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Protein

Phospholipase D B

Gene

pldB

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Plays a role in cell growth. Hydrolyzes membrane phospholipids, such as PtdCho (phosphatidylcholine), producing the free headgroup and PtdOH (phosphatidic acid; signaling molecule on its own). Involved in the inhibition of actin-based motility and endocytosis. Its inhibition causes complete collapse of F-actin organization. Plays an important role in cell migration by localizing along the anterior cell membrane. Overexpression leads to the inability to aggregate even at higher cell density. Also known as a negative regulator of quorum sensing.4 Publications

Catalytic activityi

A phosphatidylcholine + H2O = choline + a phosphatidate.

Enzyme regulationi

Inhibited by butan-1-ol.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei590 – 5901PROSITE-ProRule annotation
Active sitei592 – 5921PROSITE-ProRule annotation
Active sitei597 – 5971PROSITE-ProRule annotation
Active sitei1041 – 10411PROSITE-ProRule annotation
Active sitei1043 – 10431PROSITE-ProRule annotation
Active sitei1048 – 10481PROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Calcium bindingi209 – 22012PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • calcium ion binding Source: InterPro
  • N-acylphosphatidylethanolamine-specific phospholipase D activity Source: UniProtKB-EC
  • phospholipase D activity Source: dictyBase

GO - Biological processi

  • cell motility Source: dictyBase
  • chemotaxis to cAMP Source: dictyBase
  • gene expression Source: dictyBase
  • lipid catabolic process Source: UniProtKB-KW
  • phospholipid metabolic process Source: dictyBase
  • positive regulation of exocytosis Source: dictyBase
  • positive regulation of sorocarp spore cell differentiation Source: dictyBase
  • quorum sensing Source: dictyBase
  • regulation of actin cytoskeleton reorganization Source: dictyBase
  • regulation of aggregation involved in sorocarp development Source: dictyBase
  • regulation of G-protein coupled receptor protein signaling pathway Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Lipid degradation, Lipid metabolism

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.4.4. 1939.
ReactomeiR-DDI-1483166. Synthesis of PA.
R-DDI-2029485. Role of phospholipids in phagocytosis.

Names & Taxonomyi

Protein namesi
Recommended name:
Phospholipase D B (EC:3.1.4.4)
Alternative name(s):
Phosphatase D1
Short name:
PLD 1
Gene namesi
Name:pldB
Synonyms:pld1
ORF Names:DDB_G0279483
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
Proteomesi
  • UP000002195 Componentsi: Chromosome 3, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0279483. pldB.

Subcellular locationi

GO - Cellular componenti

  • cell cortex Source: dictyBase
  • cytoplasmic, membrane-bounded vesicle Source: UniProtKB-SubCell
  • membrane Source: dictyBase
  • protein complex Source: dictyBase
  • pseudopodium Source: dictyBase
  • vacuole Source: dictyBase
  • vesicle Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoplasmic vesicle

Pathology & Biotechi

Disruption phenotypei

Null cells show a motility defect; migration speed of vegetative cells is reduced to 73% of that of the wild-type, an aggregation ability at lower cell density and an ability to initiate and finish aggregation rapidly. Have altered cAR1 expression.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12161216Phospholipase D BPRO_0000367471Add
BLAST

Proteomic databases

PaxDbiQ54WR4.

Expressioni

Developmental stagei

Not expressed in vegetative cells. Expression is apparent by 8 hours and peaked by 16 hours. Becomes present during aggregation and throughout development.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi44689.DDB0231507.

Structurei

3D structure databases

ProteinModelPortaliQ54WR4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini196 – 23136EF-hand 1PROSITE-ProRule annotationAdd
BLAST
Domaini232 – 26736EF-hand 2PROSITE-ProRule annotationAdd
BLAST
Domaini347 – 462116PHPROSITE-ProRule annotationAdd
BLAST
Domaini585 – 61228PLD phosphodiesterase 1PROSITE-ProRule annotationAdd
BLAST
Domaini1036 – 106328PLD phosphodiesterase 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi384 – 3896Poly-Lys
Compositional biasi416 – 4194Poly-Lys
Compositional biasi843 – 8486Poly-Asn

Sequence similaritiesi

Belongs to the phospholipase D family.Curated
Contains 2 EF-hand domains.PROSITE-ProRule annotation
Contains 1 PH domain.PROSITE-ProRule annotation
Contains 2 PLD phosphodiesterase domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0044. Eukaryota.
KOG1329. Eukaryota.
COG1502. LUCA.
COG5126. LUCA.
InParanoidiQ54WR4.
KOiK01115.
OMAiSCNINDR.
PhylomeDBiQ54WR4.

