PLDB_DICDI
ID PLDB_DICDI Reviewed; 1216 AA.
AC Q54WR4;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Phospholipase D B;
DE EC=3.1.4.4;
DE AltName: Full=Phosphatase D1;
DE Short=PLD 1;
GN Name=pldB; Synonyms=pld1; ORFNames=DDB_G0279483;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [2]
RP FUNCTION.
RX PubMed=6498208; DOI=10.1016/0005-2760(84)90343-6;
RA Ellingson J.S., Dischinger H.C.;
RT "Comparison of the hydrolysis of phosphatidylethanolamine and
RT phosphatidyl(N-acyl)ethanolamine in Dictyostelium discoideum amoebae.";
RL Biochim. Biophys. Acta 796:155-162(1984).
RN [3]
RP FUNCTION.
RX PubMed=8394342; DOI=10.1016/s0021-9258(19)85353-x;
RA Cubitt A.B., Dharmawardhane S., Firtel R.A.;
RT "Developmentally regulated changes in 1,2-diacylglycerol in Dictyostelium.
RT Regulation by light and G proteins.";
RL J. Biol. Chem. 268:17431-17439(1993).
RN [4]
RP NOMENCLATURE.
RX PubMed=15225639; DOI=10.1016/j.febslet.2004.05.071;
RA Rigden D.J.;
RT "A distant evolutionary relationship between GPI-specific phospholipase D
RT and bacterial phosphatidylcholine-preferring phospholipase C.";
RL FEBS Lett. 569:229-234(2004).
RN [5]
RP ACTIVITY REGULATION, AND FUNCTION.
RX PubMed=15769249; DOI=10.1042/bj20050085;
RA Zouwail S., Pettitt T.R., Dove S.K., Chibalina M.V., Powner D.J.,
RA Haynes L., Wakelam M.J.O., Insall R.H.;
RT "Phospholipase D activity is essential for actin localization and actin-
RT based motility in Dictyostelium.";
RL Biochem. J. 389:207-214(2005).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND DEVELOPMENTAL STAGE.
RX PubMed=15821129; DOI=10.1128/ec.4.4.694-702.2005;
RA Chen Y., Rodrick V., Yan Y., Brazill D.;
RT "PldB, a putative phospholipase D homologue in Dictyostelium discoideum
RT mediates quorum sensing during development.";
RL Eukaryot. Cell 4:694-702(2005).
RN [7]
RP NOMENCLATURE.
RX PubMed=16762450; DOI=10.1016/j.ejcb.2006.04.011;
RA Vlahou G., Rivero F.;
RT "Rho GTPase signaling in Dictyostelium discoideum: insights from the
RT genome.";
RL Eur. J. Cell Biol. 85:947-959(2006).
RN [8]
RP DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
RX PubMed=18164290; DOI=10.1016/j.yexcr.2007.12.002;
RA Nagasaki A., Uyeda T.Q.P.;
RT "Screening of genes involved in cell migration in Dictyostelium.";
RL Exp. Cell Res. 314:1136-1146(2008).
CC -!- FUNCTION: Plays a role in cell growth. Hydrolyzes membrane
CC phospholipids, such as PtdCho (phosphatidylcholine), producing the free
CC headgroup and PtdOH (phosphatidic acid; signaling molecule on its own).
CC Involved in the inhibition of actin-based motility and endocytosis. Its
CC inhibition causes complete collapse of F-actin organization. Plays an
CC important role in cell migration by localizing along the anterior cell
CC membrane. Overexpression leads to the inability to aggregate even at
CC higher cell density. Also known as a negative regulator of quorum
CC sensing. {ECO:0000269|PubMed:15769249, ECO:0000269|PubMed:15821129,
CC ECO:0000269|PubMed:6498208, ECO:0000269|PubMed:8394342}.
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 -!- ACTIVITY REGULATION: Inhibited by butan-1-ol.
CC {ECO:0000269|PubMed:15769249}.
CC -!- SUBCELLULAR LOCATION: Cytoplasmic vesicle
CC {ECO:0000269|PubMed:18164290}. Cytoplasm, cell cortex
CC {ECO:0000269|PubMed:18164290}. Note=In migrating cells, localized at
CC the protruding regions of pseudopodia.
CC -!- DEVELOPMENTAL STAGE: Not expressed in vegetative cells. Expression is
CC apparent by 8 hours and peaked by 16 hours. Becomes present during
CC aggregation and throughout development. {ECO:0000269|PubMed:15821129}.
