PLDG3_ARATH
ID PLDG3_ARATH Reviewed; 866 AA.
AC Q9T052; Q9XH77;
DT 03-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Phospholipase D gamma 3 {ECO:0000303|PubMed:11891260};
DE Short=AtPLDgamma3 {ECO:0000303|PubMed:11891260};
DE Short=PLD gamma 3 {ECO:0000303|PubMed:11891260};
DE EC=3.1.4.4 {ECO:0000250|UniProtKB:Q9T053};
GN Name=PLDGAMMA3 {ECO:0000303|PubMed:11891260}; OrderedLocusNames=At4g11840;
GN ORFNames=T26M18.50;
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 SUBCELLULAR LOCATION.
RX PubMed=10198096; DOI=10.1104/pp.119.4.1371;
RA Fan L., Zheng S., Cui D., Wang X.;
RT "Subcellular distribution and tissue expression of phospholipase Dalpha,
RT Dbeta, and Dgamma in Arabidopsis.";
RL Plant Physiol. 119:1371-1378(1999).
RN [4]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=11891260; DOI=10.1104/pp.010928;
RA Qin C., Wang X.;
RT "The Arabidopsis phospholipase D family. Characterization of a calcium-
RT independent and phosphatidylcholine-selective PLD zeta 1 with distinct
RT regulatory domains.";
RL Plant Physiol. 128:1057-1068(2002).
RN [5]
RP TISSUE SPECIFICITY.
RX PubMed=17098468; DOI=10.1016/j.bbalip.2006.09.017;
RA Qin C., Li M., Qin W., Bahn S.C., Wang C., Wang X.;
RT "Expression and characterization of Arabidopsis phospholipase Dgamma2.";
RL Biochim. Biophys. Acta 1761:1450-1458(2006).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
CC -!- FUNCTION: Hydrolyzes glycerol-phospholipids at the terminal
CC phosphodiesteric bond to generate phosphatidic acids (PA). Plays an
CC important role in various cellular processes, including phytohormone
CC action, vesicular trafficking, secretion, cytoskeletal arrangement,
CC meiosis, tumor promotion, pathogenesis, membrane deterioration and
CC senescence. Can use phosphatidylserine but prefers ethanolamine-
CC containing lipids as substrates. {ECO:0000250|UniProtKB:Q9T053}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1,2-diacyl-
CC sn-glycero-3-phosphate + choline + H(+); Xref=Rhea:RHEA:14445,
CC ChEBI:CHEBI:15354, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57643, ChEBI:CHEBI:58608; EC=3.1.4.4;
CC Evidence={ECO:0000250|UniProtKB:Q9T053};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000250|UniProtKB:Q9T053};
CC Note=Ca(2+). Requires micromolar level (PIP2-dependent).
CC {ECO:0000250|UniProtKB:Q9T053};
CC -!- ACTIVITY REGULATION: Inhibited by neomycin.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10198096}. Membrane
CC {ECO:0000269|PubMed:10198096}; Peripheral membrane protein
CC {ECO:0000269|PubMed:10198096}. Note=Found mainly associated with
CC intracellular membranes but also with mitochondrial membranes, nuclei
CC and clathrin-coated vesicles. Not found in chloroplast.
CC -!- TISSUE SPECIFICITY: Highly expressed in inflorescences and old leaves,
CC moderately in stems, roots, siliques and young leaves and low in
CC flowers. {ECO:0000269|PubMed:17098468}.
CC -!- INDUCTION: Activated by wounding, heavy metal, methyl salicylate,
CC osmotic and salt stresses.
CC -!- DOMAIN: C2 domain is a calcium-binding fold, and the binding promotes
CC the protein association with membranes. In PLD gamma, all the calcium-
CC coordinating acidic amino acids are conserved. {ECO:0000305}.
CC -!- MISCELLANEOUS: Presence of a putative myristoylation site MGXXXS (Gly-
CC 14).
CC -!- SIMILARITY: Belongs to the phospholipase D family. C2-PLD subfamily.
CC {ECO:0000305}.
CC -!- CAUTION: It is uncertain whether the sequence from 46 to 76 is encoded
CC by an intron as for PLDGAMMA2. {ECO:0000305}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-11 is the initiator.
CC {ECO:0000305}.
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DR EMBL; AL078606; CAB44322.1; -; Genomic_DNA.
DR EMBL; AL161532; CAB78227.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE83056.1; -; Genomic_DNA.
DR PIR; T09343; T09343.
DR RefSeq; NP_192921.1; NM_117254.3.
DR AlphaFoldDB; Q9T052; -.
DR SMR; Q9T052; -.
DR BioGRID; 12088; 3.
DR IntAct; Q9T052; 3.
DR STRING; 3702.AT4G11840.1; -.
DR iPTMnet; Q9T052; -.
DR PaxDb; Q9T052; -.
DR PRIDE; Q9T052; -.
DR ProteomicsDB; 234965; -.
DR EnsemblPlants; AT4G11840.1; AT4G11840.1; AT4G11840.
