PLDB1_ARATH
ID PLDB1_ARATH Reviewed; 1083 AA.
AC P93733; F4ILZ0; P93745;
DT 03-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT 25-JAN-2012, sequence version 4.
DT 03-AUG-2022, entry version 163.
DE RecName: Full=Phospholipase D beta 1 {ECO:0000303|PubMed:11891260};
DE Short=AtPLDbeta1 {ECO:0000303|PubMed:11891260};
DE Short=PLD beta 1 {ECO:0000303|PubMed:11891260};
DE Short=PLDbeta {ECO:0000303|PubMed:9054397};
DE EC=3.1.4.4 {ECO:0000269|PubMed:10441386, ECO:0000269|PubMed:9054397, ECO:0000269|PubMed:9353280};
GN Name=PLDBETA1 {ECO:0000303|PubMed:11891260};
GN OrderedLocusNames=At2g42010 {ECO:0000312|Araport:AT2G42010};
GN ORFNames=T6D20.10 {ECO:0000312|EMBL:AAB63542.2};
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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 [MRNA] OF 60-1083, AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia; TISSUE=Hypocotyl;
RX PubMed=9054397; DOI=10.1074/jbc.272.11.7055;
RA Pappan K., Qin W., Dyer J.H., Zheng L., Wang X.;
RT "Molecular cloning and functional analysis of polyphosphoinositide-
RT dependent phospholipase D, PLDbeta, from Arabidopsis.";
RL J. Biol. Chem. 272:7055-7061(1997).
RN [4]
RP SEQUENCE REVISION.
RA Wang X.;
RL Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP CATALYTIC ACTIVITY, COFACTOR, AND ACTIVITY REGULATION.
RX PubMed=9353280; DOI=10.1074/jbc.272.45.28267;
RA Qin W., Pappan K., Wang X.;
RT "Molecular heterogeneity of phospholipase D (PLD). Cloning of PLDgamma and
RT regulation of plant PLDgamma, -beta, and -alpha by polyphosphoinositides
RT and calcium.";
RL J. Biol. Chem. 272:28267-28273(1997).
RN [6]
RP SUBSTRATE SPECIFICITY.
RX PubMed=9578608; DOI=10.1006/abbi.1998.0640;
RA Pappan K., Austin-Brown S., Chapman K.D., Wang X.;
RT "Substrate selectivities and lipid modulation of plant phospholipase D
RT alpha, -beta, and -gamma.";
RL Arch. Biochem. Biophys. 353:131-140(1998).
RN [7]
RP CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=10441386; DOI=10.1006/abbi.1999.1325;
RA Pappan K., Wang X.;
RT "Plant phospholipase Dalpha is an acidic phospholipase active at near-
RT physiological Ca(2+) concentrations.";
RL Arch. Biochem. Biophys. 368:347-353(1999).
RN [8]
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 [9]
RP DOMAIN, AND 3D-STRUCTURE MODELING.
RX PubMed=10777500; DOI=10.1074/jbc.m001945200;
RA Zheng L., Krishnamoorthi R., Zolkiewski M., Wang X.;
RT "Distinct Ca2+ binding properties of novel C2 domains of plant
RT phospholipase dalpha and beta.";
RL J. Biol. Chem. 275:19700-19706(2000).
RN [10]
RP INDUCTION BY WOUNDING.
RX PubMed=11090221; DOI=10.2307/3871117;
RA Wang C., Zien C.A., Afitlhile M., Welti R., Hildebrand D.F., Wang X.;
RT "Involvement of phospholipase D in wound-induced accumulation of jasmonic
RT acid in arabidopsis.";
RL Plant Cell 12:2237-2246(2000).
RN [11]
RP FUNCTION.
RX PubMed=11722757; DOI=10.1046/j.1365-313x.2001.01138.x;
RA Sang Y., Zheng S., Li W., Huang B., Wang X.;
RT "Regulation of plant water loss by manipulating the expression of
RT phospholipase Dalpha.";
RL Plant J. 28:135-144(2001).
