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Protein

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

Gene

Plcd1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

  • calcium ion binding Source: RGD
  • phosphatidylinositol-4,5-bisphosphate binding Source: RGD
  • phosphatidylinositol phospholipase C activity Source: RGD
  • phospholipid binding Source: RGD
  • signal transducer activity Source: UniProtKB-KW

GO - Biological processi

  • G-protein coupled receptor signaling pathway Source: RGD
  • intracellular signal transduction Source: InterPro
  • lipid catabolic process Source: UniProtKB-KW
  • positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway Source: RGD
  • positive regulation of inositol trisphosphate biosynthetic process Source: RGD
  • positive regulation of norepinephrine secretion Source: RGD
  • regulation of cytosolic calcium ion concentration Source: RGD
  • regulation of phospholipase C activity Source: RGD
  • response to aluminum ion Source: RGD
  • response to calcium ion Source: RGD
  • response to hyperoxia Source: RGD
  • response to organonitrogen compound Source: RGD
  • response to peptide hormone Source: RGD
  • response to prostaglandin F Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Transducer

Keywords - Biological processi

Lipid degradation, Lipid metabolism

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.4.11. 5301.
SABIO-RKP10688.

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3346. Plcd1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: RGD
  • membrane Source: RGD
  • membrane raft Source: RGD
  • mitochondrial membrane Source: RGD
  • nucleus Source: RGD
Complete GO annotation...

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)1 Publication1
Glycosylationi193O-linked (GlcNAc)1 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.
MINTiMINT-245440.
STRINGi10116.ENSRNOP00000042824.

Chemistry databases

BindingDBiP10688.

Structurei

Secondary structure

1756
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi17 – 24Combined sources8
Beta strandi26 – 35Combined sources10
Beta strandi37 – 44Combined sources8
Beta strandi48 – 53Combined sources6
Turni62 – 65Combined sources4
Beta strandi66 – 68Combined sources3
Helixi69 – 71Combined sources3
Beta strandi72 – 79Combined sources8
Helixi82 – 87Combined sources6
Helixi93 – 95Combined sources3
Beta strandi96 – 104Combined sources9
Beta strandi108 – 111Combined sources4
Helixi115 – 129Combined sources15
Beta strandi159 – 161Combined sources3
Helixi162 – 170Combined sources9
Turni171 – 173Combined sources3
Helixi178 – 180Combined sources3
Helixi181 – 188Combined sources8
Beta strandi190 – 197Combined sources8
Helixi203 – 208Combined sources6
Helixi212 – 222Combined sources11
Beta strandi225 – 229Combined sources5
Helixi230 – 239Combined sources10
Helixi248 – 258Combined sources11
Helixi262 – 266Combined sources5
Helixi272 – 280Combined sources9
Turni282 – 284Combined sources3
Beta strandi285 – 287Combined sources3
Helixi289 – 292Combined sources4
Helixi302 – 304Combined sources3
Beta strandi305 – 307Combined sources3
Beta strandi309 – 312Combined sources4
Beta strandi315 – 317Combined sources3
Beta strandi319 – 321Combined sources3
Helixi326 – 334Combined sources9
Beta strandi339 – 345Combined sources7
Helixi348 – 350Combined sources3
Beta strandi353 – 355Combined sources3
Turni357 – 360Combined sources4
Helixi366 – 376Combined sources11
Turni377 – 379Combined sources3
Beta strandi385 – 392Combined sources8
Helixi395 – 409Combined sources15
Helixi410 – 412Combined sources3
Turni428 – 433Combined sources6
Beta strandi435 – 439Combined sources5
Helixi490 – 493Combined sources4
Beta strandi496 – 502Combined sources7
Beta strandi509 – 514Combined sources6
Beta strandi519 – 524Combined sources6
Helixi525 – 545Combined sources21
Beta strandi548 – 551Combined sources4
Helixi565 – 568Combined sources4
Turni569 – 571Combined sources3
Beta strandi574 – 577Combined sources4
Helixi584 – 594Combined sources11
Helixi596 – 598Combined sources3
Beta strandi600 – 603Combined sources4
Helixi606 – 609Combined sources4
Beta strandi629 – 640Combined sources12
Helixi644 – 646Combined sources3
Beta strandi648 – 650Combined sources3
Beta strandi654 – 663Combined sources10
Helixi664 – 666Combined sources3
Beta strandi668 – 671Combined sources4
Beta strandi679 – 681Combined sources3
Beta strandi683 – 693Combined sources11
Helixi695 – 697Combined sources3
Beta strandi699 – 706Combined sources8
Beta strandi709 – 711Combined sources3
Beta strandi714 – 722Combined sources9
Helixi723 – 725Combined sources3
Beta strandi729 – 736Combined sources8
Beta strandi742 – 755Combined sources14