CC -!- DISRUPTION PHENOTYPE: Null cells show a motility defect; migration
CC speed of vegetative cells is reduced to 73% of that of the wild-type,
CC an aggregation ability at lower cell density and an ability to initiate
CC and finish aggregation rapidly. Have altered cAR1 expression.
CC {ECO:0000269|PubMed:15821129, ECO:0000269|PubMed:18164290}.
CC -!- SIMILARITY: Belongs to the phospholipase D family. {ECO:0000305}.
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DR EMBL; AAFI02000031; EAL67680.1; -; Genomic_DNA.
DR RefSeq; XP_641653.1; XM_636561.1.
DR AlphaFoldDB; Q54WR4; -.
DR SMR; Q54WR4; -.
DR STRING; 44689.DDB0231507; -.
DR PaxDb; Q54WR4; -.
DR EnsemblProtists; EAL67680; EAL67680; DDB_G0279483.
DR GeneID; 8622060; -.
DR KEGG; ddi:DDB_G0279483; -.
DR dictyBase; DDB_G0279483; pldB.
DR eggNOG; KOG0044; Eukaryota.
DR eggNOG; KOG1329; Eukaryota.
DR HOGENOM; CLU_269219_0_0_1; -.
DR InParanoid; Q54WR4; -.
DR OMA; IGSCNIN; -.
DR PhylomeDB; Q54WR4; -.
DR BRENDA; 3.1.4.4; 1939.
DR Reactome; R-DDI-1483166; Synthesis of PA.
DR Reactome; R-DDI-2029485; Role of phospholipids in phagocytosis.
DR Reactome; R-DDI-6798695; Neutrophil degranulation.
DR Reactome; R-DDI-9013149; RAC1 GTPase cycle.
DR Reactome; R-DDI-9013404; RAC2 GTPase cycle.
DR PRO; PR:Q54WR4; -.
DR Proteomes; UP000002195; Chromosome 3.
DR GO; GO:0005938; C:cell cortex; IDA:dictyBase.
DR GO; GO:0031410; C:cytoplasmic vesicle; IEA:UniProtKB-KW.
DR GO; GO:0031941; C:filamentous actin; IDA:dictyBase.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IBA:GO_Central.
DR GO; GO:0016020; C:membrane; ISS:dictyBase.
DR GO; GO:0032991; C:protein-containing complex; IDA:dictyBase.
DR GO; GO:0031143; C:pseudopodium; IDA:dictyBase.
DR GO; GO:0005773; C:vacuole; IDA:dictyBase.
DR GO; GO:0031982; C:vesicle; IDA:dictyBase.
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; IMP:dictyBase.
DR GO; GO:0048870; P:cell motility; IMP:dictyBase.
DR GO; GO:0043327; P:chemotaxis to cAMP; IMP:dictyBase.
DR GO; GO:0010467; P:gene expression; IDA:dictyBase.
DR GO; GO:0009395; P:phospholipid catabolic process; IBA:GO_Central.
DR GO; GO:0006644; P:phospholipid metabolic process; ISS:dictyBase.
DR GO; GO:0045921; P:positive regulation of exocytosis; IMP:dictyBase.
DR GO; GO:1901263; P:positive regulation of sorocarp spore cell differentiation; IMP:dictyBase.
DR GO; GO:0009372; P:quorum sensing; IMP:dictyBase.
DR GO; GO:2000249; P:regulation of actin cytoskeleton reorganization; IMP:dictyBase.
DR GO; GO:0060176; P:regulation of aggregation involved in sorocarp development; IMP:dictyBase.
DR GO; GO:0008277; P:regulation of G protein-coupled receptor signaling pathway; IMP:dictyBase.
DR GO; GO:0048837; P:sorocarp sorus development; IMP:dictyBase.
DR Gene3D; 2.30.29.30; -; 1.
DR InterPro; IPR011992; EF-hand-dom_pair.
DR InterPro; IPR018247; EF_Hand_1_Ca_BS.
DR InterPro; IPR002048; EF_hand_dom.
DR InterPro; IPR011993; PH-like_dom_sf.
DR InterPro; IPR001849; PH_domain.
DR InterPro; IPR025202; PLD-like_dom.
DR InterPro; IPR001736; PLipase_D/transphosphatidylase.
DR InterPro; IPR015679; PLipase_D_fam.
DR PANTHER; PTHR18896; PTHR18896; 1.
DR Pfam; PF00614; PLDc; 1.
