GDE1_YEAST
ID GDE1_YEAST Reviewed; 1223 AA.
AC Q02979; D6W3Q7;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Glycerophosphocholine phosphodiesterase GDE1 {ECO:0000303|PubMed:16141200};
DE EC=3.1.4.2 {ECO:0000305|PubMed:16141200};
DE AltName: Full=Glycerophosphodiester phosphodiesterase GDE1;
GN Name=GDE1 {ECO:0000303|PubMed:16141200}; OrderedLocusNames=YPL110C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX PubMed=16141200; DOI=10.1074/jbc.m507051200;
RA Fisher E., Almaguer C., Holic R., Griac P., Patton-Vogt J.;
RT "Glycerophosphocholine-dependent growth requires Gde1p (YPL110c) and Git1p
RT in Saccharomyces cerevisiae.";
RL J. Biol. Chem. 280:36110-36117(2005).
RN [6]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=16172116; DOI=10.1074/jbc.m507700200;
RA Fernandez-Murray J.P., McMaster C.R.;
RT "Glycerophosphocholine catabolism as a new route for choline formation for
RT phosphatidylcholine synthesis by the Kennedy pathway.";
RL J. Biol. Chem. 280:38290-38296(2005).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-653, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-983, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Glycerophosphocholine glycerophosphodiesterase responsible
CC for the hydrolysis of intracellular glycerophosphocholine into
CC glycerol-phosphate and choline (PubMed:16141200, PubMed:16172116). The
CC choline is used for phosphatidyl-choline synthesis. Required for
CC utilization of glycerophosphocholine as phosphate source
CC (PubMed:16141200). May also use glycerophosphoinositol as substrate in
CC vivo (PubMed:16172116). {ECO:0000269|PubMed:16141200,
CC ECO:0000269|PubMed:16172116}.
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 Evidence={ECO:0000269|PubMed:16141200};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16062;
CC Evidence={ECO:0000305|PubMed:16141200};
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;
CC Evidence={ECO:0000305|PubMed:16172116};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:16502;
CC Evidence={ECO:0000305|PubMed:16172116};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- DISRUPTION PHENOTYPE: Affects the glycerophosphocholine metabolism but
CC not the glycerophosphoinositol metabolism (PubMed:16141200).
CC -!- MISCELLANEOUS: Present with 2300 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the GDE1 family. {ECO:0000305}.
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DR EMBL; U43503; AAB68251.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11323.1; -; Genomic_DNA.
DR PIR; S62011; S62011.
DR RefSeq; NP_015215.1; NM_001183924.1.
DR AlphaFoldDB; Q02979; -.
DR SMR; Q02979; -.
DR BioGRID; 36071; 75.
DR DIP; DIP-8774N; -.
DR IntAct; Q02979; 9.
DR MINT; Q02979; -.
DR STRING; 4932.YPL110C; -.
DR SwissLipids; SLP:000000074; -.
DR iPTMnet; Q02979; -.
DR MaxQB; Q02979; -.
DR PaxDb; Q02979; -.
DR PRIDE; Q02979; -.
DR EnsemblFungi; YPL110C_mRNA; YPL110C; YPL110C.
DR GeneID; 855994; -.
DR KEGG; sce:YPL110C; -.
DR SGD; S000006031; GDE1.
DR VEuPathDB; FungiDB:YPL110C; -.
DR eggNOG; KOG0504; Eukaryota.
DR eggNOG; KOG1162; Eukaryota.
DR eggNOG; KOG2421; Eukaryota.
DR GeneTree; ENSGT00440000033970; -.
DR HOGENOM; CLU_005444_1_0_1; -.
DR InParanoid; Q02979; -.
DR OMA; HSTQLDT; -.
DR BioCyc; MetaCyc:G3O-34012-MON; -.
DR BioCyc; YEAST:G3O-34012-MON; -.
DR BRENDA; 3.1.4.46; 984.
DR PRO; PR:Q02979; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q02979; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0047389; F:glycerophosphocholine phosphodiesterase activity; IMP:SGD.
DR GO; GO:0047395; F:glycerophosphoinositol glycerophosphodiesterase activity; IEA:RHEA.
DR GO; GO:0046475; P:glycerophospholipid catabolic process; IMP:SGD.
DR Gene3D; 1.25.40.20; -; 2.
DR Gene3D; 3.20.20.190; -; 1.
DR InterPro; IPR002110; Ankyrin_rpt.
DR InterPro; IPR036770; Ankyrin_rpt-contain_sf.
DR InterPro; IPR033506; Gde1.
DR InterPro; IPR030395; GP_PDE_dom.
