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Protein

Diphosphoinositol polyphosphate phosphohydrolase 3-beta

Gene

NUDT11

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), suggesting that it may play a role in signal transduction. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5-phosphoribose 1-diphosphate.

Catalytic activityi

Diphospho-myo-inositol polyphosphate + H2O = myo-inositol polyphosphate + phosphate.
P1,P(6)-bis(5'-adenosyl)hexaphosphate + H2O = adenosine 5'-pentaphosphate + AMP.
P1,P(5)-bis(5'-adenosyl)pentaphosphate + H2O = adenosine 5'-tetraphosphate + AMP.

Cofactori

Mg2+By similarity1 Publication, Mn2+By similarity1 PublicationNote: Binds 3 Mg(2+) or Mn(2+) ions per subunit. Mn2+ may be the true cofactor in vivo.By similarity1 Publication

Kineticsi

  1. KM=0.053 µM for PP-InsP52 Publications
  2. KM=13 µM for Ap6A2 Publications
  3. KM=37 µM for Ap5A2 Publications

    pH dependencei

    Optimum pH is 8.5.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei9 – 91SubstrateBy similarity
    Binding sitei40 – 401SubstrateBy similarity
    Metal bindingi49 – 491Magnesium 1; via carbonyl oxygenBy similarity
    Metal bindingi65 – 651Magnesium 2By similarity
    Metal bindingi65 – 651Magnesium 3By similarity
    Active sitei68 – 681Proton acceptorBy similarity
    Metal bindingi69 – 691Magnesium 1By similarity

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:HS05381-MONOMER.
    BRENDAi3.6.1.52. 2681.
    3.6.1.60. 2681.
    ReactomeiREACT_150188. Synthesis of pyrophosphates in the cytosol.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diphosphoinositol polyphosphate phosphohydrolase 3-beta (EC:3.6.1.52)
    Short name:
    DIPP-3-beta
    Short name:
    DIPP3-beta
    Short name:
    hDIPP3beta
    Alternative name(s):
    Diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase 3-beta
    Diadenosine hexaphosphate hydrolase (AMP-forming) (EC:3.6.1.60)
    Nucleoside diphosphate-linked moiety X motif 11
    Short name:
    Nudix motif 11
    hAps1
    Gene namesi
    Name:NUDT11
    Synonyms:APS1, DIPP3B
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640 Componenti: Chromosome X

    Organism-specific databases

    HGNCiHGNC:18011. NUDT11.

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA31832.

    Polymorphism and mutation databases

    BioMutaiNUDT11.
    DMDMi68565927.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 164164Diphosphoinositol polyphosphate phosphohydrolase 3-betaPRO_0000057065Add
    BLAST

    Proteomic databases

    MaxQBiQ96G61.
    PaxDbiQ96G61.
    PRIDEiQ96G61.

    PTM databases

    PhosphoSiteiQ96G61.

    Expressioni

    Tissue specificityi

    Mainly expressed in testis and, at lower level in brain. According to PubMed:12121577, it is also expressed in pancreas and weakly expressed in thymus, prostate, ovary, lung, small intestine and heart.2 Publications

    Gene expression databases

    BgeeiQ96G61.
    CleanExiHS_NUDT11.
    GenevisibleiQ96G61. HS.

    Organism-specific databases

    HPAiHPA047027.

    Interactioni

    Protein-protein interaction databases

    MINTiMINT-3053121.
    STRINGi9606.ENSP00000365160.

    Structurei

    3D structure databases

    ProteinModelPortaliQ96G61.
    SMRiQ96G61. Positions 17-144.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini17 – 144128Nudix hydrolasePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni17 – 193Substrate bindingBy similarity
    Regioni89 – 913Substrate bindingBy similarity

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi50 – 7122Nudix boxAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiNOG250169.
    GeneTreeiENSGT00390000012928.
    HOGENOMiHOG000237336.
    HOVERGENiHBG053341.
    InParanoidiQ96G61.
    KOiK07766.
    OMAiCFRSELE.
    OrthoDBiEOG7T7GVQ.
    PhylomeDBiQ96G61.
    TreeFamiTF106349.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q96G61-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKCKPNQTRT YDPEGFKKRA ACLCFRSERE DEVLLVSSSR YPDRWIVPGG
    60 70 80 90 100
    GMEPEEEPGG AAVREVYEEA GVKGKLGRLL GVFEQNQDRK HRTYVYVLTV
    110 120 130 140 150
    TELLEDWEDS VSIGRKREWF KVEDAIKVLQ CHKPVHAEYL EKLKLGGSPT
    160
    NGNSMAPSSP DSDP
    Length:164
    Mass (Da):18,559
    Last modified:December 1, 2001 - v1
    Checksum:i8E7F342C8A38872F
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti39 – 391S → N.2 Publications
    VAR_022738

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK001490 mRNA. Translation: BAA91720.1.
    AL158055 Genomic DNA. Translation: CAI40294.1.
    BC009942 mRNA. Translation: AAH09942.1.
    CCDSiCCDS43952.1.
    RefSeqiNP_060629.2. NM_018159.3.
    UniGeneiHs.200016.