Family and domain databases

Gene3Di1.10.238.10. 1 hit.
2.30.29.30. 1 hit.
InterProiIPR011992. EF-hand-dom_pair.
IPR018247. EF_Hand_1_Ca_BS.
IPR002048. EF_hand_dom.
IPR011993. PH_dom-like.
IPR001849. PH_domain.
IPR025202. PLD-like_dom.
IPR001736. PLipase_D/transphosphatidylase.
IPR015679. PLipase_D_fam.
[Graphical view]
PANTHERiPTHR18896. PTHR18896. 2 hits.
PfamiPF00614. PLDc. 1 hit.
PF13091. PLDc_2. 1 hit.
[Graphical view]
SMARTiSM00054. EFh. 2 hits.
SM00233. PH. 1 hit.
SM00155. PLDc. 2 hits.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
SSF50729. SSF50729. 1 hit.
PROSITEiPS00018. EF_HAND_1. 1 hit.
PS50222. EF_HAND_2. 2 hits.
PS50003. PH_DOMAIN. 1 hit.
PS50035. PLD. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q54WR4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNLSQEHAIN QNLHKNQKNE EKIEKKTINK DGRGQMNYDG EEGQGEKSRF
60 70 80 90 100
QKMVENEKIE EPQQKDENIP NTDVIERKEV GVIERINSED VPILMTDNAT
110 120 130 140 150
DYKVLQHNLK KGKVSKKSKE QIEQISKQEE NDMLEYLKNY KSNEEFTIQL
160 170 180 190 200
EDLLSFETYF SRDELHLLYR EFKTISKSGM FMSKEDFISK LTPFSRNADL
210 220 230 240 250
TISLMNAIDR NGDQKIAFPE FVQALSIMCR GTKKERLRFT FEICDFNGDS
260 270 280 290 300
LVSRDEVYST VKAISDIFSK FGYSKDKFGD PSEAVDSIFS SGLTTNGIYL
310 320 330 340 350
HNKKELTLNE FLERGELNPD LSKCFGMFDY FYLKFIGQID LLFKDKEINM
360 370 380 390 400
NGQLTKIKPK TIFNFNISHR RTLSLRDGFL IVYKKKKFKH DEDKPSKVIF
410 420 430 440 450
LPGSTVKVVV GSQPSKKKKF LSKKFHNYYG FRVTKGNYNR FFLMENRDEA
460 470 480 490 500
LNWVNAIRFH SRQGFRFQSF SKVRSNISVE WFINGSSYYN ELAETIRRAK
510 520 530 540 550
HEIFITGWWV SPYVYLQRDN GIENMEKSRL DRILTEKAKE GVKVYVLMWN
560 570 580 590 600
ETNLGVQLGS RHAKNWLEGC HSNIHVIRHP KRYPLSWSHH QKNAIIDQQI
610 620 630 640 650
AFVGGIDICL MRYETSKFQL TDDQGKRFPG KDYGNLLGTV IRTGDPKKDQ
660 670 680 690 700
FNRRECPRMP WHDVHTKIVG PSAKDVASNF IQRWNHAIYV ERSNRFQPIL
710 720 730 740 750
VPKNYTGLPS DDAKPDKWKN LVSNIRKGFS HVSYGREKPT HYQRAGDNPK
760 770 780 790 800
VRSHTRQGAF GLQSDQIDNK IDKQKNNSTN SENSENSYSE FDEEDEEGNQ
810 820 830 840 850
EEEDEDEFDE FEKDENQKQE NSKIPFNNKP SDAGGLKSKN YKNNNNNNII
860 870 880 890 900
ESLKDEESFE LPGTPKIDLN NDKLLKSIYH LSSNMSENSC VVQMVRSICP
910 920 930 940 950
WSAGTDVEDS CYKAYLGLIK NAQHFIYIQN LFFISSCGSK LPKNRIALAI
960 970 980 990 1000
LNRVRRAITL KEKFRVIIMV PISPSGDLAL ASSRMIIGWT NRTISQGGQS
1010 1020 1030 1040 1050
ILELLKNEFP DVDLDQYISF NSIRQWEANG DRIFTEQIYV HSKVLIVDDR
1060 1070 1080 1090 1100
VAVIGSCNIN DRSMMGSRDS ELAVVVSDQS KLLITMNGKP FKVGKFPHTL
1110 1120 1130 1140 1150
RVGLWKTHLN LTDSEISSII DPITDNAFIN IWRKTARNNS IIYKEVFGDC
1160 1170 1180 1190 1200
ILENQRRLGI VQKKYIPKTN ELIVQLSQIQ GVLIEYPLDM FCESNLFNEQ
1210
VGIFTAESYV DVSIFT
Length:1,216
Mass (Da):140,700
Last modified:May 24, 2005 - v1
Checksum:i895DB744505DE04D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000031 Genomic DNA. Translation: EAL67680.1.
RefSeqiXP_641653.1. XM_636561.1.

