PLDA2_ORYSJ
ID PLDA2_ORYSJ Reviewed; 817 AA.
AC P93844; A0A0P0WYW9; Q0DB42; Q69X20;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2006, sequence version 2.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Phospholipase D alpha 2;
DE Short=PLD alpha 2;
DE EC=3.1.4.4;
DE AltName: Full=Choline phosphatase 2;
DE AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D 2;
GN Name=PLD2;
GN OrderedLocusNames=Os06g0604400 {ECO:0000312|EMBL:BAF19931.1},
GN LOC_Os06g40190 {ECO:0000305};
GN ORFNames=OsJ_21907 {ECO:0000312|EMBL:EEE65982.1}, P0481H08.5;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Koshihikari; TISSUE=Leaf;
RA Morioka S., Ueki J., Komari T.;
RT "Characterization of two Distinctive genomic clones for phospholipase D
RT from rice.";
RL (er) Plant Gene Register PGR97-076(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Hydrolyzes glycerol-phospholipids at the terminal
CC phosphodiesteric bond. Plays an important role in various cellular
CC processes.
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 -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000250};
CC -!- DOMAIN: C2 domain is a calcium-binding fold, and the binding promotes
CC the protein association with membranes. A lower affinity toward calcium
CC can be anticipated for PLD alpha due to the absence of two potential
CC calcium ligands.
CC -!- SIMILARITY: Belongs to the phospholipase D family. C2-PLD subfamily.
CC {ECO:0000305}.
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DR EMBL; AB001919; BAA19466.1; -; Genomic_DNA.
DR EMBL; AP003629; BAD35531.1; -; Genomic_DNA.
DR EMBL; AP008212; BAF19931.1; -; Genomic_DNA.
DR EMBL; AP014962; BAS98517.1; -; Genomic_DNA.
DR EMBL; CM000143; EEE65982.1; -; Genomic_DNA.
DR EMBL; AK072121; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; T03401; T03401.
DR RefSeq; XP_015643893.1; XM_015788407.1.
DR AlphaFoldDB; P93844; -.
DR SMR; P93844; -.
DR STRING; 4530.OS06T0604400-01; -.
DR PaxDb; P93844; -.
DR PRIDE; P93844; -.
DR EnsemblPlants; Os06t0604400-01; Os06t0604400-01; Os06g0604400.
DR GeneID; 4341469; -.
DR Gramene; Os06t0604400-01; Os06t0604400-01; Os06g0604400.
DR KEGG; osa:4341469; -.
DR eggNOG; KOG1329; Eukaryota.
DR HOGENOM; CLU_004684_0_0_1; -.
DR InParanoid; P93844; -.
DR OMA; GEHFAVY; -.
DR OrthoDB; 128697at2759; -.
DR PlantReactome; R-OSA-1119276; Choline biosynthesis III.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000007752; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 6.
DR Genevisible; P93844; OS.
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 2: Evidence at transcript level;
KW Calcium; Hydrolase; Lipid degradation; Lipid metabolism; Metal-binding;
KW Reference proteome; Repeat.
FT CHAIN 1..817
FT /note="Phospholipase D alpha 2"
FT /id="PRO_0000218821"
FT DOMAIN 1..130
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 333..372
FT /note="PLD phosphodiesterase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT DOMAIN 663..690
FT /note="PLD phosphodiesterase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 338
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 340
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 345
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 668
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 670
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 675
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT BINDING 192
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 338
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 378
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
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 529
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 668
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 730
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT CONFLICT 111
FT /note="G -> D (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 122
FT /note="S -> C (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 365
FT /note="G -> R (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 387
FT /note="A -> G (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 391
FT /note="D -> Y (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 395
FT /note="P -> A (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 480
FT /note="G -> WA (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 520
FT /note="A -> R (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 550
FT /note="A -> P (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 690
FT /note="S -> P (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 694..695
FT /note="GR -> EG (in Ref. 1; BAA19466)"
FT /evidence="ECO:0000305"
FT CONFLICT 729
FT /note="Y -> F (in Ref. 6; AK072121)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 817 AA; 91319 MW; 948AE6A40B32E12F CRC64;
MAHLLLHGTL EATILEADHL SNPTRATGAA PGIFRKFVEG FEDSLGLGKG ATRLYATIDL
GRARVGRTRV VDDEPVNPRW YEVFHIYCAH FAADVVFSVK AAQPIGATLI GRAYLPVREL
LSGEAIERRL DILDAGRRRI SHGPTIHVRL QFRDVAGDRH GWGRGVSGAR YPGVPYTFFS
QRPGCRVTLY QDAHVPDAFA PRIPLAGGGY YRQGRCWEDV FDAISNAKHL IYLTGWSVYT
EITLIRDGTR QRPGGDATLG ELLKRKASEG VRVLLLVWDD RTSVESLGMK WGFMSTHDAE
TADYFRGTDV RCVLCPRNPD AGRSAIMGAQ IAYMITHHQK TVIVDHDMPV PRGGGSRRIV
SFVGGLDLCD GRYDTQFHSL FRTLDTAHHS DFHQPNLDGA AVTKGGPREP WHDIHSKIEG
PAAWDVLYNF EQRWRKQGGD KDLLLDLKAM ADLIIPPSPV MFPDDGEAWS VQLFRSIDGG
ACFGFPSTPE AAARSGLVSG KNNTIDRSIQ DAYIHAIRRA KNFIYIENQY FLGSSFAWKA
DGIRPEDIEA LHLIPREISL KIVNKIEAGE RFAVYVVLPM WPEGPPASGS VQAILDWQRR
TMEMMYYDIA VALEAKRINA DPRDYLTFFC LGNREVKLNG EYEPAGRPLD GTDYAKAQKA
RRFMIYVHSK MMIVDDEYII VGSANINQRS MDGGRDSEIA MGAFQPCHLN TKGLVARGQI
HGFRMSLWYE HLGMLHDNFL NPESLECVQR VNKMADKYWD LYASDELNDD LPGHLLTYPV
RVTKEGTVTE LPGAKFFPDT QAPVIGTKGN LPPFLTT