DR InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR InterPro; IPR004331; SPX_dom.
DR PANTHER; PTHR22958:SF1; PTHR22958:SF1; 1.
DR Pfam; PF12796; Ank_2; 1.
DR Pfam; PF03009; GDPD; 1.
DR Pfam; PF03105; SPX; 2.
DR SMART; SM00248; ANK; 7.
DR SUPFAM; SSF48403; SSF48403; 1.
DR SUPFAM; SSF51695; SSF51695; 1.
DR PROSITE; PS50297; ANK_REP_REGION; 1.
DR PROSITE; PS50088; ANK_REPEAT; 2.
DR PROSITE; PS51704; GP_PDE; 1.
DR PROSITE; PS51382; SPX; 1.
PE 1: Evidence at protein level;
KW ANK repeat; Cytoplasm; Hydrolase; Phosphoprotein; Reference proteome;
KW Repeat.
FT CHAIN 1..1223
FT /note="Glycerophosphocholine phosphodiesterase GDE1"
FT /id="PRO_0000233009"
FT DOMAIN 1..213
FT /note="SPX"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00714"
FT REPEAT 427..456
FT /note="ANK 1"
FT REPEAT 472..502
FT /note="ANK 2"
FT REPEAT 504..533
FT /note="ANK 3"
FT REPEAT 538..567
FT /note="ANK 4"
FT REPEAT 572..601
FT /note="ANK 5"
FT REPEAT 605..634
FT /note="ANK 6"
FT DOMAIN 872..1217
FT /note="GP-PDE"
FT REGION 43..64
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 653
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 983
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
SQ SEQUENCE 1223 AA; 138014 MW; C42E74B3CB7FB382 CRC64;
MKFGKTFANH RIPEWSSQYV GYKSLKKMIK EITRLQEDIY RAHNKNSYDE GRPPTKMRDS
SNSAQNYLDS PKIQKLLASF FFAVDRDIEK VDTFYNSQYA EYKKRFERLL SSNQFNEIKS
TLVVDANKED AVAQTLLTKD TREMNMLLKG TSQASRLSYH KDDLIEIQSI LAELRKQFRN
LKWYAELNKR AFGKILKKLD KKVGTNQQMS TMKTRILPLQ FANDSLITKD LSLLKTIWEQ
VTFRINSYER VMRSTSPNAN ANDNTEFFKI ICVFIEEDDS KGLIRELTNL YSELSLIPTR
IMISVLNKAA LSKSLACIDA ILKVIPSLND SEDINRRNFF HHHIIAIGKL IRKQEILSRK
KKSQPSKYTN SEGEIVTDLR TLHTTLSAPA ESDSITEEEK SSACTLSYIL EELPIHLRPC
LFQHDNYKRT PLHYSCQYGL SEVTKLIIKL MKEWNIWNEI PIDDVSAFGD AESLTPLHLC
VLGAHPKTTE VLLQSLDPNV KLKSSSLLHL ATEWNNYPLL HVLLSSKRFD INYQDNELHE
TPLYLACRLN FFEAAVCLLY NGADLEIREK LFGWTAIFVA AAEGFTDIVK LLIANNANFD
IEDEGGWTPM EHAVLRGHLH IADMVQIRDE LVTHPHSQLN SGSEEKEPLN EISAGELNER
NENGNGGNKG SLGKLAGPIK SYGHRFLDNN ESLILITLGS NDTRNKSPSI SLSSEALAKV
IGLETDCALS LVISCNDSID KSSVILDLPL DDNVDAVDFK VPFKVDYSHT LYFDIVPTYG
TRSLETHNRI DCQKNNNNYV MARGVSMLNK SYSSVGVNRS ILNGSVTVPI IANHTLEILG
TLKFEYIIIT PFEHPQLPLE RTETYWKSLV STRVIGHRGL GKNNPNKSLQ IGENTVESFI
MAASLGASYV EFDVQLTKDN VPVVYHDFLV AETGVDIPMH ELTLEQFLDL NNADKEHIQR
GAGHSPHHVN GADTALQKYR GRSVDDSDVS TLRRAWDLHD NDPNGKSNNA HWSDNRMRLT
KTFKKNNFKG NARGHSIASS FVTLKELFKK IPANVGFNIE CKFPMLDEAE EEELGQIMME
MNHWVDTVLK VVFDNANGRD IIFSSFHPDI CIMLSLKQPV IPILFLTEGG SEQMADLRAS
SLQNGIRFAK KWNLLGIVSA AAPILKAPRL VQVVKSNGLV CVTYGVDNND PENASIQIEA
GVDAVIVDSV LAIRRGLTKK NEK
