GPCP1_HUMAN
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 03-AUG-2022, entry version 166.
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; Q9NPB8; -.
DR PeptideAtlas; Q9NPB8; -.
DR PRIDE; Q9NPB8; -.
DR ProteomicsDB; 81961; -.
DR Antibodypedia; 23917; 27 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 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; YHTAEGL; -.
DR OrthoDB; 687958at2759; -.
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; 12 hits in 1068 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 187 other tissues.
DR ExpressionAtlas; Q9NPB8; baseline and differential.
DR Genevisible; Q9NPB8; HS.
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 Gene3D; 2.60.40.10; -; 1.
DR Gene3D; 3.20.20.190; -; 1.
DR InterPro; IPR013784; Carb-bd-like_fold.
DR InterPro; IPR034839; CBM20_GPCPD1.
DR InterPro; IPR002044; CBM_fam20.
DR InterPro; IPR033506; Gde1.
DR InterPro; IPR030395; GP_PDE_dom.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR PANTHER; PTHR22958:SF1; PTHR22958:SF1; 1.
DR Pfam; PF00686; CBM_20; 1.
DR Pfam; PF03009; GDPD; 1.
DR SMART; SM01065; CBM_2; 1.
DR SUPFAM; SSF49452; SSF49452; 1.
DR SUPFAM; SSF51695; SSF51695; 1.
DR PROSITE; PS51166; CBM20; 1.
DR PROSITE; PS51704; GP_PDE; 1.
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
