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Protein

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1

Gene

Plcd1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. Essential for trophoblast and placental development.

Catalytic activityi

1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H2O = 1D-myo-inositol 1,4,5-trisphosphate + diacylglycerol.

Cofactori

Ca2+Note: Binds 3 Ca2+ ions per subunit. Two of the Ca2+ ions are bound to the C2 domain.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei3111
Metal bindingi312Calcium 1; catalytic1
Metal bindingi341Calcium 1; catalytic1
Metal bindingi343Calcium 1; catalytic1
Active sitei3561
Metal bindingi390Calcium 1; catalytic1
Binding sitei438Substrate1
Binding sitei440Substrate1
Binding sitei522Substrate1
Binding sitei549Substrate1
Metal bindingi651Calcium 2; via carbonyl oxygen1
Metal bindingi653Calcium 21
Metal bindingi677Calcium 21
Metal bindingi706Calcium 31
Metal bindingi707Calcium 3; via carbonyl oxygen1
Metal bindingi708Calcium 31

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Calcium bindingi153 – 1641PROSITE-ProRule annotationAdd BLAST12
Calcium bindingi189 – 2002PROSITE-ProRule annotationAdd BLAST12

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase, Transducer
Biological processLipid degradation, Lipid metabolism
LigandCalcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.4.11 5301
SABIO-RKiP10688

Chemistry databases

SwissLipidsiSLP:000001066

Names & Taxonomyi

Protein namesi
Recommended name:
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 (EC:3.1.4.11)
Alternative name(s):
Phosphoinositide phospholipase C-delta-1
Phospholipase C-III
Short name:
PLC-III
Phospholipase C-delta-1
Short name:
PLC-delta-1
Gene namesi
Name:Plcd1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3346 Plcd1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi311H → A: Lowers activity 10000-fold. 1 Publication1
Mutagenesisi312N → A: Lowers activity 10000-fold. 1 Publication1
Mutagenesisi320L → A: Lowers activity 3-fold. 1 Publication1
Mutagenesisi341E → A, H or Q: Lowers activity 200000-fold. 1 Publication1
Mutagenesisi343D → A: Lowers activity 1000-fold. 1 Publication1
Mutagenesisi343D → R: Lowers activity 100000-fold. 1 Publication1
Mutagenesisi356H → A: Lowers activity 1000-fold. 1 Publication1
Mutagenesisi360F → A: Lowers activity 4-fold. 1 Publication1
Mutagenesisi390E → A, H or K: Lowers activity 1000-fold. 1 Publication1
Mutagenesisi390E → Q: Lowers activity 200-fold. 1 Publication1
Mutagenesisi438K → A: Lowers activity very slightly. 1 Publication1
Mutagenesisi440K → A: No effect on activity towards phosphatidylinositol 4-monophosphate. Lowers activity 5-fold towards phosphatidylinositol 4,5-bisphosphate. 1 Publication1
Mutagenesisi522S → A: Lowers activity 10000-fold. 1 Publication1
Mutagenesisi549R → A: Lowers activity 600-fold. 1 Publication1
Mutagenesisi551Y → A: Lowers activity 600-fold. 1 Publication1
Mutagenesisi555W → A: Lowers activity very slightly. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL1914273

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000885061 – 7561-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1Add BLAST756

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi191O-linked (GlcNAc) serine1 Publication1
Glycosylationi193O-linked (GlcNAc) threonine1 Publication1
Modified residuei457PhosphothreonineBy similarity1
Modified residuei460PhosphoserineBy similarity1

Keywords - PTMi

Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiP10688
PRIDEiP10688

PTM databases

iPTMnetiP10688
PhosphoSitePlusiP10688

Interactioni

Protein-protein interaction databases

BioGridi246790, 1 interactor
STRINGi10116.ENSRNOP00000042824

Chemistry databases

BindingDBiP10688

Structurei

Secondary structure

1756
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

DisProtiDP00055
ProteinModelPortaliP10688
SMRiP10688
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP10688

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini21 – 130PHPROSITE-ProRule annotationAdd BLAST110
Domaini140 – 175EF-hand 1PROSITE-ProRule annotationAdd BLAST36
Domaini176 – 211EF-hand 2PROSITE-ProRule annotationAdd BLAST36
Domaini296 – 440PI-PLC X-boxPROSITE-ProRule annotationAdd BLAST145
Domaini492 – 609PI-PLC Y-boxPROSITE-ProRule annotationAdd BLAST118
Domaini630 – 720C2PROSITE-ProRule annotationAdd BLAST91

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni30 – 57Substrate bindingAdd BLAST28

