ID   GPCP1_HUMAN             Reviewed;         672 AA.
AC   Q9NPB8; D3DW06; Q9BQL8; Q9NUX0;
DT   10-OCT-2002, integrated into UniProtKB/Swiss-Prot.
DT   10-OCT-2002, sequence version 2.
DT   27-MAR-2024, entry version 173.
DE   RecName: Full=Glycerophosphocholine phosphodiesterase GPCPD1;
DE            EC=3.1.4.2;
DE   AltName: Full=Glycerophosphodiester phosphodiesterase 5;
GN   Name=GPCPD1; Synonyms=GDE5, KIAA1434;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Brain;
RX   PubMed=10718198; DOI=10.1093/dnares/7.1.65;
RA   Nagase T., Kikuno R., Ishikawa K., Hirosawa M., Ohara O.;
RT   "Prediction of the coding sequences of unidentified human genes. XVI. The
RT   complete sequences of 150 new cDNA clones from brain which code for large
RT   proteins in vitro.";
RL   DNA Res. 7:65-73(2000).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=11780052; DOI=10.1038/414865a;
RA   Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R.,
RA   Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L.,
RA   Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P.,
RA   Bird C.P., Blakey S.E., Bridgeman A.M., Brown A.J., Buck D., Burrill W.D.,
RA   Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G.,
RA   Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E.,
RA   Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D.,
RA   Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P.,
RA   Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E.,
RA   Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J.,
RA   Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D.,
RA   Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S.,
RA   Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D.,
RA   Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A.,
RA   Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T.,
RA   Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I.,
RA   Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M.,
RA   Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D.,
RA   Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M.,
RA   Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A.,
RA   Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L.,
RA   Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L.,
RA   Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.;
RT   "The DNA sequence and comparative analysis of human chromosome 20.";
RL   Nature 414:865-871(2001).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA   Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA   Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA   Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA   Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA   Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA   Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA   Hunkapiller M.W., Myers E.W., Venter J.C.;
RL   Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Testis;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 413-672.
RC   TISSUE=Placenta;
RX   PubMed=14702039; DOI=10.1038/ng1285;
RA   Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA   Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA   Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA   Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA   Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA   Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA   Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA   Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA   Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA   Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA   Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA   Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA   Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA   Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA   Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA   Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA   Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA   Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA   Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA   Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA   Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA   Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA   Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA   Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA   Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA   Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA   Isogai T., Sugano S.;
RT   "Complete sequencing and characterization of 21,243 full-length human
RT   cDNAs.";
RL   Nat. Genet. 36:40-45(2004).
RN   [6]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA   Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA   Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA   Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT   "N-terminal acetylome analyses and functional insights of the N-terminal
RT   acetyltransferase NatB.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-175, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Erythroleukemia;
RX   PubMed=23186163; DOI=10.1021/pr300630k;
RA   Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA   Mohammed S.;
RT   "Toward a comprehensive characterization of a human cancer cell
RT   phosphoproteome.";
RL   J. Proteome Res. 12:260-271(2013).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-120 IN COMPLEX WITH PHOSPHATE.
RG   RIKEN structural genomics initiative (RSGI);
RT   "Crystal structure of CBM20 domain of human putative glycerophosphodiester
RT   phosphodiesterase 5 (KIAA1434).";
RL   Submitted (MAY-2008) to the PDB data bank.
CC   -!- FUNCTION: May be involved in the negative regulation of skeletal muscle
CC       differentiation, independently of its glycerophosphocholine
CC       phosphodiesterase activity. {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + sn-glycerol 3-phosphocholine = choline + H(+) + sn-
CC         glycerol 3-phosphate; Xref=Rhea:RHEA:16061, ChEBI:CHEBI:15354,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16870,
CC         ChEBI:CHEBI:57597; EC=3.1.4.2;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000250}.
CC   -!- TISSUE SPECIFICITY: Widely expressed, with highest expression in spinal
CC       chord.
CC   -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC       family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAA91994.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC       Sequence=BAA92672.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; AB037855; BAA92672.1; ALT_INIT; mRNA.
DR   EMBL; AL109935; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CH471133; EAX10414.1; -; Genomic_DNA.
DR   EMBL; CH471133; EAX10415.1; -; Genomic_DNA.
DR   EMBL; BC027588; AAH27588.1; -; mRNA.
DR   EMBL; AK001947; BAA91994.1; ALT_INIT; mRNA.
DR   CCDS; CCDS13090.1; -.