DR GeneID; 826790; -.
DR Gramene; AT4G11840.1; AT4G11840.1; AT4G11840.
DR KEGG; ath:AT4G11840; -.
DR Araport; AT4G11840; -.
DR TAIR; locus:2137035; AT4G11840.
DR eggNOG; KOG1329; Eukaryota.
DR HOGENOM; CLU_004684_0_0_1; -.
DR InParanoid; Q9T052; -.
DR OrthoDB; 181485at2759; -.
DR PhylomeDB; Q9T052; -.
DR BioCyc; ARA:AT4G11840-MON; -.
DR PRO; PR:Q9T052; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9T052; baseline and differential.
DR Genevisible; Q9T052; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0070290; F:N-acylphosphatidylethanolamine-specific phospholipase D activity; IEA:UniProtKB-EC.
DR GO; GO:0004630; F:phospholipase D activity; IBA:GO_Central.
DR GO; GO:0046470; P:phosphatidylcholine metabolic process; IEA:InterPro.
DR GO; GO:0009395; P:phospholipid catabolic process; IBA:GO_Central.
DR Gene3D; 2.60.40.150; -; 1.
DR InterPro; IPR000008; C2_dom.
DR InterPro; IPR035892; C2_domain_sf.
DR InterPro; IPR001736; PLipase_D/transphosphatidylase.
DR InterPro; IPR024632; PLipase_D_C.
DR InterPro; IPR015679; PLipase_D_fam.
DR InterPro; IPR011402; PLipase_D_pln.
DR PANTHER; PTHR18896; PTHR18896; 1.
DR Pfam; PF00168; C2; 1.
DR Pfam; PF12357; PLD_C; 1.
DR Pfam; PF00614; PLDc; 2.
DR PIRSF; PIRSF036470; PLD_plant; 1.
DR SMART; SM00239; C2; 1.
DR SMART; SM00155; PLDc; 2.
DR SUPFAM; SSF49562; SSF49562; 1.
DR PROSITE; PS50004; C2; 1.
DR PROSITE; PS50035; PLD; 2.
PE 1: Evidence at protein level;
KW Calcium; Cytoplasm; Hydrolase; Lipid degradation; Lipid metabolism;
KW Membrane; Metal-binding; Phosphoprotein; Reference proteome; Repeat.
FT CHAIN 1..866
FT /note="Phospholipase D gamma 3"
FT /id="PRO_0000218814"
FT DOMAIN 31..170
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 371..406
FT /note="PLD phosphodiesterase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT DOMAIN 712..739
FT /note="PLD phosphodiesterase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 376
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 378
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 383
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 717
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 719
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 724
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT BINDING 232
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 376
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 412
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 444
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 572
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 717
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 780
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT MOD_RES 692
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9T053"
SQ SEQUENCE 866 AA; 97482 MW; 6748F62F7CD4636E CRC64;
MAYHPVYNET MSMGGGSSNE FGQWLDKQLV PFDTSSGSLR VELLHGNLDI WVKEAKHLPN
MDGFHNTLVG GMFFGLGRRN HKVDGENSSK ITSDPYVTVS ISGAVIGRTF VISNSENPVW
MQHFDVPVAH SAAKVHFVVK DSDIIGSQII GAVEIPTEQL CSGNRIEGLF PILNSRGKPC
KQGAVLSLSI QYIPMERMRL YQKGVGFGVE CVGVPGTYFP LRKGGRVTLY QDAHVDDGTL
PSVHLDGGIQ YRHGKCWEDM ADAIRRARRL IYITGWSVFH PVRLVRRNND PTQGTLGELL
KVKSQEGVRV LVLVWDDPTS RSLLGFSTKG LMNTSDEETR RFFKHSSVQV LLCPRYGGKG
HSFIKKSEVE TIYTHHQKTM IVDAEAAQNR RKIVAFVGGL DLCNGRFDTP KHPLFRTLKT
IHKDDFHNPN FVTTADDGPR EPWHDLHSKI DGPAAYDVLA NFEERWMKAS KPRGIGRLRT
SSDDSLLRLD RIPDIMGLSE ASSANDNDPE SWHVQVFRSI DSSSVKGFPK DPKEATGRNL
LCGKNILIDM SIHAAYVKAI RSAQHFIYIE NQYFLGSSFN WDSNKNLGAN NLIPMEIALK
IANKIRAREK FAAYIVIPMW PEGAPTSNPI QRILYWQHKT MQMMYQTIYK ALVEVGLDGQ
LEPQDFLNFF CLGTREVGTR EVPDGTVSVY NSPRKPPQLN AAQVQALKSR RFMIYVHSKG
MVVDDEFVLI GSANINQRSL EGTRDTEIAM GGYQPHHSWA KKGSRPRGQI FGYRMSLWAE
HLGFLEQEFE EPENMECVRR VRQLSELNWR QYAAEEVTEM PGHLLKYPVQ VDRTGKVSSL
PGYETFPDLG GKIIGSFLVV EENLTI