RN [12]
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 [13]
RP FUNCTION.
RX PubMed=23577648; DOI=10.1111/nph.12256;
RA Zhao J., Devaiah S.P., Wang C., Li M., Welti R., Wang X.;
RT "Arabidopsis phospholipase Dbeta1 modulates defense responses to bacterial
RT and fungal pathogens.";
RL New Phytol. 199:228-240(2013).
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. Involved in regulating stomatal movement and plant-water
CC status (PubMed:11722757). Can use phosphatidylserine (PS) and
CC phosphatidylethanolamine (PE) as substrates only in the presence of
CC PIP2. Can use phosphatidylcholine (PC), phosphatidylglycerol (PG) or N-
CC acylphosphatidylethanolamine (NAPE) as substrates in the presence of PE
CC and PIP2 (PubMed:9578608). Modulates defense responses to bacterial and
CC fungal pathogens (PubMed:23577648). {ECO:0000269|PubMed:11722757,
CC ECO:0000269|PubMed:23577648, ECO:0000269|PubMed:9578608}.
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:0000269|PubMed:10441386, ECO:0000269|PubMed:9054397,
CC ECO:0000269|PubMed:9353280};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:9054397, ECO:0000269|PubMed:9353280};
CC Note=Ca(2+). Requires micromolar level (PIP2-dependent).
CC {ECO:0000269|PubMed:9054397, ECO:0000269|PubMed:9353280};
CC -!- ACTIVITY REGULATION: Inhibited by neomycin. Up-regulated by PIP2
CC binding. {ECO:0000269|PubMed:9054397, ECO:0000269|PubMed:9353280}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.5 to 7.5. {ECO:0000269|PubMed:10441386};
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. {ECO:0000269|PubMed:11090221}.
CC -!- DOMAIN: C2 domain is a calcium-binding fold, and the binding induces
CC conformational changes, promoting the protein association with
CC membranes. These conformational changes occure at micromolar Ca(2+)
CC concentrations. Exhibits three Ca(2+)-binding sites. Binds also PIP2.
CC {ECO:0000269|PubMed:10777500}.
CC -!- SIMILARITY: Belongs to the phospholipase D family. C2-PLD subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB63542.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAC49656.2; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U90439; AAB63542.2; ALT_INIT; Genomic_DNA.
DR EMBL; CP002685; AEC10063.1; -; Genomic_DNA.
DR EMBL; U84568; AAC49656.2; ALT_SEQ; mRNA.
DR PIR; H84848; H84848.
DR RefSeq; NP_565963.2; NM_129765.4.
DR AlphaFoldDB; P93733; -.
DR SMR; P93733; -.
DR BioGRID; 4139; 3.
DR IntAct; P93733; 1.
DR STRING; 3702.AT2G42010.1; -.
DR iPTMnet; P93733; -.
DR PaxDb; P93733; -.
DR PRIDE; P93733; -.
DR ProteomicsDB; 235007; -.
DR EnsemblPlants; AT2G42010.1; AT2G42010.1; AT2G42010.
DR GeneID; 818802; -.
DR Gramene; AT2G42010.1; AT2G42010.1; AT2G42010.
DR KEGG; ath:AT2G42010; -.
DR Araport; AT2G42010; -.
DR TAIR; locus:2064607; AT2G42010.
DR eggNOG; KOG1329; Eukaryota.
DR HOGENOM; CLU_004684_0_1_1; -.
DR InParanoid; P93733; -.
DR BioCyc; ARA:AT2G42010-MON; -.
DR BioCyc; MetaCyc:AT2G42010-MON; -.
DR BRENDA; 3.1.4.4; 399.
DR PRO; PR:P93733; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; P93733; baseline and differential.
DR Genevisible; P93733; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0070290; F:N-acylphosphatidylethanolamine-specific phospholipase D activity; IEA:UniProtKB-EC.
