GDPD3_MOUSE
ID GDPD3_MOUSE Reviewed; 330 AA.
AC Q99LY2; Q9D1C0;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 14-APR-2009, sequence version 2.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Lysophospholipase D GDPD3 {ECO:0000305};
DE EC=3.1.4.- {ECO:0000269|PubMed:25528375, ECO:0000269|PubMed:27637550};
DE AltName: Full=Glycerophosphodiester phosphodiesterase 7 {ECO:0000303|PubMed:25528375};
DE AltName: Full=Glycerophosphodiester phosphodiesterase domain-containing protein 3;
GN Name=Gdpd3 {ECO:0000312|MGI:MGI:1915866};
GN Synonyms=Gde7 {ECO:0000303|PubMed:25528375};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Embryo;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 62-330.
RC TISSUE=Mammary tumor;
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 [3]
RP SUBCELLULAR LOCATION, TISSUE SPECIFICITY, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND FUNCTION.
RX PubMed=25528375; DOI=10.1074/jbc.m114.614537;
RA Ohshima N., Kudo T., Yamashita Y., Mariggio S., Araki M., Honda A.,
RA Nagano T., Isaji C., Kato N., Corda D., Izumi T., Yanaka N.;
RT "New members of the mammalian glycerophosphodiester phosphodiesterase
RT family: GDE4 and GDE7 produce lysophosphatidic acid by lysophospholipase D
RT activity.";
RL J. Biol. Chem. 290:4260-4271(2015).
RN [4]
RP CATALYTIC ACTIVITY, FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=27637550; DOI=10.1016/j.bbalip.2016.09.008;
RA Rahman I.A., Tsuboi K., Hussain Z., Yamashita R., Okamoto Y., Uyama T.,
RA Yamazaki N., Tanaka T., Tokumura A., Ueda N.;
RT "Calcium-dependent generation of N-acylethanolamines and lysophosphatidic
RT acids by glycerophosphodiesterase GDE7.";
RL Biochim. Biophys. Acta 1861:1881-1892(2016).
CC -!- FUNCTION: Hydrolyzes lysoglycerophospholipids to produce
CC lysophosphatidic acid (LPA) and the corresponding amines
CC (PubMed:25528375, PubMed:27637550). Shows a preference for 1-O-alkyl-
CC sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylcholine (lyso-
CC PC) and N-acylethanolamine lysophospholipids (PubMed:25528375). Does
CC not display glycerophosphodiester phosphodiesterase activity, since it
CC cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine
CC (PubMed:25528375). {ECO:0000269|PubMed:25528375,
CC ECO:0000269|PubMed:27637550}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-hexadecanoyl-sn-glycero-3-phosphocholine + H2O = 1-
CC hexadecanoyl-sn-glycero-3-phosphate + choline + H(+);
CC Xref=Rhea:RHEA:38975, ChEBI:CHEBI:15354, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57518, ChEBI:CHEBI:72998;
CC Evidence={ECO:0000269|PubMed:25528375, ECO:0000269|PubMed:27637550};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:38976;
CC Evidence={ECO:0000269|PubMed:25528375};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-O-hexadecyl-sn-glycero-3-phosphocholine + H2O = 1-O-
CC hexadecyl-sn-glycero-3-phosphate + choline + H(+);
CC Xref=Rhea:RHEA:41143, ChEBI:CHEBI:15354, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:64496, ChEBI:CHEBI:77580;
CC Evidence={ECO:0000269|PubMed:25528375};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:41144;
CC Evidence={ECO:0000269|PubMed:25528375};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-O-(1Z-octadecenyl)-sn-glycero-3-phospho-N-hexadecanoyl-
CC ethanolamine + H2O = 1-O-(1Z-octadecenyl)-sn-glycero-3-phosphate +
CC H(+) + N-hexadecanoylethanolamine; Xref=Rhea:RHEA:53184,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:71464,
CC ChEBI:CHEBI:137009, ChEBI:CHEBI:137017;
CC Evidence={ECO:0000269|PubMed:27637550};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:53185;
CC Evidence={ECO:0000305|PubMed:27637550};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-1-(9Z-octadecenoyl)-
CC sn-glycero-3-phosphoethanolamine = 1-(9Z-octadecenoyl)-sn-glycero-3-
CC phosphate + H(+) + N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine;
CC Xref=Rhea:RHEA:45544, ChEBI:CHEBI:2700, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:74544, ChEBI:CHEBI:85223;
CC Evidence={ECO:0000269|PubMed:27637550};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:45545;
CC Evidence={ECO:0000305|PubMed:27637550};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N,1-di-(9Z-octadecenoyl)-sn-glycero-3-
CC phosphoethanolamine = 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate +
CC H(+) + N-(9Z-octadecenoyl) ethanolamine; Xref=Rhea:RHEA:56460,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:71466,
CC ChEBI:CHEBI:74544, ChEBI:CHEBI:85222;
CC Evidence={ECO:0000269|PubMed:27637550};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:56461;
CC Evidence={ECO:0000305|PubMed:27637550};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-hexadecanoyl-1-(9Z-octadecenoyl)-sn-glycero-3-
CC phosphoethanolamine = 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate +
CC H(+) + N-hexadecanoylethanolamine; Xref=Rhea:RHEA:53168,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:71464,
CC ChEBI:CHEBI:74544, ChEBI:CHEBI:85217;
CC Evidence={ECO:0000269|PubMed:27637550};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:53169;
CC Evidence={ECO:0000305|PubMed:27637550};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-hexadecanoyl-sn-glycero-3-phosphocholine + H2O = H(+) +
CC hexadecanoate + sn-glycerol 3-phosphocholine; Xref=Rhea:RHEA:40435,
CC ChEBI:CHEBI:7896, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16870, ChEBI:CHEBI:72998;
CC Evidence={ECO:0000250|UniProtKB:Q7L5L3};
CC -!- ACTIVITY REGULATION: Lysophospholipase D activity is stimulated by
CC calcium. Loss of lysophospholipase D activity in presence of EDTA.