DR Pfam; PF13091; PLDc_2; 1.
DR SMART; SM00054; EFh; 2.
DR SMART; SM00233; PH; 1.
DR SMART; SM00155; PLDc; 2.
DR SUPFAM; SSF47473; SSF47473; 1.
DR PROSITE; PS00018; EF_HAND_1; 1.
DR PROSITE; PS50222; EF_HAND_2; 2.
DR PROSITE; PS50003; PH_DOMAIN; 1.
DR PROSITE; PS50035; PLD; 2.
PE 2: Evidence at transcript level;
KW Calcium; Cytoplasm; Cytoplasmic vesicle; Hydrolase; Lipid degradation;
KW Lipid metabolism; Metal-binding; Reference proteome; Repeat.
FT CHAIN 1..1216
FT /note="Phospholipase D B"
FT /id="PRO_0000367471"
FT DOMAIN 196..231
FT /note="EF-hand 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT DOMAIN 232..267
FT /note="EF-hand 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT DOMAIN 347..462
FT /note="PH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00145"
FT DOMAIN 585..612
FT /note="PLD phosphodiesterase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT DOMAIN 1036..1063
FT /note="PLD phosphodiesterase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT REGION 1..48
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 732..844
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 13..48
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 732..751
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 787..813
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 821..844
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 590
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 592
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 597
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 1041
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 1043
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 1048
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT BINDING 209
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 211
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 213
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 215
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 220
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
SQ SEQUENCE 1216 AA; 140700 MW; 895DB744505DE04D CRC64;
MNLSQEHAIN QNLHKNQKNE EKIEKKTINK DGRGQMNYDG EEGQGEKSRF QKMVENEKIE
EPQQKDENIP NTDVIERKEV GVIERINSED VPILMTDNAT DYKVLQHNLK KGKVSKKSKE
QIEQISKQEE NDMLEYLKNY KSNEEFTIQL EDLLSFETYF SRDELHLLYR EFKTISKSGM
FMSKEDFISK LTPFSRNADL TISLMNAIDR NGDQKIAFPE FVQALSIMCR GTKKERLRFT
FEICDFNGDS LVSRDEVYST VKAISDIFSK FGYSKDKFGD PSEAVDSIFS SGLTTNGIYL
HNKKELTLNE FLERGELNPD LSKCFGMFDY FYLKFIGQID LLFKDKEINM NGQLTKIKPK
TIFNFNISHR RTLSLRDGFL IVYKKKKFKH DEDKPSKVIF LPGSTVKVVV GSQPSKKKKF
LSKKFHNYYG FRVTKGNYNR FFLMENRDEA LNWVNAIRFH SRQGFRFQSF SKVRSNISVE
WFINGSSYYN ELAETIRRAK HEIFITGWWV SPYVYLQRDN GIENMEKSRL DRILTEKAKE
GVKVYVLMWN ETNLGVQLGS RHAKNWLEGC HSNIHVIRHP KRYPLSWSHH QKNAIIDQQI
AFVGGIDICL MRYETSKFQL TDDQGKRFPG KDYGNLLGTV IRTGDPKKDQ FNRRECPRMP
WHDVHTKIVG PSAKDVASNF IQRWNHAIYV ERSNRFQPIL VPKNYTGLPS DDAKPDKWKN
LVSNIRKGFS HVSYGREKPT HYQRAGDNPK VRSHTRQGAF GLQSDQIDNK IDKQKNNSTN
SENSENSYSE FDEEDEEGNQ EEEDEDEFDE FEKDENQKQE NSKIPFNNKP SDAGGLKSKN
YKNNNNNNII ESLKDEESFE LPGTPKIDLN NDKLLKSIYH LSSNMSENSC VVQMVRSICP
WSAGTDVEDS CYKAYLGLIK NAQHFIYIQN LFFISSCGSK LPKNRIALAI LNRVRRAITL
KEKFRVIIMV PISPSGDLAL ASSRMIIGWT NRTISQGGQS ILELLKNEFP DVDLDQYISF
NSIRQWEANG DRIFTEQIYV HSKVLIVDDR VAVIGSCNIN DRSMMGSRDS ELAVVVSDQS
KLLITMNGKP FKVGKFPHTL RVGLWKTHLN LTDSEISSII DPITDNAFIN IWRKTARNNS
IIYKEVFGDC ILENQRRLGI VQKKYIPKTN ELIVQLSQIQ GVLIEYPLDM FCESNLFNEQ
VGIFTAESYV DVSIFT
