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Protein

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

Gene

PLCD1

Organism
Homo sapiens (Human)
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+By similarityNote: Binds 3 Ca2+ ions per subunit. Two of the Ca2+ ions are bound to the C2 domain.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei311PROSITE-ProRule annotation1
Metal bindingi312Calcium 1; catalyticBy similarity1
Metal bindingi341Calcium 1; catalyticBy similarity1
Metal bindingi343Calcium 1; catalyticBy similarity1
Active sitei356PROSITE-ProRule annotation1
Metal bindingi390Calcium 1; catalyticBy similarity1
Binding sitei438SubstrateBy similarity1
Binding sitei440SubstrateBy similarity1
Binding sitei522SubstrateBy similarity1
Binding sitei549SubstrateBy similarity1
Metal bindingi651Calcium 2; via carbonyl oxygenBy similarity1
Metal bindingi653Calcium 2By similarity1
Metal bindingi677Calcium 2By similarity1
Metal bindingi706Calcium 3By similarity1
Metal bindingi707Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi708Calcium 3By similarity1

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

BioCyciMetaCyc:HS07195-MONOMER
BRENDAi3.1.4.11 2681
ReactomeiR-HSA-1855204 Synthesis of IP3 and IP4 in the cytosol

Chemistry databases

SwissLipidsiSLP:000001065

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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000187091.13
HGNCiHGNC:9060 PLCD1
MIMi602142 gene
neXtProtiNX_P51178

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

Involvement in diseasei

Nail disorder, non-syndromic congenital, 3 (NDNC3)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA nail disorder characterized by a white appearance of the nail plate (true leukonychia), the nail bed (pseudoleukonychia), or neither (apparent leukonychia). Leukonychia may involve all of the nail (leukonychia totalis) or only part of the nail (leukonychia partialis), or can appear as one or more transverse bands (leukonychia striata) or white spots (leukonychia punctata).
See also OMIM:151600
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_066399209T → R in NDNC3. 1 Publication1
Natural variantiVAR_066400574I → T in NDNC3. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi5333
MalaCardsiPLCD1
MIMi151600 phenotype
OpenTargetsiENSG00000187091
Orphaneti2387 Leukonychia totalis
PharmGKBiPA33388

Chemistry databases

ChEMBLiCHEMBL3727

Polymorphism and mutation databases

BioMutaiPLCD1
DMDMi206729887

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000885041 – 7561-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1Add BLAST756

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi191O-linked (GlcNAc) serineBy similarity1
Glycosylationi193O-linked (GlcNAc) threonineBy similarity1
Modified residuei457PhosphothreonineBy similarity1
Modified residuei460PhosphoserineCombined sources1

Keywords - PTMi

Glycoprotein, Phosphoprotein

Proteomic databases

EPDiP51178
MaxQBiP51178
PaxDbiP51178
PeptideAtlasiP51178
PRIDEiP51178
ProteomicsDBi56300
56301 [P51178-2]

2D gel databases

REPRODUCTION-2DPAGEiIPI00746030

PTM databases

iPTMnetiP51178
PhosphoSitePlusiP51178
SwissPalmiP51178

Expressioni

Gene expression databases

BgeeiENSG00000187091 Expressed in 225 organ(s), highest expression level in male germ cell
CleanExiHS_PLCD1
GenevisibleiP51178 HS

Organism-specific databases

HPAiCAB009913
HPA020107
HPA021677

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111349, 17 interactors
IntActiP51178, 3 interactors
MINTiP51178
STRINGi9606.ENSP00000430344

Chemistry databases

BindingDBiP51178

Structurei

3D structure databases

ProteinModelPortaliP51178
SMRiP51178
ModBaseiSearch...
MobiDBiSearch...

