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Q9NPB8

- GPCP1_HUMAN

UniProt

Q9NPB8 - GPCP1_HUMAN

Protein

Glycerophosphocholine phosphodiesterase GPCPD1

Gene

GPCPD1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 2 (10 Oct 2002)
      Previous versions | rss
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    Functioni

    May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.By similarity

    Catalytic activityi

    sn-glycero-3-phosphocholine + H2O = choline + sn-glycerol 3-phosphate.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei70 – 701SubstrateSequence Analysis

    GO - Molecular functioni

    1. glycerophosphocholine phosphodiesterase activity Source: UniProtKB-EC
    2. glycerophosphodiester phosphodiesterase activity Source: InterPro
    3. starch binding Source: InterPro

    GO - Biological processi

    1. glycerol metabolic process Source: InterPro
    2. glycerophospholipid biosynthetic process Source: Reactome
    3. phospholipid metabolic process Source: Reactome
    4. small molecule metabolic process Source: Reactome

    Keywords - Molecular functioni

    Hydrolase

    Enzyme and pathway databases

    ReactomeiREACT_120785. Hydrolysis of LPE.
    REACT_120977. Hydrolysis of LPC.

    Protein family/group databases

    CAZyiCBM20. Carbohydrate-Binding Module Family 20.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycerophosphocholine phosphodiesterase GPCPD1 (EC:3.1.4.2)
    Alternative name(s):
    Glycerophosphodiester phosphodiesterase 5
    Gene namesi
    Name:GPCPD1
    Synonyms:GDE5, KIAA1434
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 20

    Organism-specific databases

    HGNCiHGNC:26957. GPCPD1.

    Subcellular locationi

    Cytoplasmcytosol By similarity

    GO - Cellular componenti

    1. cytosol Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA165392351.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 672672Glycerophosphocholine phosphodiesterase GPCPD1PRO_0000050797Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei608 – 6081PhosphotyrosineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ9NPB8.
    PaxDbiQ9NPB8.
    PRIDEiQ9NPB8.

    PTM databases

    PhosphoSiteiQ9NPB8.

    Expressioni

    Tissue specificityi

    Widely expressed, with highest expression in spinal chord.

    Gene expression databases

    ArrayExpressiQ9NPB8.
    BgeeiQ9NPB8.
    GenevestigatoriQ9NPB8.

    Organism-specific databases

    HPAiHPA039556.
    HPA042987.

    Interactioni

    Protein-protein interaction databases

    BioGridi121125. 1 interaction.
    IntActiQ9NPB8. 1 interaction.
    MINTiMINT-4650772.
    STRINGi9606.ENSP00000368305.

    Structurei

    Secondary structure

    1
    672
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 118
    Beta strandi19 – 268
    Helixi27 – 293
    Turni30 – 323
    Helixi34 – 363
    Beta strandi49 – 5810
    Beta strandi64 – 7411
    Beta strandi84 – 907
    Beta strandi97 – 993
    Beta strandi103 – 11210

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2Z0BX-ray2.00A/B/C/D/E/F3-120[»]
    ProteinModelPortaliQ9NPB8.
    SMRiQ9NPB8. Positions 3-115, 321-611.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9NPB8.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 115115CBM20PROSITE-ProRule annotationAdd
    BLAST
    Domaini318 – 618301GP-PDEAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni88 – 892Substrate bindingSequence Analysis

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi169 – 1724Poly-Asp

    Sequence similaritiesi

    Contains 1 CBM20 (carbohydrate binding type-20) domain.PROSITE-ProRule annotation
    Contains 1 GP-PDE domain.Curated

    Phylogenomic databases

    eggNOGiCOG0584.
    HOGENOMiHOG000231653.
    HOVERGENiHBG080384.
    InParanoidiQ9NPB8.
    OMAiHDLTCCI.
    OrthoDBiEOG7RNJZM.
    PhylomeDBiQ9NPB8.
    TreeFamiTF314722.

