GPDL1_ARATH
ID GPDL1_ARATH Reviewed; 763 AA.
AC Q7Y208; Q9FZI1;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 2.
DT 25-MAY-2022, entry version 115.
DE RecName: Full=Glycerophosphodiester phosphodiesterase GDPDL1 {ECO:0000305};
DE EC=3.1.4.46 {ECO:0000269|PubMed:21323773};
DE AltName: Full=Glycerophosphodiester phosphodiesterase-like 1 {ECO:0000303|PubMed:21323773};
DE Short=ATGDPDL1 {ECO:0000303|PubMed:21323773};
DE AltName: Full=Glycerophosphodiesterase-like 3 {ECO:0000303|PubMed:18718934};
DE AltName: Full=Protein SHV3-LIKE 2 {ECO:0000303|PubMed:18718934};
DE Flags: Precursor;
GN Name=GDPDL1 {ECO:0000303|PubMed:21323773};
GN Synonyms=GDPL3 {ECO:0000303|PubMed:18718934},
GN SVL2 {ECO:0000303|PubMed:18718934}; OrderedLocusNames=At1g66970;
GN ORFNames=F1O19.5;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP TISSUE SPECIFICITY.
RX PubMed=18718934; DOI=10.1093/pcp/pcn120;
RA Hayashi S., Ishii T., Matsunaga T., Tominaga R., Kuromori T., Wada T.,
RA Shinozaki K., Hirayama T.;
RT "The glycerophosphoryl diester phosphodiesterase-like proteins SHV3 and its
RT homologs play important roles in cell wall organization.";
RL Plant Cell Physiol. 49:1522-1535(2008).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=21323773; DOI=10.1111/j.1365-313x.2011.04538.x;
RA Cheng Y., Zhou W., El Sheery N.I., Peters C., Li M., Wang X., Huang J.;
RT "Characterization of the Arabidopsis glycerophosphodiester
RT phosphodiesterase (GDPD) family reveals a role of the plastid-localized
RT AtGDPD1 in maintaining cellular phosphate homeostasis under phosphate
RT starvation.";
RL Plant J. 66:781-795(2011).
CC -!- FUNCTION: Hydrolyzes glycerolphosphoglycerol, glycerophosphocholine and
CC glycerophosphoethanolamine in vitro. {ECO:0000269|PubMed:21323773}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a sn-glycero-3-phosphodiester + H2O = an alcohol + H(+) + sn-
CC glycerol 3-phosphate; Xref=Rhea:RHEA:12969, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30879, ChEBI:CHEBI:57597,
CC ChEBI:CHEBI:83408; EC=3.1.4.46;
CC Evidence={ECO:0000269|PubMed:21323773};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:21323773};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=2.3 umol/min/mg enzyme toward glycerolphosphoglycerol
CC {ECO:0000269|PubMed:21323773};
CC Vmax=2.6 umol/min/mg enzyme toward glycerophosphocholine
CC {ECO:0000269|PubMed:21323773};
CC Vmax=2.8 umol/min/mg enzyme toward glycerophosphoethanolamine
CC {ECO:0000269|PubMed:21323773};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass type I
CC membrane protein {ECO:0000255}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q7Y208-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in rosette and cauline leaves, stems,
CC flowers and siliques. {ECO:0000269|PubMed:21323773}.
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
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DR EMBL; AC007152; AAF98209.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE34579.1; -; Genomic_DNA.
DR EMBL; BT008653; AAP40466.1; -; mRNA.
DR PIR; F96693; F96693.
DR RefSeq; NP_176869.2; NM_105368.3. [Q7Y208-1]
DR AlphaFoldDB; Q7Y208; -.
DR SMR; Q7Y208; -.
DR STRING; 3702.AT1G66970.2; -.
DR PaxDb; Q7Y208; -.
DR PRIDE; Q7Y208; -.
DR ProteomicsDB; 248508; -. [Q7Y208-1]
DR EnsemblPlants; AT1G66970.1; AT1G66970.1; AT1G66970. [Q7Y208-1]
DR GeneID; 843015; -.