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
Domaini616 – 720C2PROSITE-ProRule annotationAdd BLAST105

Region

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0169 Eukaryota
ENOG410XPSW LUCA
GeneTreeiENSGT00760000118936
HOGENOMiHOG000006871
HOVERGENiHBG053610
InParanoidiP51178
KOiK05857
OMAiCKTIWQE
OrthoDBiEOG091G02KH
PhylomeDBiP51178
TreeFamiTF313216

Family and domain databases

Gene3Di2.30.29.30, 1 hit
2.60.40.150, 1 hit
3.20.20.190, 2 hits
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
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

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: P51178-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MDSGRDFLTL HGLQDDEDLQ ALLKGSQLLK VKSSSWRRER FYKLQEDCKT
60 70 80 90 100
IWQESRKVMR TPESQLFSIE DIQEVRMGHR TEGLEKFARD VPEDRCFSIV
110 120 130 140 150
FKDQRNTLDL IAPSPADAQH WVLGLHKIIH HSGSMDQRQK LQHWIHSCLR
160 170 180 190 200
KADKNKDNKM SFKELQNFLK ELNIQVDDSY ARKIFRECDH SQTDSLEDEE
210 220 230 240 250
IEAFYKMLTQ RVEIDRTFAE AAGSGETLSV DQLVTFLQHQ QREEAAGPAL
260 270 280 290 300
ALSLIERYEP SETAKAQRQM TKDGFLMYLL SADGSAFSLA HRRVYQDMGQ
310 320 330 340 350
PLSHYLVSSS HNTYLLEDQL AGPSSTEAYI RALCKGCRCL ELDCWDGPNQ
360 370 380 390 400
EPIIYHGYTF TSKILFCDVL RAIRDYAFKA SPYPVILSLE NHCTLEQQRV
410 420 430 440 450
MARHLHAILG PMLLNRPLDG VTNSLPSPEQ LKGKILLKGK KLGGLLPPGG
460 470 480 490 500
EGGPEATVVS DEDEAAEMED EAVRSRVQHK PKEDKLRLAQ ELSDMVIYCK
510 520 530 540 550
SVHFGGFSSP GTPGQAFYEM ASFSENRALR LLQESGNGFV RHNVGHLSRI
560 570 580 590 600
YPAGWRTDSS NYSPVEMWNG GCQIVALNFQ TPGPEMDVYQ GRFQDNGACG
610 620 630 640 650
YVLKPAFLRD PNGTFNPRAL AQGPWWARKR LNIRVISGQQ LPKVNKNKNS
660 670 680 690 700
IVDPKVTVEI HGVSRDVASR QTAVITNNGF NPWWDTEFAF EVVVPDLALI
710 720 730 740 750
RFLVEDYDAS SKNDFIGQST IPLNSLKQGY RHVHLMSKNG DQHPSATLFV

KISLQD
Length:756
Mass (Da):85,665
Last modified:September 23, 2008 - v2
Checksum:i6C6FD7F89BA08C83
GO
Isoform 2 (identifier: P51178-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-11: MDSGRDFLTLH → MQCLGIRSRSRSRELYLQERSLKVAALNGRRL

Note: No experimental confirmation available.
Show »
Length:777
Mass (Da):88,135
Checksum:i6260C76BE397266B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti224S → P in AAA73567 (PubMed:7890667).Curated1
Sequence conflicti264A → T in AAA73567 (PubMed:7890667).Curated1
Sequence conflicti591G → D in AAA73567 (PubMed:7890667).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_066399209T → R in NDNC3. 1 Publication1
Natural variantiVAR_046560257R → H. Corresponds to variant dbSNP:rs933135Ensembl.1
Natural variantiVAR_066400574I → T in NDNC3. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0429191 – 11MDSGRDFLTLH → MQCLGIRSRSRSRELYLQER SLKVAALNGRRL in isoform 2. 1 PublicationAdd BLAST11

