PLDA1_ORYSJ
ID PLDA1_ORYSJ Reviewed; 812 AA.
AC Q43007; A0A0P0UZ48; Q0JQB1;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2006, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Phospholipase D alpha 1;
DE Short=PLD alpha 1;
DE EC=3.1.4.4;
DE AltName: Full=Choline phosphatase 1;
DE AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D 1;
DE Flags: Precursor;
GN Name=PLD1;
GN OrderedLocusNames=Os01g0172400 {ECO:0000312|EMBL:BAF04067.1},
GN LOC_Os01g07760 {ECO:0000305};
GN ORFNames=OsJ_00559 {ECO:0000312|EMBL:EEE53959.1};
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 [MRNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=cv. Koshihikari;
RX PubMed=7551587; DOI=10.1093/oxfordjournals.pcp.a078837;
RA Ueki J., Morioka S., Komari T., Kumashiro T.;
RT "Purification and characterization of phospholipase D (PLD) from rice
RT (Oryza sativa L.) and cloning of cDNA for PLD from rice and maize (Zea mays
RT L.).";
RL Plant Cell Physiol. 36:903-914(1995).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [4]
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 [5]
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 [6]
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 [7]
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).
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;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.0.;
CC Temperature dependence:
CC Stable from 4 to 37 degrees Celsius. Activity is reduced to one third
CC of the original level after incubation at 50 degrees Celsius for 30
CC minutes.;
CC -!- SUBUNIT: Monomer.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, roots, developing seeds and
CC cultured cells.
CC -!- DEVELOPMENTAL STAGE: The transcript begins to emerged in seeds as early
CC as the second day after imbibition and increased after radicle
CC emergence on the third day. Strongly expressed in the leaves, roots and
CC residual grain of seedling eight days after imbibition. Undetectable in
CC mature dry seeds.
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; D73411; BAA11136.1; -; mRNA.
DR EMBL; AB001920; BAA19467.1; -; Genomic_DNA.
DR EMBL; AP003215; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AP003282; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AP008207; BAF04067.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS70634.1; -; Genomic_DNA.
DR EMBL; CM000138; EEE53959.1; -; Genomic_DNA.
DR PIR; T03402; T03402.
DR RefSeq; XP_015646609.1; XM_015791123.1.
DR AlphaFoldDB; Q43007; -.
DR SMR; Q43007; -.
DR STRING; 4530.OS01T0172400-03; -.
DR PaxDb; Q43007; -.
DR PRIDE; Q43007; -.
DR EnsemblPlants; Os01t0172400-02; Os01t0172400-02; Os01g0172400.
DR EnsemblPlants; Os01t0172400-03; Os01t0172400-03; Os01g0172400.
DR GeneID; 4327647; -.
DR Gramene; Os01t0172400-02; Os01t0172400-02; Os01g0172400.
DR Gramene; Os01t0172400-03; Os01t0172400-03; Os01g0172400.
DR KEGG; osa:4327647; -.
DR eggNOG; KOG1329; Eukaryota.
DR InParanoid; Q43007; -.
DR OMA; PNWGRGI; -.
DR OrthoDB; 128697at2759; -.
DR PlantReactome; R-OSA-1119276; Choline biosynthesis III.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR ExpressionAtlas; Q43007; baseline and differential.
DR Genevisible; Q43007; 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 1: Evidence at protein level;
KW Calcium; Direct protein sequencing; Hydrolase; Lipid degradation;
KW Lipid metabolism; Metal-binding; Reference proteome; Repeat.
FT PROPEP 1..46
FT /id="PRO_0000024655"
FT CHAIN 47..812
FT /note="Phospholipase D alpha 1"
FT /id="PRO_0000024656"
FT DOMAIN 1..130
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 330..368
FT /note="PLD phosphodiesterase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT DOMAIN 658..685
FT /note="PLD phosphodiesterase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 335
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 337
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 342
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 663
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 665
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 670
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT BINDING 190
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 335
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 374
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 408
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 524
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 663
FT /ligand="a 1,2-diacyl-sn-glycero-3-phosphate"
FT /ligand_id="ChEBI:CHEBI:58608"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT BINDING 724
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:Q38882"
FT CONFLICT 139
FT /note="P -> S (in Ref. 1 and 2)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 812 AA; 92219 MW; 6AE267E6C8B1DC5E CRC64;
MAQMLLHGTL HATIFEAASL SNPHRASGSA PKFIRKFVEG IEDTVGVGKG ATKVYSTIDL
EKARVGRTRM ITNEPINPRW YESFHIYCAH MASNVIFTVK IDNPIGATNI GRAYLPVQEL
LNGEEIDRWL DICDNNREPV GESKIHVKLQ YFDVSKDRNW ARGVRSTKYP GVPYTFFSQR
QGCKVTLYQD AHVPDNFIPK IPLADGKNYE PHRCWEDIFD AISNAQHLIY ITGWSVYTEI
TLVRDSNRPK PGGDVTLGEL LKKKASEGVR VLMLVWDDRT SVGLLKRDGL MATHDEETEN
YFHGSDVNCV LCPRNPDDSG SIVQDLSIST MFTHHQKIVV VDHELPNQGS QQRRIVSFVG
GLDLCDGRYD TQYHSLFRTL DSTHHDDFHQ PNFATASIKK GGPREPWHDI HSRLEGPIAW
DVLYNFEQRW RKQGGKDLLL QLRDLSDTII PPSPVMFPED RETWNVQLFR SIDGGAAFGF
PDTPEEAAKA GLVSGKDQII DRSIQDAYIH AIRRAKNFIY IENQYFLGSS YAWKPEGIKP
EDIGALHLIP KELALKVVSK IEAGERFTVY VVVPMWPEGV PESGSVQAIL DWQRRTMEMM
YTDITEALQA KGIEANPKDY LTFFCLGNRE VKQAGEYQPE EQPEADTDYS RAQEARRFMI
YVHTKMMIVD DEYIIIGSAN INQRSMDGAR DSEIAMGGYQ PYHLATRQPA RGQIHGFRMA
LWYEHLGMLD DVFQRPESLE CVQKVNRIAE KYWDMYSSDD LQQDLPGHLL SYPIGVASDG
VVTELPGMEY FPDTRARVLG AKSDYMPPIL TS