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...

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

Sequence similaritiesi

Contains 1 C2 domain.PROSITE-ProRule annotation
Contains 2 EF-hand domains.PROSITE-ProRule annotation
Contains 1 PH domain.PROSITE-ProRule annotation
Contains 1 PI-PLC X-box domain.PROSITE-ProRule annotation
Contains 1 PI-PLC Y-box domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0169. Eukaryota.
ENOG410XPSW. LUCA.
HOGENOMiHOG000006871.
HOVERGENiHBG053610.
InParanoidiP10688.
KOiK05857.
PhylomeDBiP10688.

Family and domain databases

Gene3Di1.10.238.10. 2 hits.
2.30.29.30. 1 hit.
2.60.40.150. 1 hit.
3.20.20.190. 2 hits.
InterProiIPR000008. C2_dom.
IPR011992. EF-hand-dom_pair.
IPR018247. EF_Hand_1_Ca_BS.
IPR002048. EF_hand_dom.
IPR011993. PH_dom-like.
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.
[Graphical view]
PANTHERiPTHR10336. PTHR10336. 1 hit.
PTHR10336:SF80. PTHR10336:SF80. 1 hit.
PfamiPF00168. 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.
[Graphical view]
PRINTSiPR00390. PHPHLIPASEC.
SMARTiSM00239. C2. 1 hit.
SM00054. EFh. 2 hits.
SM00233. PH. 1 hit.
SM00148. PLCXc. 1 hit.
SM00149. PLCYc. 1 hit.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
SSF49562. SSF49562. 1 hit.
SSF50729. SSF50729. 1 hit.
SSF51695. SSF51695. 1 hit.
PROSITEiPS50004. 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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

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

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.
MINTiMINT-245440.
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-RKP10688.

Miscellaneous databases

EvolutionaryTraceiP10688.
PROiP10688.

Family and domain databases

Gene3Di1.10.238.10. 2 hits.
2.30.29.30. 1 hit.
2.60.40.150. 1 hit.
3.20.20.190. 2 hits.
InterProiIPR000008. C2_dom.
IPR011992. EF-hand-dom_pair.
IPR018247. EF_Hand_1_Ca_BS.
IPR002048. EF_hand_dom.
IPR011993. PH_dom-like.
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.
[Graphical view]
PANTHERiPTHR10336. PTHR10336. 1 hit.
PTHR10336:SF80. PTHR10336:SF80. 1 hit.
PfamiPF00168. 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.
[Graphical view]
PRINTSiPR00390. PHPHLIPASEC.
SMARTiSM00239. C2. 1 hit.
SM00054. EFh. 2 hits.
SM00233. PH. 1 hit.
SM00148. PLCXc. 1 hit.
SM00149. PLCYc. 1 hit.
[Graphical view]
SUPFAMiSSF47473. SSF47473. 1 hit.
SSF49562. SSF49562. 1 hit.
SSF50729. SSF50729. 1 hit.
SSF51695. SSF51695. 1 hit.
PROSITEiPS50004. 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.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPLCD1_RAT
AccessioniPrimary (citable) accession number: P10688
Secondary accession number(s): Q80WI4
, Q9QVD3, Q9QVD4, Q9QVD5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: November 2, 2016
This is version 172 of the entry and version 1 of the sequence. [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
  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.