DR   RefSeq; NP_062539.1; NM_019593.3.
DR   RefSeq; XP_005260815.1; XM_005260758.4.
DR   RefSeq; XP_006723659.1; XM_006723596.3.
DR   PDB; 2Z0B; X-ray; 2.00 A; A/B/C/D/E/F=3-120.
DR   PDBsum; 2Z0B; -.
DR   AlphaFoldDB; Q9NPB8; -.
DR   SMR; Q9NPB8; -.
DR   BioGRID; 121125; 5.
DR   IntAct; Q9NPB8; 2.
DR   MINT; Q9NPB8; -.
DR   STRING; 9606.ENSP00000368305; -.
DR   BindingDB; Q9NPB8; -.
DR   CAZy; CBM20; Carbohydrate-Binding Module Family 20.
DR   iPTMnet; Q9NPB8; -.
DR   PhosphoSitePlus; Q9NPB8; -.
DR   BioMuta; GPCPD1; -.
DR   DMDM; 23821811; -.
DR   EPD; Q9NPB8; -.
DR   jPOST; Q9NPB8; -.
DR   MassIVE; Q9NPB8; -.
DR   MaxQB; Q9NPB8; -.
DR   PaxDb; 9606-ENSP00000368305; -.
DR   PeptideAtlas; Q9NPB8; -.
DR   ProteomicsDB; 81961; -.
DR   Pumba; Q9NPB8; -.
DR   Antibodypedia; 23917; 42 antibodies from 10 providers.
DR   DNASU; 56261; -.
DR   Ensembl; ENST00000379019.7; ENSP00000368305.4; ENSG00000125772.14.
DR   GeneID; 56261; -.
DR   KEGG; hsa:56261; -.
DR   MANE-Select; ENST00000379019.7; ENSP00000368305.4; NM_019593.5; NP_062539.1.
DR   UCSC; uc002wme.5; human.
DR   AGR; HGNC:26957; -.
DR   CTD; 56261; -.
DR   DisGeNET; 56261; -.
DR   GeneCards; GPCPD1; -.
DR   HGNC; HGNC:26957; GPCPD1.
DR   HPA; ENSG00000125772; Tissue enhanced (bone).
DR   MIM; 614124; gene.
DR   neXtProt; NX_Q9NPB8; -.
DR   OpenTargets; ENSG00000125772; -.
DR   PharmGKB; PA165392351; -.
DR   VEuPathDB; HostDB:ENSG00000125772; -.
DR   eggNOG; KOG2421; Eukaryota.
DR   GeneTree; ENSGT00440000033970; -.
DR   HOGENOM; CLU_013007_2_0_1; -.
DR   InParanoid; Q9NPB8; -.
DR   OMA; LKVYHTA; -.
DR   OrthoDB; 1005457at2759; -.
DR   PhylomeDB; Q9NPB8; -.
DR   TreeFam; TF314722; -.
DR   BRENDA; 3.1.4.46; 2681.
DR   PathwayCommons; Q9NPB8; -.
DR   Reactome; R-HSA-1483115; Hydrolysis of LPC.
DR   Reactome; R-HSA-1483152; Hydrolysis of LPE.
DR   SignaLink; Q9NPB8; -.
DR   BioGRID-ORCS; 56261; 13 hits in 1146 CRISPR screens.
DR   ChiTaRS; GPCPD1; human.
DR   EvolutionaryTrace; Q9NPB8; -.
DR   GenomeRNAi; 56261; -.
DR   Pharos; Q9NPB8; Tdark.
DR   PRO; PR:Q9NPB8; -.
DR   Proteomes; UP000005640; Chromosome 20.
DR   RNAct; Q9NPB8; Protein.
DR   Bgee; ENSG00000125772; Expressed in palpebral conjunctiva and 189 other cell types or tissues.
DR   ExpressionAtlas; Q9NPB8; baseline and differential.
DR   GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR   GO; GO:0047389; F:glycerophosphocholine phosphodiesterase activity; IBA:GO_Central.
DR   GO; GO:2001070; F:starch binding; IEA:InterPro.
DR   GO; GO:0046475; P:glycerophospholipid catabolic process; IBA:GO_Central.
DR   GO; GO:0007519; P:skeletal muscle tissue development; IEA:Ensembl.
DR   CDD; cd05814; CBM20_Prei4; 1.