Genome annotation databases

EnsemblProtistsiDDB0231507; DDB0231507; DDB_G0279483.
GeneIDi8622060.
KEGGiddi:DDB_G0279483.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000031 Genomic DNA. Translation: EAL67680.1.
RefSeqiXP_641653.1. XM_636561.1.

3D structure databases

ProteinModelPortaliQ54WR4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0231507.

Proteomic databases

PaxDbiQ54WR4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0231507; DDB0231507; DDB_G0279483.
GeneIDi8622060.
KEGGiddi:DDB_G0279483.

Organism-specific databases

dictyBaseiDDB_G0279483. pldB.

Phylogenomic databases

eggNOGiKOG0044. Eukaryota.
KOG1329. Eukaryota.
COG1502. LUCA.
COG5126. LUCA.
InParanoidiQ54WR4.
KOiK01115.
OMAiSCNINDR.
PhylomeDBiQ54WR4.

Enzyme and pathway databases

BRENDAi3.1.4.4. 1939.
ReactomeiR-DDI-1483166. Synthesis of PA.
R-DDI-2029485. Role of phospholipids in phagocytosis.

Miscellaneous databases

PROiQ54WR4.

Family and domain databases

Gene3Di1.10.238.10. 1 hit.
2.30.29.30. 1 hit.
InterProiIPR011992. EF-hand-dom_pair.
IPR018247. EF_Hand_1_Ca_BS.
IPR002048. EF_hand_dom.
IPR011993. PH_dom-like.
IPR001849. PH_domain.
IPR025202. PLD-like_dom.
IPR001736. PLipase_D/transphosphatidylase.
IPR015679. PLipase_D_fam.
[Graphical view]
PANTHERiPTHR18896. PTHR18896. 2 hits.
PfamiPF00614. PLDc. 1 hit.
PF13091. PLDc_2. 1 hit.
[Graphical view]
SMARTiSM00054. EFh. 2 hits.
SM00233. PH. 1 hit.
SM00155. PLDc. 2 hits.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
SSF50729. SSF50729. 1 hit.
PROSITEiPS00018. EF_HAND_1. 1 hit.
PS50222. EF_HAND_2. 2 hits.
PS50003. PH_DOMAIN. 1 hit.
PS50035. PLD. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.
  2. "Comparison of the hydrolysis of phosphatidylethanolamine and phosphatidyl(N-acyl)ethanolamine in Dictyostelium discoideum amoebae."
    Ellingson J.S., Dischinger H.C.
    Biochim. Biophys. Acta 796:155-162(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  3. "Developmentally regulated changes in 1,2-diacylglycerol in Dictyostelium. Regulation by light and G proteins."
    Cubitt A.B., Dharmawardhane S., Firtel R.A.
    J. Biol. Chem. 268:17431-17439(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C."
    Rigden D.J.
    FEBS Lett. 569:229-234(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  5. "Phospholipase D activity is essential for actin localization and actin-based motility in Dictyostelium."
    Zouwail S., Pettitt T.R., Dove S.K., Chibalina M.V., Powner D.J., Haynes L., Wakelam M.J.O., Insall R.H.
    Biochem. J. 389:207-214(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION, FUNCTION.
  6. "PldB, a putative phospholipase D homologue in Dictyostelium discoideum mediates quorum sensing during development."
    Chen Y., Rodrick V., Yan Y., Brazill D.
    Eukaryot. Cell 4:694-702(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, DEVELOPMENTAL STAGE.
  7. "Rho GTPase signaling in Dictyostelium discoideum: insights from the genome."
    Vlahou G., Rivero F.
    Eur. J. Cell Biol. 85:947-959(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  8. "Screening of genes involved in cell migration in Dictyostelium."
    Nagasaki A., Uyeda T.Q.P.
    Exp. Cell Res. 314:1136-1146(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiPLDB_DICDI
AccessioniPrimary (citable) accession number: Q54WR4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 24, 2005
Last modified: March 16, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.