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0169 Eukaryota
ENOG410XPSW LUCA
HOGENOMiHOG000006871
HOVERGENiHBG053610
InParanoidiP10688
KOiK05857
PhylomeDBiP10688

Family and domain databases

Gene3Di2.30.29.30, 1 hit
2.60.40.150, 1 hit
3.20.20.190, 1 hit
InterProiView protein in InterPro
IPR000008 C2_dom
IPR035892 C2_domain_sf
IPR011992 EF-hand-dom_pair
IPR018247 EF_Hand_1_Ca_BS
IPR002048 EF_hand_dom
IPR011993 PH-like_dom_sf
IPR001849 PH_domain
IPR001192 PI-PLC_fam
IPR028391 PLC-delta1
IPR017946 PLC-like_Pdiesterase_TIM-brl
IPR015359 PLC_EF-hand-like
IPR000909 PLipase_C_PInositol-sp_X_dom
IPR001711 PLipase_C_Pinositol-sp_Y
PANTHERiPTHR10336 PTHR10336, 1 hit
PTHR10336:SF80 PTHR10336:SF80, 1 hit
PfamiView protein in Pfam
PF00168 C2, 1 hit
PF09279 EF-hand_like, 1 hit
PF16457 PH_12, 1 hit
PF00388 PI-PLC-X, 1 hit
PF00387 PI-PLC-Y, 1 hit
PRINTSiPR00390 PHPHLIPASEC
SMARTiView protein in SMART
SM00239 C2, 1 hit
SM00054 EFh, 2 hits
SM00233 PH, 1 hit
SM00148 PLCXc, 1 hit
SM00149 PLCYc, 1 hit
SUPFAMiSSF47473 SSF47473, 1 hit
SSF51695 SSF51695, 1 hit
PROSITEiView protein in PROSITE
PS50004 C2, 1 hit
PS00018 EF_HAND_1, 2 hits
PS50222 EF_HAND_2, 2 hits
PS50003 PH_DOMAIN, 1 hit
PS50007 PIPLC_X_DOMAIN, 1 hit
PS50008 PIPLC_Y_DOMAIN, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

P10688-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDSGRDFLTL HGLQDDPDLQ ALLKGSQLLK VKSSSWRRER FYKLQEDCKT
60 70 80 90 100
IWQESRKVMR SPESQLFSIE DIQEVRMGHR TEGLEKFARD IPEDRCFSIV
110 120 130 140 150
FKDQRNTLDL IAPSPADAQH WVQGLRKIIH HSGSMDQRQK LQHWIHSCLR
160 170 180 190 200
KADKNKDNKM NFKELKDFLK ELNIQVDDGY ARKIFRECDH SQTDSLEDEE
210 220 230 240 250
IETFYKMLTQ RAEIDRAFEE AAGSAETLSV ERLVTFLQHQ QREEEAGPAL
260 270 280 290 300
ALSLIERYEP SETAKAQRQM TKDGFLMYLL SADGNAFSLA HRRVYQDMDQ
310 320 330 340 350
PLSHYLVSSS HNTYLLEDQL TGPSSTEAYI RALCKGCRCL ELDCWDGPNQ
360 370 380 390 400
EPIIYHGYTF TSKILFCDVL RAIRDYAFKA SPYPVILSLE NHCSLEQQRV
410 420 430 440 450
MARHLRAILG PILLDQPLDG VTTSLPSPEQ LKGKILLKGK KLGGLLPAGG
460 470 480 490 500
ENGSEATDVS DEVEAAEMED EAVRSQVQHK PKEDKLKLVP ELSDMIIYCK
510 520 530 540 550
SVHFGGFSSP GTSGQAFYEM ASFSESRALR LLQESGNGFV RHNVSCLSRI
560 570 580 590 600
YPAGWRTDSS NYSPVEMWNG GCQIVALNFQ TPGPEMDVYL GCFQDNGGCG
610 620 630 640 650
YVLKPAFLRD PNTTFNSRAL TQGPWWRPER LRVRIISGQQ LPKVNKNKNS
660 670 680 690 700
IVDPKVIVEI HGVGRDTGSR QTAVITNNGF NPRWDMEFEF EVTVPDLALV
710 720 730 740 750
RFMVEDYDSS SKNDFIGQST IPWNSLKQGY RHVHLLSKNG DQHPSATLFV

KISIQD
Length:756
Mass (Da):85,962
Last modified:July 1, 1989 - v1
Checksum:iE33F2313AC81E9F9
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
G3V9D1G3V9D1_RAT
Phosphoinositide phospholipase C
Plcd1 rCG_25198
756Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti627 – 629RPE → APK in AAP31521 (PubMed:1684614).Curated3

