GDE1_RAT
ID GDE1_RAT Reviewed; 331 AA.
AC Q9JL55; Q6IRJ6;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 2.
DT 03-AUG-2022, entry version 96.
DE RecName: Full=Glycerophosphodiester phosphodiesterase 1 {ECO:0000305};
DE AltName: Full=Glycerophosphoinositol glycerophosphodiesterase GDE1 {ECO:0000305};
DE EC=3.1.4.44 {ECO:0000269|PubMed:12576545};
DE AltName: Full=Lysophospholipase D GDE1 {ECO:0000305};
DE EC=3.1.4.- {ECO:0000250|UniProtKB:Q9JL56};
DE AltName: Full=Membrane-interacting protein of RGS16 {ECO:0000303|PubMed:10760272};
GN Name=Gde1 {ECO:0000312|RGD:621788};
GN Synonyms=Mir16 {ECO:0000303|PubMed:10760272};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], INTERACTION WITH RGS16, SUBCELLULAR LOCATION,
RP GLYCOSYLATION, AND TISSUE SPECIFICITY.
RX PubMed=10760272; DOI=10.1073/pnas.97.8.3999;
RA Zheng B., Chen D., Farquhar M.G.;
RT "MIR16, a putative membrane glycerophosphodiester phosphodiesterase,
RT interacts with RGS16.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:3999-4004(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Lung;
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 FUNCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, MEMBRANE
RP TOPOLOGY, MUTAGENESIS OF GLU-97; ASP-99 AND HIS-112, AND COFACTOR.
RX PubMed=12576545; DOI=10.1073/pnas.0337605100;
RA Zheng B., Berrie C.P., Corda D., Farquhar M.G.;
RT "GDE1/MIR16 is a glycerophosphoinositol phosphodiesterase regulated by
RT stimulation of G protein-coupled receptors.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:1745-1750(2003).
CC -!- FUNCTION: Hydrolyzes the phosphodiester bond of glycerophosphodiesters
CC such as glycerophosphoinositol (GroPIns) and glycerophosphoethanolamine
CC (GroPEth), to yield a glycerol phosphate and an alcohol
CC (PubMed:12576545). Hydrolyzes glycerophospho-N-acylethanolamines to N-
CC acylethanolamines in the brain and participates in bioactive N-
CC acylethanolamine biosynthesis such as anandamide (an endocannabinoid),
CC N-palmitoylethanolamine (an anti-inflammatory), and N-
CC oleoylethanolamine (an anorexic). In addition, has a lysophospholipase
CC D activity by hydrolyzing N-acyl-lysoplasmenylethanolamine (N-acyl-
CC lysoPlsEt) to N-acylethanolamine. However lysophospholipase D activity
CC is lower than glycerophosphodiester phosphodiesterase activity (By
CC similarity). Has little or no activity towards glycerophosphocholine
CC (PubMed:12576545). {ECO:0000250|UniProtKB:Q9JL56,
CC ECO:0000269|PubMed:12576545}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + sn-glycero-3-phospho-1D-myo-inositol = H(+) + myo-
CC inositol + sn-glycerol 3-phosphate; Xref=Rhea:RHEA:16501,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17268,
CC ChEBI:CHEBI:57597, ChEBI:CHEBI:58444; EC=3.1.4.44;
CC Evidence={ECO:0000269|PubMed:12576545};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16502;
CC Evidence={ECO:0000305|PubMed:12576545};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-O-(1Z-octadecenyl)-sn-glycero-3-phospho-(N-5Z,8Z,11Z,14Z-
CC eicosatetraenoyl)-ethanolamine + H2O = 1-O-(1Z-octadecenyl)-sn-
CC glycero-3-phosphate + H(+) + N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-
CC ethanolamine; Xref=Rhea:RHEA:53192, ChEBI:CHEBI:2700,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:137016,
CC ChEBI:CHEBI:137017; Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:53193;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1-O-(1Z-octadecenyl)-sn-glycero-3-phospho-(N-9Z-octadecenoyl)-
CC ethanolamine + H2O = 1-O-(1Z-octadecenyl)-sn-glycero-3-phosphate +
CC H(+) + N-(9Z-octadecenoyl) ethanolamine; Xref=Rhea:RHEA:53188,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:71466,