CC {ECO:0000250|UniProtKB:Q7L5L3}.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Multi-pass membrane
CC protein {ECO:0000305}. Cytoplasm, perinuclear region
CC {ECO:0000269|PubMed:25528375}. Endoplasmic reticulum membrane
CC {ECO:0000269|PubMed:25528375}; Multi-pass membrane protein
CC {ECO:0000305}. Note=Partially colocalized with CANX (PubMed:25528375).
CC {ECO:0000269|PubMed:25528375}.
CC -!- TISSUE SPECIFICITY: Highly expressed in stomach and kidney. In stomach
CC detected in the glandular epithelium. Predominantly expressed in the
CC stomach (at protein level). {ECO:0000269|PubMed:25528375,
CC ECO:0000269|PubMed:27637550}.
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BC002172; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305};
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DR EMBL; AK003726; BAB22961.1; -; mRNA.
DR EMBL; BC002172; -; NOT_ANNOTATED_CDS; mRNA.
DR CCDS; CCDS40130.1; -.
DR RefSeq; NP_077190.2; NM_024228.2.
DR AlphaFoldDB; Q99LY2; -.
DR SMR; Q99LY2; -.
DR STRING; 10090.ENSMUSP00000032944; -.
DR SwissLipids; SLP:000001719; -.
DR iPTMnet; Q99LY2; -.
DR PhosphoSitePlus; Q99LY2; -.
DR PaxDb; Q99LY2; -.
DR PRIDE; Q99LY2; -.
DR ProteomicsDB; 272950; -.
DR Antibodypedia; 51979; 128 antibodies from 17 providers.
DR DNASU; 68616; -.
DR Ensembl; ENSMUST00000032944; ENSMUSP00000032944; ENSMUSG00000030703.
DR GeneID; 68616; -.
DR KEGG; mmu:68616; -.
DR UCSC; uc009jso.1; mouse.
DR CTD; 79153; -.
DR MGI; MGI:1915866; Gdpd3.
DR VEuPathDB; HostDB:ENSMUSG00000030703; -.
DR eggNOG; KOG2258; Eukaryota.
DR GeneTree; ENSGT00940000160759; -.
DR HOGENOM; CLU_030006_5_0_1; -.
DR InParanoid; Q99LY2; -.
DR OMA; KWAIMRK; -.
DR OrthoDB; 1218115at2759; -.
DR PhylomeDB; Q99LY2; -.
DR TreeFam; TF328545; -.
DR BRENDA; 3.1.4.39; 3474.
DR BioGRID-ORCS; 68616; 3 hits in 74 CRISPR screens.
DR ChiTaRS; Gdpd3; mouse.
DR PRO; PR:Q99LY2; -.
DR Proteomes; UP000000589; Chromosome 7.
DR RNAct; Q99LY2; protein.
DR Bgee; ENSMUSG00000030703; Expressed in plantaris and 122 other tissues.
DR Genevisible; Q99LY2; MM.
DR GO; GO:0005783; C:endoplasmic reticulum; ISO:MGI.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IDA:UniProtKB.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:UniProtKB.
DR GO; GO:0004622; F:lysophospholipase activity; EXP:Reactome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008081; F:phosphoric diester hydrolase activity; IMP:UniProtKB.
DR GO; GO:0046475; P:glycerophospholipid catabolic process; IBA:GO_Central.
DR GO; GO:0070291; P:N-acylethanolamine metabolic process; IMP:UniProtKB.
DR GO; GO:0034638; P:phosphatidylcholine catabolic process; IDA:UniProtKB.
DR GO; GO:0006644; P:phospholipid metabolic process; IDA:UniProtKB.
DR Gene3D; 3.20.20.190; -; 1.
DR InterPro; IPR030395; GP_PDE_dom.
DR InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR Pfam; PF03009; GDPD; 1.
DR SUPFAM; SSF51695; SSF51695; 1.
DR PROSITE; PS51704; GP_PDE; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Endoplasmic reticulum; Hydrolase; Lipid metabolism; Membrane;
KW Metal-binding; Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..330
FT /note="Lysophospholipase D GDPD3"
FT /id="PRO_0000251937"
FT TOPO_DOM 1
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 2..22
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 23..200
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 201..221
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 222..330
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 39..308
FT /note="GP-PDE"
FT REGION 311..330
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 71
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 73
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 86
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
SQ SEQUENCE 330 AA; 38488 MW; BE90FD27E56EBAB4 CRC64;
MIPLLYFVLP TLGSYVMLSI FFLRRPHLLH TPRAPVFPIR LAAHRGGSGE RLENTMEAVE
NSMAQRADLL EFDCQLTRDG VVVVSHDKNL SRQSGLNKDV NTLDFEELPL YKEELEIYFS
PGHFAHGSDR HMISLEDVFQ KFPRTPMCLE VKERNEELIH KVANLTRRFD RNEITIWAAE
KSSVMKRCRA ANPEMPMAFT IWRSFWILLL YYLGLLPFVS IPEKFFFCFL PTIINRTYFP
FRCGWMNQLS ATITKWIIMR KSLIRHLQDR GVQVLFWCLN EESDFEVAFS LGANGVMTDY
PTALRHYLDK QEEETQPPQP EALSCLSLKK