DR Gramene; AT1G66970.1; AT1G66970.1; AT1G66970. [Q7Y208-1]
DR KEGG; ath:AT1G66970; -.
DR Araport; AT1G66970; -.
DR eggNOG; KOG2258; Eukaryota.
DR HOGENOM; CLU_010414_0_1_1; -.
DR InParanoid; Q7Y208; -.
DR OMA; YKLNSCM; -.
DR PhylomeDB; Q7Y208; -.
DR SABIO-RK; Q7Y208; -.
DR PRO; PR:Q7Y208; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q7Y208; baseline and differential.
DR Genevisible; Q7Y208; AT.
DR GO; GO:0031225; C:anchored component of membrane; IDA:UniProtKB.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IDA:UniProtKB.
DR GO; GO:0005509; F:calcium ion binding; IDA:UniProtKB.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IDA:UniProtKB.
DR GO; GO:0006071; P:glycerol metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0006629; P:lipid metabolic process; IEA:InterPro.
DR Gene3D; 3.20.20.190; -; 2.
DR InterPro; IPR030395; GP_PDE_dom.
DR InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR Pfam; PF03009; GDPD; 2.
DR SUPFAM; SSF51695; SSF51695; 2.
DR PROSITE; PS51704; GP_PDE; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell membrane; Glycerol metabolism; Glycoprotein;
KW Hydrolase; Membrane; Reference proteome; Repeat; Signal; Transmembrane;
KW Transmembrane helix.
FT SIGNAL 1..35
FT /evidence="ECO:0000255"
FT CHAIN 36..763
FT /note="Glycerophosphodiester phosphodiesterase GDPDL1"
FT /id="PRO_0000251277"
FT TOPO_DOM 36..744
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 745..762
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 763
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 50..350
FT /note="GP-PDE 1"
FT DOMAIN 366..668
FT /note="GP-PDE 2"
FT CARBOHYD 105
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 192
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 248
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 257
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 315
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 359
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 430
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 534
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 547
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 654
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CONFLICT 672
FT /note="C -> Y (in Ref. 3; AAP40466)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 763 AA; 83788 MW; CFFAD6E6334D30BB CRC64;
MNSRPSNPTK LVIRSSTLLF CGVVLIHLFA AQIDAQRSTS RWQTLNGDAP LVIARGGFSG
LYPDSSIAAY QLATLTSVAD VVLWCDLQLT KDGLGICFPD LNLANASTID RVYPNREKSY
SVNGVTTKGW FPNDFSLTEL QNFLLIRGIL SRTDRFDGNG YLISTIEDVV TTLNREGFWL
NVQHDAFYEQ QNLSMSSFLL SVSRTVSIDF ISSPEVNFFK KITGSFGRNG PTFVFQFLGK
EDFEPTTNRT YGSILSNLTF VKTFASGILV PKSYILPLDD EQYLVPHTSL VQDAHKAGLQ
VYVSGFANDV DIAYNYSSDP VSEYLSFVDN GDFSVDGVLS DFPITASAAV DCFSHIGRNA
TKQVDFLVIS KDGASGDYPG CTDLAYEKAI KDGADVIDCS VQMSSDGVPF CLRSIDLRNS
IAALQNTFSN RSTSVPEISS VPGIFTFSLT WPEIQSLTPA ISNPFRVYRI FRNPREKNSG
KLISLSQFLD LAKTYTSLSG VLISVENAAY LREKQGLDVV QAVLDTLTEA GYSNGTTTTK
VMIQSTNSSV LVDFKKQSKY ETVYKIEETI GNIRDSAIED IKKFANAVVI NKDSVFPNSD
SFLTGQTNVV ERLQKSQLPV YVELFRNEFV SQAYDFFSDA TVEINAYIYG AGINGTITEF
PFTAARYKRN RCLGREEVPP YMLPVNPGGL LNVMSPLSLP PAQAPNQDFI EADVTEPPLS
PVIAKAPTST PGTPSTIAQA PSGQTRLKLS LLLSVFFLSL LLL