CC ChEBI:CHEBI:137010, ChEBI:CHEBI:137017;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:53189;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
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:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:53185;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-sn-glycero-3-
CC phosphoethanolamine = H(+) + N-(4Z,7Z,10Z,13Z,16Z,19Z)-
CC docosahexaenoyl ethanolamine + sn-glycerol 3-phosphate;
CC Xref=Rhea:RHEA:45444, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57597, ChEBI:CHEBI:85250, ChEBI:CHEBI:85252;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:45445;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-eicosanoyl-sn-glycero-3-phosphoethanolamine = H(+) +
CC N-eicosanoyl ethanolamine + sn-glycerol 3-phosphate;
CC Xref=Rhea:RHEA:45440, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57597, ChEBI:CHEBI:85228, ChEBI:CHEBI:85253;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:45441;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-hexadecanoyl-sn-glycero-3-phosphoethanolamine = H(+) +
CC N-hexadecanoylethanolamine + sn-glycerol 3-phosphate;
CC Xref=Rhea:RHEA:45436, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57597, ChEBI:CHEBI:71464, ChEBI:CHEBI:85226;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:45437;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine =
CC H(+) + N-(9Z-octadecenoyl) ethanolamine + sn-glycerol 3-phosphate;
CC Xref=Rhea:RHEA:45432, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57597, ChEBI:CHEBI:71466, ChEBI:CHEBI:85229;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:45433;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-
CC phosphoethanolamine = H(+) + N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-
CC ethanolamine + sn-glycerol 3-phosphate; Xref=Rhea:RHEA:45428,
CC ChEBI:CHEBI:2700, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57597, ChEBI:CHEBI:85230;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:45429;
CC Evidence={ECO:0000250|UniProtKB:Q9JL56};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:12576545};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA, calcium chloride, and zinc
CC chloride. Enhanced by magnesium chloride (By similarity).
CC Glycerophosphodiester phosphodiesterase activity can be modulated by G-
CC protein signaling pathways (PubMed:12576545).
CC {ECO:0000250|UniProtKB:Q9JL56, ECO:0000269|PubMed:12576545}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=12 mM for glycerophosphoinositol {ECO:0000269|PubMed:12576545};
CC Vmax=3000 pmol/min/mg enzyme {ECO:0000269|PubMed:12576545};
CC Note=Measured in the presence of 10 mM magnesium chloride at 37
CC degrees Celsius.;
CC -!- SUBUNIT: Interacts with PRAF2 (By similarity). Interacts with RGS16
CC (PubMed:10760272). {ECO:0000250|UniProtKB:Q9NZC3,
CC ECO:0000269|PubMed:10760272}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:10760272,
CC ECO:0000269|PubMed:12576545}; Multi-pass membrane protein
CC {ECO:0000255}. Cytoplasmic vesicle membrane
CC {ECO:0000269|PubMed:10760272, ECO:0000269|PubMed:12576545}; Multi-pass
CC membrane protein {ECO:0000255}. Note=Perinuclear vesicles and cell
CC membrane. {ECO:0000305|PubMed:12576545}.
CC -!- TISSUE SPECIFICITY: Detected in heart, brain, lung, liver, skeletal
CC muscle, kidney, pituitary and testis. {ECO:0000269|PubMed:10760272}.
CC -!- PTM: N-glycosylated. {ECO:0000269|PubMed:10760272}.
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
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DR EMBL; AF212861; AAF65233.1; -; mRNA.
DR EMBL; BC070897; AAH70897.1; -; mRNA.
DR RefSeq; NP_116004.2; NM_032615.2.