    Genome annotation databases

    EnsembliENST00000375992; ENSP00000365160; ENSG00000196368.
    GeneIDi55190.
    KEGGihsa:55190.
    UCSCiuc010njt.3. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK001490 mRNA. Translation: BAA91720.1.
    AL158055 Genomic DNA. Translation: CAI40294.1.
    BC009942 mRNA. Translation: AAH09942.1.
    CCDSiCCDS43952.1.
    RefSeqiNP_060629.2. NM_018159.3.
    UniGeneiHs.200016.

    3D structure databases

    ProteinModelPortaliQ96G61.
    SMRiQ96G61. Positions 17-144.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    MINTiMINT-3053121.
    STRINGi9606.ENSP00000365160.

    PTM databases

    PhosphoSiteiQ96G61.

    Polymorphism and mutation databases

    BioMutaiNUDT11.
    DMDMi68565927.

    Proteomic databases

    MaxQBiQ96G61.
    PaxDbiQ96G61.
    PRIDEiQ96G61.

    Protocols and materials databases

    DNASUi55190.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000375992; ENSP00000365160; ENSG00000196368.
    GeneIDi55190.
    KEGGihsa:55190.
    UCSCiuc010njt.3. human.

    Organism-specific databases

    CTDi55190.
    GeneCardsiGC0XM051232.
    HGNCiHGNC:18011. NUDT11.
    HPAiHPA047027.
    MIMi300528. gene.
    neXtProtiNX_Q96G61.
    PharmGKBiPA31832.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiNOG250169.
    GeneTreeiENSGT00390000012928.
    HOGENOMiHOG000237336.
    HOVERGENiHBG053341.
    InParanoidiQ96G61.
    KOiK07766.
    OMAiCFRSELE.
    OrthoDBiEOG7T7GVQ.
    PhylomeDBiQ96G61.
    TreeFamiTF106349.

    Enzyme and pathway databases

    BioCyciMetaCyc:HS05381-MONOMER.
    BRENDAi3.6.1.52. 2681.
    3.6.1.60. 2681.
    ReactomeiREACT_150188. Synthesis of pyrophosphates in the cytosol.

    Miscellaneous databases

    GeneWikiiNUDT11.
    GenomeRNAii55190.
    NextBioi59039.
    PROiQ96G61.
    SOURCEiSearch...

    Gene expression databases

    BgeeiQ96G61.
    CleanExiHS_NUDT11.
    GenevisibleiQ96G61. HS.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "An adjacent pair of human NUDT genes on chromosome X are preferentially expressed in testis and encode two new isoforms of diphosphoinositol polyphosphate phosphohydrolase."
      Hidaka K., Caffrey J.J., Hua L., Zhang T., Falck J.R., Nickel G.C., Carrel L., Barnes L.D., Shears S.B.
      J. Biol. Chem. 277:32730-32738(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, TISSUE SPECIFICITY.
    2. "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], VARIANT ASN-39.
    3. "The DNA sequence of the human X chromosome."
      Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
      , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
      Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "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].
      Tissue: Uterus.
    5. "Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases."
      Leslie N.R., McLennan A.G., Safrany S.T.
      BMC Biochem. 3:20-20(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, TISSUE SPECIFICITY, VARIANT ASN-39.
    6. "Nudix hydrolases that degrade dinucleoside and diphosphoinositol polyphosphates also have 5-phosphoribosyl 1-pyrophosphate (PRPP) pyrophosphatase activity that generates the glycolytic activator ribose 1,5-bisphosphate."
      Fisher D.I., Safrany S.T., Strike P., McLennan A.G., Cartwright J.L.
      J. Biol. Chem. 277:47313-47317(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY.
    7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiNUD11_HUMAN
    AccessioniPrimary (citable) accession number: Q96G61
    Secondary accession number(s): Q9NVN0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 5, 2005
    Last sequence update: December 1, 2001
    Last modified: July 22, 2015
    This is version 127 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

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome X
      Human chromosome X: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. 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.