GPDL5_ARATH
ID GPDL5_ARATH Reviewed; 729 AA.
AC F4JEQ1; Q84W64;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 68.
DE RecName: Full=Glycerophosphodiester phosphodiesterase GDPDL5 {ECO:0000305};
DE EC=3.1.4.46 {ECO:0000250|UniProtKB:Q7Y208};
DE AltName: Full=Glycerophosphodiester phosphodiesterase-like 5 {ECO:0000303|PubMed:21323773};
DE Short=ATGDPDL5 {ECO:0000303|PubMed:21323773};
DE AltName: Full=Glycerophosphodiesterase-like 4 {ECO:0000303|PubMed:18718934};
DE AltName: Full=Protein SHV3-LIKE 3 {ECO:0000303|PubMed:18718934};
DE Flags: Precursor;
GN Name=GDPDL5 {ECO:0000303|PubMed:21323773};
GN Synonyms=GDPL4 {ECO:0000303|PubMed:18718934},
GN SVL3 {ECO:0000303|PubMed:18718934};
GN OrderedLocusNames=At3g20520 {ECO:0000312|Araport:AT3G20520};
GN ORFNames=K10D20;
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 {ECO:0000312|EMBL:AEE76390.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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 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 -!- 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:0000250|UniProtKB:Q7Y208};
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000255}; Single-pass membrane
CC protein {ECO:0000255}.
CC -!- TISSUE SPECIFICITY: Expressed in stems, flowers and siliques.
CC {ECO:0000269|PubMed:21323773}.
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
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DR EMBL; AC011664; AAF14830.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76390.1; -; Genomic_DNA.
DR EMBL; BT004193; AAO42211.1; -; mRNA.
DR RefSeq; NP_188688.1; NM_112944.3.
DR AlphaFoldDB; F4JEQ1; -.
DR SMR; F4JEQ1; -.
DR STRING; 3702.AT3G20520.1; -.
DR PaxDb; F4JEQ1; -.
DR PRIDE; F4JEQ1; -.
DR ProteomicsDB; 247029; -.
DR EnsemblPlants; AT3G20520.1; AT3G20520.1; AT3G20520.
DR GeneID; 821598; -.
DR Gramene; AT3G20520.1; AT3G20520.1; AT3G20520.
DR KEGG; ath:AT3G20520; -.
DR Araport; AT3G20520; -.
DR TAIR; locus:2085710; AT3G20520.
DR eggNOG; KOG2258; Eukaryota.
DR HOGENOM; CLU_010414_0_0_1; -.
DR InParanoid; F4JEQ1; -.
DR OMA; YMINEEV; -.
DR OrthoDB; 285275at2759; -.
DR PRO; PR:F4JEQ1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; F4JEQ1; baseline and differential.
DR Genevisible; F4JEQ1; AT.
DR GO; GO:0031225; C:anchored component of membrane; TAS:TAIR.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IBA:GO_Central.
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; 1.
DR SUPFAM; SSF51695; SSF51695; 2.
DR PROSITE; PS51704; GP_PDE; 2.
PE 2: Evidence at transcript level;
KW Glycerol metabolism; Glycoprotein; Hydrolase; Membrane; Reference proteome;
KW Signal; Transmembrane; Transmembrane helix.
FT SIGNAL 1..22
FT /evidence="ECO:0000255"
FT CHAIN 23..729
FT /note="Glycerophosphodiester phosphodiesterase GDPDL5"
FT /evidence="ECO:0000255"
FT /id="PRO_0000430615"
FT TRANSMEM 709..729
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 33..320
FT /note="GP-PDE 1"
FT /evidence="ECO:0000255"
FT DOMAIN 337..645
FT /note="GP-PDE 2"
FT /evidence="ECO:0000255"
FT CARBOHYD 88
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 162
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 218
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 227
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 285
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 302
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 390
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 401
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 507
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CONFLICT 425
FT /note="Q -> K (in Ref. 3; AAO42211)"
FT CONFLICT 656
FT /note="T -> A (in Ref. 3; AAO42211)"
FT CONFLICT 726
FT /note="F -> S (in Ref. 3; AAO42211)"
SQ SEQUENCE 729 AA; 81360 MW; B87535F8E58F1EFC CRC64;
MACPRVIFLI LITFFILQTA FSSSWQTLSG KPPAVIARGG FSGMFPDSSI QAYQLVNITT
SPDVMLWCDL QLTKDGVGIC FPNLKLDNGS NVIRIDPHYK ERFSVDFTWK ELSDVKLAQG
VVSRPYIFDD VSSILAIEEV AKLTASGLWL NIQDSAFYAK HNLSMRNSVV SLSRRLKVNF
ISSPGISFLK SMKNSVKPTV TKLIFRFLKQ EHIEPFTNQS YGSLAKNLSY IRTFSSGILV
PKSYIWPVDS ALYLQPHTSL VTDAHKEGLQ VFASEFANDF VIAYNYSYDP TAEYLSFIDN
GNFSVDGFLS DFPVTPYRAI NCFSHVDPKR AKEQAKITII SKNGASGDFP GCTDLAYQRA
ASDGADILDC NVQMSKDKIP FCMSSFDLIN STNVIETSFR NLSSVVSEIN PRRSGIYTFS
LTMSQIQTLK PTISNLEKDS GLFRNPRNNK AGKFLTLSEF LFLPNRYSSL LGLLIEVENA
AYLVEHQGIS VVDAVLDELK RATTQQNKTS ARTILIQSTD KSVLMKFKEK NKMNHDELVY
RVDDNIRDVA DSAIKDIKNF AGSIVISKKS VFPYKGFIIL EKETNIASKL KSNGLRVYVE
RFSNECVTHA FDFYDDPTLE IDSFVRDVQI DGIITDFPAT TARYRKNKCY GEFGLTTTGE
LITFANPMLL PPAEAPYPAL LDSDVTEPPL PEARSQPPAS SPSKAEEKAI EVPFAFIAMA
ILVCFFISV
