B., O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K., Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L., Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G., Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W., Platzer M., Shimizu N., Lander E.S.
      Nature 439:331-335(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Uterus.
    4. "Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2."
      Takagi Y., Setoyama D., Ito R., Kamiya H., Yamagata Y., Sekiguchi M.
      J. Biol. Chem. 287:21541-21549(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, FUNCTION.
    5. "Crystal structure of the nudix domain of human nudt18."
      Structural genomics consortium (SGC)
      Submitted (MAR-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 26-179.

    Entry informationi

    Entry nameiNUD18_HUMAN
    AccessioniPrimary (citable) accession number: Q6ZVK8
    Secondary accession number(s): Q8IZ75, Q9H687
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 18, 2008
    Last sequence update: March 6, 2013
    Last modified: October 1, 2014
    This is version 90 of the entry and version 3 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 8
      Human chromosome 8: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3