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09117 mRNA Translation: AAA73567.1
AK090774 mRNA Translation: BAG52226.1
AC144536 Genomic DNA No translation available.
CH471055 Genomic DNA Translation: EAW64507.1
BC050382 mRNA Translation: AAH50382.2
CCDSiCCDS2671.1 [P51178-1]
CCDS46793.1 [P51178-2]
PIRiA55943
RefSeqiNP_001124436.1, NM_001130964.1 [P51178-2]
NP_006216.2, NM_006225.3 [P51178-1]
UniGeneiHs.80776

Genome annotation databases

EnsembliENST00000334661; ENSP00000335600; ENSG00000187091 [P51178-1]
ENST00000463876; ENSP00000430344; ENSG00000187091 [P51178-2]
GeneIDi5333
KEGGihsa:5333
UCSCiuc003chm.4 human [P51178-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09117 mRNA Translation: AAA73567.1
AK090774 mRNA Translation: BAG52226.1
AC144536 Genomic DNA No translation available.
CH471055 Genomic DNA Translation: EAW64507.1
BC050382 mRNA Translation: AAH50382.2
CCDSiCCDS2671.1 [P51178-1]
CCDS46793.1 [P51178-2]
PIRiA55943
RefSeqiNP_001124436.1, NM_001130964.1 [P51178-2]
NP_006216.2, NM_006225.3 [P51178-1]
UniGeneiHs.80776

3D structure databases

ProteinModelPortaliP51178
SMRiP51178
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111349, 17 interactors
IntActiP51178, 3 interactors
MINTiP51178
STRINGi9606.ENSP00000430344

Chemistry databases

BindingDBiP51178
ChEMBLiCHEMBL3727
SwissLipidsiSLP:000001065

PTM databases

iPTMnetiP51178
PhosphoSitePlusiP51178
SwissPalmiP51178

Polymorphism and mutation databases

BioMutaiPLCD1
DMDMi206729887

2D gel databases

REPRODUCTION-2DPAGEiIPI00746030

Proteomic databases

EPDiP51178
MaxQBiP51178
PaxDbiP51178
PeptideAtlasiP51178
PRIDEiP51178
ProteomicsDBi56300
56301 [P51178-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000334661; ENSP00000335600; ENSG00000187091 [P51178-1]
ENST00000463876; ENSP00000430344; ENSG00000187091 [P51178-2]
GeneIDi5333
KEGGihsa:5333
UCSCiuc003chm.4 human [P51178-1]

Organism-specific databases

CTDi5333
DisGeNETi5333
EuPathDBiHostDB:ENSG00000187091.13
GeneCardsiPLCD1
H-InvDBiHIX0003175
HGNCiHGNC:9060 PLCD1
HPAiCAB009913
HPA020107
HPA021677
MalaCardsiPLCD1
MIMi151600 phenotype
602142 gene
neXtProtiNX_P51178
OpenTargetsiENSG00000187091
Orphaneti2387 Leukonychia totalis
PharmGKBiPA33388
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0169 Eukaryota
ENOG410XPSW LUCA
GeneTreeiENSGT00760000118936
HOGENOMiHOG000006871
HOVERGENiHBG053610
InParanoidiP51178
KOiK05857
OMAiCKTIWQE
OrthoDBiEOG091G02KH
PhylomeDBiP51178
TreeFamiTF313216

Enzyme and pathway databases

BioCyciMetaCyc:HS07195-MONOMER
BRENDAi3.1.4.11 2681
ReactomeiR-HSA-1855204 Synthesis of IP3 and IP4 in the cytosol

Miscellaneous databases

ChiTaRSiPLCD1 human
GeneWikiiPLCD1
GenomeRNAii5333
PROiPR:P51178
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000187091 Expressed in 225 organ(s), highest expression level in male germ cell
CleanExiHS_PLCD1
GenevisibleiP51178 HS

Family and domain databases

Gene3Di2.30.29.30, 1 hit
2.60.40.150, 1 hit
3.20.20.190, 2 hits
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
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_HUMAN
AccessioniPrimary (citable) accession number: P51178
Secondary accession number(s): B3KR14, Q86VN8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: September 23, 2008
Last modified: September 12, 2018
This is version 190 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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