    Family and domain databases

    Gene3Di2.60.40.10. 1 hit.
    3.20.20.190. 1 hit.
    InterProiIPR013784. Carb-bd-like_fold.
    IPR002044. CBM_fam20.
    IPR013783. Ig-like_fold.
    IPR017946. PLC-like_Pdiesterase_TIM-brl.
    [Graphical view]
    PfamiPF00686. CBM_20. 1 hit.
    [Graphical view]
    SMARTiSM01065. CBM_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF49452. SSF49452. 1 hit.
    SSF51695. SSF51695. 1 hit.
    PROSITEiPS51166. CBM20. 1 hit.
    PS51704. GP_PDE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9NPB8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTPSQVAFEI RGTLLPGEVF AICGSCDALG NWNPQNAVAL LPENDTGESM    50
    LWKATIVLSR GVSVQYRYFK GYFLEPKTIG GPCQVIVHKW ETHLQPRSIT 100
    PLESEIIIDD GQFGIHNGVE TLDSGWLTCQ TEIRLRLHYS EKPPVSITKK 150
    KLKKSRFRVK LTLEGLEEDD DDRVSPTVLH KMSNSLEISL ISDNEFKCRH 200
    SQPECGYGLQ PDRWTEYSIQ TMEPDNLELI FDFFEEDLSE HVVQGDALPG 250
    HVGTACLLSS TIAESGKSAG ILTLPIMSRN SRKTIGKVRV DYIIIKPLPG 300
    YSCDMKSSFS KYWKPRIPLD VGHRGAGNST TTAQLAKVQE NTIASLRNAA 350
    SHGAAFVEFD VHLSKDFVPV VYHDLTCCLT MKKKFDADPV ELFEIPVKEL 400
    TFDQLQLLKL THVTALKSKD RKESVVQEEN SFSENQPFPS LKMVLESLPE 450
    DVGFNIEIKW ICQQRDGMWD GNLSTYFDMN LFLDIILKTV LENSGKRRIV 500
    FSSFDADICT MVRQKQNKYP ILFLTQGKSE IYPELMDLRS RTTPIAMSFA 550
    QFENLLGINV HTEDLLRNPS YIQEAKAKGL VIFCWGDDTN DPENRRKLKE 600
    LGVNGLIYDR IYDWMPEQPN IFQVEQLERL KQELPELKSC LCPTVSRFVP 650
    SSLCGESDIH VDANGIDNVE NA 672
    Length:672
    Mass (Da):76,035
    Last modified:October 10, 2002 - v2
    Checksum:i9AA17024D231AD74
    GO

    Sequence cautioni

    The sequence BAA91994.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence BAA92672.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti273 – 2731T → I.
    Corresponds to variant rs2273373 [ dbSNP | Ensembl ].
    VAR_022060

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB037855 mRNA. Translation: BAA92672.1. Different initiation.
    AL109935 Genomic DNA. Translation: CAB91047.2.
    CH471133 Genomic DNA. Translation: EAX10414.1.
    CH471133 Genomic DNA. Translation: EAX10415.1.
    BC027588 mRNA. Translation: AAH27588.1.
    AK001947 mRNA. Translation: BAA91994.1. Different initiation.
    CCDSiCCDS13090.1.
    RefSeqiNP_062539.1. NM_019593.3.
    XP_005260815.1. XM_005260758.2.
    XP_006723658.1. XM_006723595.1.
    XP_006723659.1. XM_006723596.1.
    UniGeneiHs.636359.

    Genome annotation databases

    EnsembliENST00000379019; ENSP00000368305; ENSG00000125772.
    GeneIDi56261.
    KEGGihsa:56261.
    UCSCiuc002wmd.4. human.

