GDPD1_ARATH
ID GDPD1_ARATH Reviewed; 361 AA.
AC Q9SGA2; Q84WI7;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Glycerophosphodiester phosphodiesterase GDPD1, chloroplastic {ECO:0000305};
DE EC=3.1.4.46 {ECO:0000269|PubMed:21323773};
DE AltName: Full=Glycerophosphodiester phosphodiesterase 1 {ECO:0000303|PubMed:21323773};
DE Short=AtGDPD1 {ECO:0000303|PubMed:21323773};
DE AltName: Full=Protein SENESCENCE-RELATED GENE 3 {ECO:0000303|PubMed:8883383};
DE Flags: Precursor;
GN Name=GDPD1 {ECO:0000303|PubMed:21323773};
GN Synonyms=SRG3 {ECO:0000303|PubMed:8883383};
GN OrderedLocusNames=At3g02040 {ECO:0000312|Araport:AT3G02040};
GN ORFNames=F1C9.18 {ECO:0000312|EMBL:AAF14831.1};
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=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 INDUCTION BY SENESCENCE.
RX PubMed=8883383; DOI=10.1104/pp.112.2.705;
RA Callard D., Axelos M., Mazzolini L.;
RT "Novel molecular markers for late phases of the growth cycle of Arabidopsis
RT thaliana cell-suspension cultures are expressed during organ senescence.";
RL Plant Physiol. 112:705-715(1996).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION, GENE FAMILY,
RP NOMENCLATURE, AND DISRUPTION PHENOTYPE.
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. May be involved in release of
CC inorganic phosphate (Pi) from phospholipids during Pi starvation.
CC {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=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:21323773};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=13.1 umol/min/mg enzyme toward glycerolphosphoglycerol
CC {ECO:0000269|PubMed:21323773};
CC Vmax=12.4 umol/min/mg enzyme toward glycerophosphocholine
CC {ECO:0000269|PubMed:21323773};
CC Vmax=10.1 umol/min/mg enzyme toward glycerophosphoethanolamine
CC {ECO:0000269|PubMed:21323773};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:21323773}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, shoots, rosette leaves, stems,
CC flowers and siliques. {ECO:0000269|PubMed:21323773}.
CC -!- INDUCTION: By senescence (PubMed:8883383) and phosphate starvation
CC (PubMed:21323773). {ECO:0000269|PubMed:21323773,
CC ECO:0000269|PubMed:8883383}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but mutant plants show reduced glycerophosphodiester
CC phosphodiesterase activity under phosphate starvation.
CC {ECO:0000269|PubMed:21323773}.
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
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DR EMBL; AC011664; AAF14831.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73752.1; -; Genomic_DNA.
DR EMBL; AY072127; AAL59949.1; -; mRNA.
DR EMBL; AY114073; AAM45121.1; -; mRNA.
DR EMBL; BT003327; AAO29946.1; -; mRNA.
DR RefSeq; NP_566159.1; NM_111070.4.
DR AlphaFoldDB; Q9SGA2; -.
DR SMR; Q9SGA2; -.
DR STRING; 3702.AT3G02040.1; -.
DR PaxDb; Q9SGA2; -.
DR PRIDE; Q9SGA2; -.
DR ProteomicsDB; 221999; -.
DR EnsemblPlants; AT3G02040.1; AT3G02040.1; AT3G02040.
DR GeneID; 821175; -.
DR Gramene; AT3G02040.1; AT3G02040.1; AT3G02040.
DR KEGG; ath:AT3G02040; -.
DR Araport; AT3G02040; -.
DR TAIR; locus:2078603; AT3G02040.
DR eggNOG; KOG2421; Eukaryota.
DR HOGENOM; CLU_013007_0_0_1; -.
DR InParanoid; Q9SGA2; -.
DR OMA; GGTELYY; -.
DR OrthoDB; 687958at2759; -.
DR PhylomeDB; Q9SGA2; -.
DR SABIO-RK; Q9SGA2; -.
DR PRO; PR:Q9SGA2; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SGA2; baseline and differential.
DR Genevisible; Q9SGA2; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IDA:TAIR.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030643; P:cellular phosphate ion homeostasis; IMP:TAIR.
DR GO; GO:0071456; P:cellular response to hypoxia; HEP:TAIR.
DR GO; GO:0006071; P:glycerol metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0046475; P:glycerophospholipid catabolic process; IBA:GO_Central.
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 Chloroplast; Glycerol metabolism; Hydrolase; Plastid; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..53
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 54..361
FT /note="Glycerophosphodiester phosphodiesterase GDPD1,
FT chloroplastic"
FT /evidence="ECO:0000255"
FT /id="PRO_0000430607"
FT DOMAIN 54..323
FT /note="GP-PDE"
FT /evidence="ECO:0000255"
FT CONFLICT 169
FT /note="G -> V (in Ref. 3; AAO29946)"
SQ SEQUENCE 361 AA; 40715 MW; 5791268298959BC7 CRC64;
MSLKAIHVSE VPSLDHFPEN PSLICSSRKA NNKFVVVGHR GHGMNMSQSP DLRFSALKEN
SILSFNAASK FPLDFIEFDV QVTRDGCPII FHDDFIYSEE QGVVYEKRVT EVCLSEFMSY
GPQRDTGKTG KPLLRKSKEG KIHKWSVATD DSFCTLQEAF EKVENPNLGF NIELKLDDNV
FYSSDHLSRL LLPILQVVSD IGNDRTIIFS SFHPDAALLV RKLQTTYPVF FLTNGGTEMY
HDTRRNSLEE AIKVCLEGGL QGIVSEVKGV FRNPALVNKI KESKLSLMTY GKLNNVAEAV
YMQHLMGIEG VIVDHVEEIT EAVREMMKPS NRDADGTKPK PNFSDRELSF LLKLIPELIQ
H
