PLDB2_ARATH
ID PLDB2_ARATH Reviewed; 927 AA.
AC O23078; F4JH27;
DT 03-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT 14-DEC-2011, sequence version 3.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Phospholipase D beta 2 {ECO:0000303|PubMed:11891260};
DE Short=AtPLDbeta2 {ECO:0000303|PubMed:11891260};
DE Short=PLD beta 2 {ECO:0000303|PubMed:11891260};
DE EC=3.1.4.4 {ECO:0000250|UniProtKB:Q38882};
DE AltName: Full=PLDdelta1;
GN Name=PLDBETA2 {ECO:0000303|PubMed:11891260}; OrderedLocusNames=At4g00240;
GN ORFNames=A_IG005I10.13, F5I10.13;
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 TISSUE SPECIFICITY.
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 INDUCTION BY LOW PHOSPHATE.
RX PubMed=16384909; DOI=10.1104/pp.105.070995;
RA Li M., Qin C., Welti R., Wang X.;
RT "Double knockouts of phospholipases Dzeta1 and Dzeta2 in Arabidopsis affect
RT root elongation during phosphate-limited growth but do not affect root hair
RT patterning.";
RL Plant Physiol. 140:761-770(2006).
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 or N-
CC acylphosphatidylethanolamine as substrates.
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:Q38882};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000250|UniProtKB:Q38882};
CC Note=Ca(2+). Requires micromolar level (PIP2-dependent).
CC {ECO:0000250|UniProtKB:Q38882};
CC -!- ACTIVITY REGULATION: Inhibited by neomycin.
CC -!- INTERACTION:
CC O23078; Q9C9L2: TCP15; NbExp=3; IntAct=EBI-25512318, EBI-4426144;
CC O23078; Q9LQF0: TCP23; NbExp=3; IntAct=EBI-25512318, EBI-15192297;
CC O23078; Q9FMX2: TCP7; NbExp=3; IntAct=EBI-25512318, EBI-15192677;
CC O23078; O64647: TCP9; NbExp=3; IntAct=EBI-25512318, EBI-9838721;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q38882}.
CC Membrane {ECO:0000250|UniProtKB:Q38882}; Peripheral membrane protein
CC {ECO:0000250|UniProtKB:Q38882}.
CC -!- TISSUE SPECIFICITY: Expressed in stems, and to a lower amount in
CC leaves, flowers and siliques. {ECO:0000269|PubMed:10198096}.
CC -!- INDUCTION: Activated by wounding, methyl jasmonate, heavy metal,
CC osmotic and salt stresses. Up-regulated by phosphate limitation
CC (PubMed:16384909). {ECO:0000269|PubMed:16384909}.
CC -!- DOMAIN: C2 domain is a calcium-binding fold, and the binding promotes
CC the protein association with membranes. In PLD beta, all the calcium-
CC coordinating acidic amino acids are conserved. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the phospholipase D family. C2-PLD subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB62845.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAF02803.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80782.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF013293; AAB62845.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AF195115; AAF02803.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161471; CAB80782.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE81845.1; -; Genomic_DNA.
DR RefSeq; NP_567160.1; NM_116245.2.
DR AlphaFoldDB; O23078; -.
DR SMR; O23078; -.
DR BioGRID; 11972; 4.
DR IntAct; O23078; 4.
DR STRING; 3702.AT4G00240.1; -.
DR PaxDb; O23078; -.
DR PRIDE; O23078; -.
DR ProteomicsDB; 234919; -.
DR EnsemblPlants; AT4G00240.1; AT4G00240.1; AT4G00240.
DR GeneID; 826673; -.
DR Gramene; AT4G00240.1; AT4G00240.1; AT4G00240.
DR KEGG; ath:AT4G00240; -.
DR Araport; AT4G00240; -.
DR TAIR; locus:2126001; AT4G00240.
DR eggNOG; KOG1329; Eukaryota.
DR HOGENOM; CLU_004684_0_0_1; -.
DR InParanoid; O23078; -.
DR OrthoDB; 133306at2759; -.
DR BioCyc; ARA:AT4G00240-MON; -.
DR PRO; PR:O23078; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O23078; baseline and differential.
DR Genevisible; O23078; 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; IDA:TAIR.
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; Reference proteome; Repeat.
FT CHAIN 1..927
FT /note="Phospholipase D beta 2"
FT /id="PRO_0000218811"
FT DOMAIN 104..237
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 439..474
FT /note="PLD phosphodiesterase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT DOMAIN 773..800
FT /note="PLD phosphodiesterase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 444
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 446
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 451
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 778
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 780
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 785
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT BINDING 299
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 444
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 480
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 512
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 640
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 778
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 841
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
SQ SEQUENCE 927 AA; 104155 MW; 157E2505B1E077E3 CRC64;
MENYGWNYPY YPYRPPRPNP PYPAPPHHHG SMSHSGPLDH HHPPMSYYAS FDYQHQPPPP
YPPVSYYASF SSHSDLSYSG RLDSSGHGFT STASPHSPGM HIVPFGKASL KVLLLHGNLD
IWVSCANNLP NLDLFHKTLG VVFGGMTNMI EGQLSKKITS DPYVSISVAG AVIGRTYVIS
NSENPVWQQH FYVPVAHHAA EVHFVVKDSD AVGSQLIGIV TIPVEQIYSG ARIEGTYSIR
DSNGKPCKPG ATLSLSIQYT SMNKLSVYHS GVGAGPYYQG VPGTYFPLRE GGSVTLYQDA
HVPEGMLPGI KLGNGMCYEH GKCWHDMFHA ICQARRLIYI TGWSVWHNVR LVRDKEDPSS
ECRLGELLRS KSQEGVRVLL LVWDDPTSQN ILGYMTDGVM GTHDEETRRF FKDSSVQVLL
CPRNAGKRHS WVKQREVGTI YTHHQKNLIV DADAGGNRRK IVAFVGGLDL CDGRYDTPQH
PLFRTLQTDH NGDYHNPTFT GNVSGCPREP WHDLHSKIDG PAAYDVLTNF EERWLKAAKP
HRINKLKTSY DDALLRIDRI PDILRVLDAP TVSANDPEAW HVQIFRSIDS NSVKGFPKDP
KYATSKNLVC GKNVLIDMSI HTAYVKAIRA AQHFIYIENQ YFIGSSYDWN AHKDIGANNL
IPMEIALKIA DKIRAKERFA AYIVIPMWPE GVPTGAATQR ILYWQHKTMQ MMYGTIYNAL
VEAGLEDEYS PQDYLNFFCL GNREMVNGNN ESGTGSASNE NTPQGLCRKS RRFMIYVHSK
GMVVDDEYVV IGSANINQRS MEGTRDTEIA MGAYQPQHTW ARRQSGPRGQ IYGYRMSLWA
EHMALLDDCF VEPESLGCVR KVRTVAEENW EQFRSEEVSE MRGHLMKYPV EVDRKGKVRP
LPGSEEFPDV GGNVVGSFLA IQENLTI