    Polymorphism databases

    DMDMi23821811.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB037855 mRNA. Translation: BAA92672.1 . Different initiation.
    AL109935 Genomic DNA. Translation: CAB91047.2 .
    CH471133 Genomic DNA. Translation: EAX10414.1 .
    CH471133 Genomic DNA. Translation: EAX10415.1 .
    BC027588 mRNA. Translation: AAH27588.1 .
    AK001947 mRNA. Translation: BAA91994.1 . Different initiation.
    CCDSi CCDS13090.1.
    RefSeqi NP_062539.1. NM_019593.3.
    XP_005260815.1. XM_005260758.2.
    XP_006723658.1. XM_006723595.1.
    XP_006723659.1. XM_006723596.1.
    UniGenei Hs.636359.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2Z0B X-ray 2.00 A/B/C/D/E/F 3-120 [» ]
    ProteinModelPortali Q9NPB8.
    SMRi Q9NPB8. Positions 3-115, 321-611.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 121125. 1 interaction.
    IntActi Q9NPB8. 1 interaction.
    MINTi MINT-4650772.
    STRINGi 9606.ENSP00000368305.

    Chemistry

    BindingDBi Q9NPB8.

    Protein family/group databases

    CAZyi CBM20. Carbohydrate-Binding Module Family 20.

    PTM databases

    PhosphoSitei Q9NPB8.

    Polymorphism databases

    DMDMi 23821811.

    Proteomic databases

    MaxQBi Q9NPB8.
    PaxDbi Q9NPB8.
    PRIDEi Q9NPB8.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000379019 ; ENSP00000368305 ; ENSG00000125772 .
    GeneIDi 56261.
    KEGGi hsa:56261.
    UCSCi uc002wmd.4. human.

    Organism-specific databases

    CTDi 56261.
    GeneCardsi GC20M005525.
    HGNCi HGNC:26957. GPCPD1.
    HPAi HPA039556.
    HPA042987.
    MIMi 614124. gene.
    neXtProti NX_Q9NPB8.
    PharmGKBi PA165392351.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG0584.
    HOGENOMi HOG000231653.
    HOVERGENi HBG080384.
    InParanoidi Q9NPB8.
    OMAi HDLTCCI.
    OrthoDBi EOG7RNJZM.
    PhylomeDBi Q9NPB8.
    TreeFami TF314722.

    Enzyme and pathway databases

    Reactomei REACT_120785. Hydrolysis of LPE.
    REACT_120977. Hydrolysis of LPC.

    Miscellaneous databases

    ChiTaRSi GPCPD1. human.
    EvolutionaryTracei Q9NPB8.
    GenomeRNAii 56261.
    NextBioi 61917.
    PROi Q9NPB8.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9NPB8.
    Bgeei Q9NPB8.
    Genevestigatori Q9NPB8.

    Family and domain databases

    Gene3Di 2.60.40.10. 1 hit.
    3.20.20.190. 1 hit.
    InterProi IPR013784. Carb-bd-like_fold.
    IPR002044. CBM_fam20.
    IPR013783. Ig-like_fold.
    IPR017946. PLC-like_Pdiesterase_TIM-brl.
    [Graphical view ]
    Pfami PF00686. CBM_20. 1 hit.
    [Graphical view ]
    SMARTi SM01065. CBM_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF49452. SSF49452. 1 hit.
    SSF51695. SSF51695. 1 hit.
    PROSITEi PS51166. CBM20. 1 hit.
    PS51704. GP_PDE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro."
      Nagase T., Kikuno R., Ishikawa K., Hirosawa M., Ohara O.
      DNA Res. 7:65-73(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    2. "The DNA sequence and comparative analysis of human chromosome 20."
      Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E.
      , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
      Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. 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: Testis.
    5. "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] OF 413-672.
      Tissue: Placenta.
    6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. "Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)."
      RIKEN structural genomics initiative (RSGI)
      Submitted (MAY-2008) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-120 IN COMPLEX WITH PHOSPHATE.

    Entry informationi

    Entry nameiGPCP1_HUMAN
    AccessioniPrimary (citable) accession number: Q9NPB8
    Secondary accession number(s): D3DW06, Q9BQL8, Q9NUX0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 10, 2002
    Last sequence update: October 10, 2002
    Last modified: October 1, 2014
    This is version 117 of the entry and version 2 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 20
      Human chromosome 20: 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3