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti412I → M in SHR. 1 Publication1
Natural varianti423T → S in SHR. 1 Publication1
Natural varianti463V → D in SHR. 1 Publication1
Natural varianti668G → A in SHR. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M20637 mRNA Translation: AAA41886.1
S74591 mRNA Translation: AAP31521.1
PIRiB28821
RefSeqiNP_058731.1, NM_017035.1
UniGeneiRn.12324

Genome annotation databases

GeneIDi24655
KEGGirno:24655
UCSCiRGD:3346 rat

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M20637 mRNA Translation: AAA41886.1
S74591 mRNA Translation: AAP31521.1
PIRiB28821
RefSeqiNP_058731.1, NM_017035.1
UniGeneiRn.12324

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DJGX-ray2.60A/B133-756[»]
1DJHX-ray2.50A/B133-756[»]
1DJIX-ray2.50A/B133-756[»]
1DJWX-ray2.45A/B133-756[»]
1DJXX-ray2.30A/B133-756[»]
1DJYX-ray2.80A/B133-756[»]
1DJZX-ray2.95A/B133-756[»]
1MAIX-ray1.90A11-140[»]
1QASX-ray2.40A/B135-756[»]
1QATX-ray3.00A/B135-756[»]
2ISDX-ray2.50A/B133-756[»]
DisProtiDP00055
ProteinModelPortaliP10688
SMRiP10688
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi246790, 1 interactor
STRINGi10116.ENSRNOP00000042824

Chemistry databases

BindingDBiP10688
ChEMBLiCHEMBL1914273
SwissLipidsiSLP:000001066

PTM databases

iPTMnetiP10688
PhosphoSitePlusiP10688

Proteomic databases

PaxDbiP10688
PRIDEiP10688

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi24655
KEGGirno:24655
UCSCiRGD:3346 rat

Organism-specific databases

CTDi5333
RGDi3346 Plcd1

Phylogenomic databases

eggNOGiKOG0169 Eukaryota
ENOG410XPSW LUCA
HOGENOMiHOG000006871
HOVERGENiHBG053610
InParanoidiP10688
KOiK05857
PhylomeDBiP10688

Enzyme and pathway databases

BRENDAi3.1.4.11 5301
SABIO-RKiP10688

Miscellaneous databases

EvolutionaryTraceiP10688
PROiPR:P10688

Family and domain databases

Gene3Di2.30.29.30, 1 hit
2.60.40.150, 1 hit
3.20.20.190, 1 hit
InterProiView protein in InterPro
IPR000008 C2_dom
IPR035892 C2_domain_sf
IPR011992 EF-hand-dom_pair
IPR018247 EF_Hand_1_Ca_BS
IPR002048 EF_hand_dom
IPR011993 PH-like_dom_sf
IPR001849 PH_domain
IPR001192 PI-PLC_fam
IPR028391 PLC-delta1
IPR017946 PLC-like_Pdiesterase_TIM-brl
IPR015359 PLC_EF-hand-like
IPR000909 PLipase_C_PInositol-sp_X_dom
IPR001711 PLipase_C_Pinositol-sp_Y
PANTHERiPTHR10336 PTHR10336, 1 hit
PTHR10336:SF80 PTHR10336:SF80, 1 hit
PfamiView protein in Pfam
PF00168 C2, 1 hit
PF09279 EF-hand_like, 1 hit
PF16457 PH_12, 1 hit
PF00388 PI-PLC-X, 1 hit
PF00387 PI-PLC-Y, 1 hit
PRINTSiPR00390 PHPHLIPASEC
SMARTiView protein in SMART
SM00239 C2, 1 hit
SM00054 EFh, 2 hits
SM00233 PH, 1 hit
SM00148 PLCXc, 1 hit
SM00149 PLCYc, 1 hit
SUPFAMiSSF47473 SSF47473, 1 hit
SSF51695 SSF51695, 1 hit
PROSITEiView protein in PROSITE
PS50004 C2, 1 hit
PS00018 EF_HAND_1, 2 hits
PS50222 EF_HAND_2, 2 hits
PS50003 PH_DOMAIN, 1 hit
PS50007 PIPLC_X_DOMAIN, 1 hit
PS50008 PIPLC_Y_DOMAIN, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPLCD1_RAT
AccessioniPrimary (citable) accession number: P10688
Secondary accession number(s): Q80WI4
, Q9QVD3, Q9QVD4, Q9QVD5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: June 20, 2018
This is version 181 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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