DR   CDD; cd08607; GDPD_GDE5; 1.
DR   Gene3D; 2.60.40.10; Immunoglobulins; 1.
DR   Gene3D; 3.20.20.190; Phosphatidylinositol (PI) phosphodiesterase; 1.
DR   InterPro; IPR013784; Carb-bd-like_fold.
DR   InterPro; IPR034839; CBM20_GPCPD1.
DR   InterPro; IPR002044; CBM_fam20.
DR   InterPro; IPR030395; GP_PDE_dom.
DR   InterPro; IPR013783; Ig-like_fold.
DR   InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR   PANTHER; PTHR22958:SF1; GLYCEROPHOSPHOCHOLINE PHOSPHODIESTERASE GPCPD1; 1.
DR   PANTHER; PTHR22958; GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE; 1.
DR   Pfam; PF00686; CBM_20; 1.
DR   Pfam; PF03009; GDPD; 1.
DR   SMART; SM01065; CBM_2; 1.
DR   SUPFAM; SSF51695; PLC-like phosphodiesterases; 1.
DR   SUPFAM; SSF49452; Starch-binding domain-like; 1.
DR   PROSITE; PS51166; CBM20; 1.
DR   PROSITE; PS51704; GP_PDE; 1.
DR   Genevisible; Q9NPB8; HS.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Hydrolase; Phosphoprotein; Reference proteome.
FT   CHAIN           1..672
FT                   /note="Glycerophosphocholine phosphodiesterase GPCPD1"
FT                   /id="PRO_0000050797"
FT   DOMAIN          1..115
FT                   /note="CBM20"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00594"
FT   DOMAIN          318..618
FT                   /note="GP-PDE"
FT   BINDING         70
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255"
FT   BINDING         88..89
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255"
FT   MOD_RES         175
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:23186163"
FT   MOD_RES         424
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:Q8C0L9"
FT   MOD_RES         608
FT                   /note="Phosphotyrosine"
FT                   /evidence="ECO:0000250|UniProtKB:Q8C0L9"
FT   VARIANT         273
FT                   /note="T -> I (in dbSNP:rs2273373)"
FT                   /id="VAR_022060"
FT   STRAND          4..11
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   STRAND          19..26
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   HELIX           27..29
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   TURN            30..32
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   HELIX           34..36
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   STRAND          49..58
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   STRAND          64..74
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   STRAND          84..90
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   STRAND          97..99
FT                   /evidence="ECO:0007829|PDB:2Z0B"
FT   STRAND          103..112
FT                   /evidence="ECO:0007829|PDB:2Z0B"
SQ   SEQUENCE   672 AA;  76035 MW;  9AA17024D231AD74 CRC64;
     MTPSQVAFEI RGTLLPGEVF AICGSCDALG NWNPQNAVAL LPENDTGESM LWKATIVLSR
     GVSVQYRYFK GYFLEPKTIG GPCQVIVHKW ETHLQPRSIT PLESEIIIDD GQFGIHNGVE
     TLDSGWLTCQ TEIRLRLHYS EKPPVSITKK KLKKSRFRVK LTLEGLEEDD DDRVSPTVLH
     KMSNSLEISL ISDNEFKCRH SQPECGYGLQ PDRWTEYSIQ TMEPDNLELI FDFFEEDLSE
     HVVQGDALPG HVGTACLLSS TIAESGKSAG ILTLPIMSRN SRKTIGKVRV DYIIIKPLPG
     YSCDMKSSFS KYWKPRIPLD VGHRGAGNST TTAQLAKVQE NTIASLRNAA SHGAAFVEFD
     VHLSKDFVPV VYHDLTCCLT MKKKFDADPV ELFEIPVKEL TFDQLQLLKL THVTALKSKD
     RKESVVQEEN SFSENQPFPS LKMVLESLPE DVGFNIEIKW ICQQRDGMWD GNLSTYFDMN
     LFLDIILKTV LENSGKRRIV FSSFDADICT MVRQKQNKYP ILFLTQGKSE IYPELMDLRS
     RTTPIAMSFA QFENLLGINV HTEDLLRNPS YIQEAKAKGL VIFCWGDDTN DPENRRKLKE
     LGVNGLIYDR IYDWMPEQPN IFQVEQLERL KQELPELKSC LCPTVSRFVP SSLCGESDIH
     VDANGIDNVE NA
//