GPDL3_ARATH
ID GPDL3_ARATH Reviewed; 759 AA.
AC Q9SZ11; Q93ZT1;
DT 29-AUG-2003, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 3.
DT 25-MAY-2022, entry version 135.
DE RecName: Full=Glycerophosphodiester phosphodiesterase GDPDL3 {ECO:0000305};
DE EC=3.1.4.46 {ECO:0000250|UniProtKB:Q7Y208};
DE AltName: Full=Glycerophosphodiester phosphodiesterase-like 3 {ECO:0000303|PubMed:21323773};
DE Short=ATGDPDL3 {ECO:0000303|PubMed:21323773};
DE AltName: Full=Glycerophosphodiesterase-like 2 {ECO:0000303|PubMed:18718934};
DE AltName: Full=Protein MUTANT ROOT HAIR 5 {ECO:0000303|PubMed:16367956};
DE AltName: Full=Protein SHAVEN 3 {ECO:0000303|PubMed:18718934};
DE Flags: Precursor;
GN Name=GDPDL3 {ECO:0000303|PubMed:21323773};
GN Synonyms=GPDL2 {ECO:0000303|PubMed:18718934},
GN MRH5 {ECO:0000303|PubMed:16367956}, SHV3 {ECO:0000303|PubMed:18718934};
GN OrderedLocusNames=At4g26690; ORFNames=F10M23.30;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 DISRUPTION PHENOTYPE.
RX PubMed=16367956; DOI=10.1111/j.1365-313x.2005.02609.x;
RA Jones M.A., Raymond M.J., Smirnoff N.;
RT "Analysis of the root-hair morphogenesis transcriptome reveals the
RT molecular identity of six genes with roles in root-hair development in
RT Arabidopsis.";
RL Plant J. 45:83-100(2006).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DISRUPTION
RP PHENOTYPE.
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 [6]
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: Involved in primary cell wall organization. Required for the
CC accumulation of crystalline cellulose. {ECO:0000269|PubMed:18718934}.
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: Cell membrane {ECO:0000269|PubMed:18718934};
CC Single-pass type I membrane protein {ECO:0000255}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, shoots, rosette and cauline
CC leaves, stems, flowers and siliques. {ECO:0000269|PubMed:18718934,
CC ECO:0000269|PubMed:21323773}.
CC -!- DISRUPTION PHENOTYPE: Defective in root hair formation
CC (PubMed:16367956, PubMed:18718934). This phenotype is partially
CC suppressed by application of exogenous borate (PubMed:18718934).
CC {ECO:0000269|PubMed:16367956, ECO:0000269|PubMed:18718934}.
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB36515.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79524.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL035440; CAB36515.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161565; CAB79524.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE85238.1; -; Genomic_DNA.
DR EMBL; AY056280; AAL07129.1; -; mRNA.
DR PIR; T04792; T04792.
DR RefSeq; NP_567755.1; NM_118803.5.
DR AlphaFoldDB; Q9SZ11; -.
DR SMR; Q9SZ11; -.
DR BioGRID; 14063; 2.
DR STRING; 3702.AT4G26690.1; -.
DR PaxDb; Q9SZ11; -.
DR PRIDE; Q9SZ11; -.
DR ProteomicsDB; 247176; -.
DR EnsemblPlants; AT4G26690.1; AT4G26690.1; AT4G26690.
DR GeneID; 828776; -.
DR Gramene; AT4G26690.1; AT4G26690.1; AT4G26690.
DR KEGG; ath:AT4G26690; -.
DR Araport; AT4G26690; -.
DR TAIR; locus:2116377; AT4G26690.
DR eggNOG; KOG2258; Eukaryota.
DR HOGENOM; CLU_010414_0_1_1; -.
DR InParanoid; Q9SZ11; -.
DR OMA; CTNIANV; -.
DR OrthoDB; 211520at2759; -.
DR PRO; PR:Q9SZ11; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SZ11; baseline and differential.
DR Genevisible; Q9SZ11; AT.
DR GO; GO:0031225; C:anchored component of membrane; TAS:TAIR.
DR GO; GO:0046658; C:anchored component of plasma membrane; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IDA:TAIR.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0009932; P:cell tip growth; IMP:TAIR.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0006071; P:glycerol metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0006629; P:lipid metabolic process; IEA:InterPro.
DR GO; GO:0010053; P:root epidermal cell differentiation; IMP:TAIR.
DR GO; GO:0048765; P:root hair cell differentiation; IMP:TAIR.
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 Cell membrane; Cell wall biogenesis/degradation; Glycerol metabolism;
KW Glycoprotein; Hydrolase; Membrane; Reference proteome; Repeat; Signal;
KW Transmembrane; Transmembrane helix.
FT SIGNAL 1..27
FT /evidence="ECO:0000255"
FT CHAIN 28..759
FT /note="Glycerophosphodiester phosphodiesterase GDPDL3"
FT /id="PRO_0000012599"
FT TOPO_DOM 28..738
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 739..759
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 44..344
FT /note="GP-PDE 1"
FT DOMAIN 360..661
FT /note="GP-PDE 2"
FT REGION 702..734
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CARBOHYD 99
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 186
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 242
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 251
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 326
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 353
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 413
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 424
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 488
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 528
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 540
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 647
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CONFLICT 148
FT /note="E -> K (in Ref. 3; AAL07129)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 759 AA; 82562 MW; C20B45292AD1B068 CRC64;
MRGLLRASSL LLCGVILIQL LAAQIHAQSK KPKSPWPTLT GDPPLVIARG GFSGLFPDSS
YDAYNFAILT SVPDAVLWCD VQLTKDALGI CFPDLTMRNS SSIEAVYPTR QKSYPVNGVP
TSGWFTIDFS LKDLKDVNLI RGILSRSEKF DGNSNPIMTV QSVSTQMKPS FFWLNVQHDA
FYAQHNLSMS SFLVAASKTV LIDFISSPEV NFFKKIAGRF GRNGPSLVFR FLGQDEFEPT
TNRTYGSILS NLTFVKTFAS GILVPKSYIL PLDDQQYLLP HTSLVQDAHK AGLEVFVSGF
ANDIDIAHDY SFDPVSEYLS FVDNGNFSVD GVLSDFPITA SASLDCFSHV GRNATKQVDF
LVITKDGASG DYPGCTDLAY KKAIKDGADV IDCSVQLSSD GTPFCLSSID LGNSTTVSLT
AFRNRSTTVP ELGSLGAIYT FSLTWAEIQT LTPAISNPYR VTSLFRNPKQ KNAGKLFSLS
DFLSLAKNST SLSGVLISVE NAAYLREEQG LDVVKAVLDT LTQTGYSNST ATKVMIQSTN
SSVLVDFKKQ SQYETVYKVE ENIRDILDSA IEDIKKFADA VVIQKLSVFP VAQSFITTQT
NVVEKLQKSQ LPVYVELFQN EFLSQPYDFF ADATVEINSY ITGAGINGTI TEFPFTAARY
KRNLCLGRKE TIPYMAPAQP GALLTLVSPT AFPPAEAPNP VFTDADVTEP PLPPVTAKAP
TSSPGTPSTN AQAPSGQTRI TLSLLLSVFA MVLASLLLL