DR GO; GO:0005546; F:phosphatidylinositol-4,5-bisphosphate binding; IDA:TAIR.
DR GO; GO:0004630; F:phospholipase D activity; IDA:TAIR.
DR GO; GO:0042742; P:defense response to bacterium; IEP:TAIR.
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 PANTHER; PTHR18896; PTHR18896; 1.
DR Pfam; PF00168; C2; 1.
DR Pfam; PF12357; PLD_C; 1.
DR Pfam; PF00614; PLDc; 2.
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..1083
FT /note="Phospholipase D beta 1"
FT /id="PRO_0000218810"
FT DOMAIN 252..393
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 595..630
FT /note="PLD phosphodiesterase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT DOMAIN 929..956
FT /note="PLD phosphodiesterase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT REGION 26..231
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 26..65
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 66..87
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 115..147
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 148..180
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 192..231
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 600
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 602
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 607
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 934
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 936
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 941
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT BINDING 455
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 600
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 636
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 668
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 796
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 934
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 997
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
SQ SEQUENCE 1083 AA; 121101 MW; 4A3558560FF8CFEB CRC64;
MDNHGPRYPY PYGQYPYPYP YPAPYRPPSS EPYPPPPTNQ YSAPYYPYPP PPYATPPPYA
SPPPPHQHTS GSHSGPLDYS HNPQPSSLAA APPEYHRHSF DYQPSPYPYQ PQGNFGAYGP
PPPHYSYQEP AQYPPPETKP QEPLPPPQQT QGFQEYRRQD CLSTGGTGHD NVSNSGSSYP
PVDELLGGLH ISTNQPGPSV PQLSSLPSNS WQSRPGDLYG YPNSSFPSNS HLPQLGRVDS
SSSYYASTES PHSADMQMTL FGKGSLKVLL LHGNLDIWIY HAKNLPNMDM FHKTLGDMFG
RLPGKIEGQL TSKITSDPYV SVSVAGAVIG RTYVMSNSEN PVWMQHFYVP VAHHAAEVHF
VVKDSDVVGS QLIGLVTIPV EQIYSGAKIE GTYPILNSNG KPCKPGANLS LSIQYTPMDK
LSVYHHGVGA GPDYQGVPGT YFPLRKGGTV RLYQDAHVPE GMLPGIRLDN GMSYEHGKCW
HDMFDAIRQA RRLIYITGWS VWHKVKLIRD KLGPASECTL GELLRSKSQE GVRVLLLIWD
DPTSRSILGY KTDGVMATHD EETRRFFKHS SVQVLLCPRN AGKRHSWVKQ REVGTIYTHH
QKNVIVDADA GGNRRKIIAF VGGLDLCDGR YDTPQHPLFR TLQTIHKDDF HNPTFTGNLS
GCPREPWHDL HSKIDGPAAY DVLTNFEERW LKAAKPSGIK KFKTSYDDAL LRIDRIPDIL
GVSDTPTVSE NDPEAWHVQI FRSIDSNSVK GFPKDPKDAT CKNLVCGKNV LIDMSIHTAY
VKAIRAAQHF IYIENQYFIG SSYNWNAHKD IGANNLIPME IALKIAEKIR ANERFAAYIV
IPMWPEGVPT GAATQRILYW QHKTIQMMYE TIYKALVETG LEGAFSPQDY LNFFCLGNRE
MVDGIDNSGT GSPSNANTPQ ALSRKSRRFM VYVHSKGMVV DDEYVVIGSA NINQRSMEGT
RDTEIAMGAY QPQHTWARKH SGPRGQIYGY RMSLWAEHMA TLDDCFTQPE SIECVRKVRT
MGERNWKQFA AEEVSDMRGH LLKYPVEVDR KGKVRPLPGS ETFPDVGGNI VGSFIAIQEN
LTI