DR AlphaFoldDB; Q9JL55; -.
DR SMR; Q9JL55; -.
DR STRING; 10116.ENSRNOP00000064735; -.
DR GlyGen; Q9JL55; 1 site.
DR PhosphoSitePlus; Q9JL55; -.
DR jPOST; Q9JL55; -.
DR PaxDb; Q9JL55; -.
DR PRIDE; Q9JL55; -.
DR GeneID; 60418; -.
DR KEGG; rno:60418; -.
DR CTD; 51573; -.
DR RGD; 621788; Gde1.
DR eggNOG; KOG2258; Eukaryota.
DR InParanoid; Q9JL55; -.
DR OrthoDB; 1218115at2759; -.
DR PhylomeDB; Q9JL55; -.
DR Reactome; R-RNO-6814848; Glycerophospholipid catabolism.
DR SABIO-RK; Q9JL55; -.
DR PRO; PR:Q9JL55; -.
DR Proteomes; UP000002494; Unplaced.
DR GO; GO:0030659; C:cytoplasmic vesicle membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IDA:RGD.
DR GO; GO:0016020; C:membrane; ISO:RGD.
DR GO; GO:0005886; C:plasma membrane; ISS:UniProtKB.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; ISS:UniProtKB.
DR GO; GO:0047395; F:glycerophosphoinositol glycerophosphodiesterase activity; ISS:UniProtKB.
DR GO; GO:0004622; F:lysophospholipase activity; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008081; F:phosphoric diester hydrolase activity; ISO:RGD.
DR GO; GO:0006580; P:ethanolamine metabolic process; ISS:UniProtKB.
DR GO; GO:0007186; P:G protein-coupled receptor signaling pathway; NAS:RGD.
DR GO; GO:0070291; P:N-acylethanolamine metabolic process; ISS:UniProtKB.
DR GO; GO:0006644; P:phospholipid metabolic process; ISS: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 Cell membrane; Cytoplasmic vesicle; Glycoprotein; Hydrolase;
KW Lipid metabolism; Magnesium; Membrane; Metal-binding; Reference proteome;
KW Transmembrane; Transmembrane helix.
FT CHAIN 1..331
FT /note="Glycerophosphodiester phosphodiesterase 1"
FT /id="PRO_0000251946"
FT TOPO_DOM 1..3
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 4..24
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 25..248
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT TRANSMEM 249..269
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 270..331
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 65..331
FT /note="GP-PDE"
FT BINDING 97
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT BINDING 99
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT BINDING 174
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT CARBOHYD 168
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT MUTAGEN 97
FT /note="E->A: Strongly reduced activity; when associated
FT with A-99."
FT /evidence="ECO:0000269|PubMed:12576545"
FT MUTAGEN 99
FT /note="D->A: Strongly reduced activity; when associated
FT with A-97."
FT /evidence="ECO:0000269|PubMed:12576545"
FT MUTAGEN 112
FT /note="H->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12576545"
FT CONFLICT 326
FT /note="D -> N (in Ref. 1; AAF65233)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 331 AA; 37634 MW; D946067B5768035F CRC64;
MWLWEDQGGL LGPFSFVLVL LLVVTRSPFN ACVLTGSLYL LLRFFSFEPV PSRRALQVLK
PRDRVSAIAH RGGSHDAPEN TLAAIRQAAK NGATGVELDI EFTSDGVPVL MHDNTVDRTT
DGSGRLCDLT FEQVRKLNPA ANHRLRNEFP DERIPTLREA VTECLCHNLT IFFDVKGHAD
MASAALKNIY MEFPQLYNNS MVCSFLPEVI YKMRQTDQKV ITALTHRPWS LSHTGDGKPR
YSVFWKQSVF VVLDILLDWS MHNVLWYLCG ISAFLMQKDF VSPDYLKKWS AKGIQVVSWT
VNTFDEKNYY ESHLGSSYIT DSMLEDCAPH F
