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Protein

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3-A

Gene

plcd3a

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Hydrolyzes the phosphatidylinositol 4,5-bisphosphate (PIP2) to generate 2 second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). DAG mediates the activation of protein kinase C (PKC), while IP3 releases Ca2+ from intracellular stores (By similarity).By similarity

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 Ca(2+) ions per subunit. Two of the Ca2+ ions are bound to the C2 domain.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei328 – 3281PROSITE-ProRule annotation
Metal bindingi329 – 3291Calcium 1; catalyticBy similarity
Metal bindingi358 – 3581Calcium 1; catalyticBy similarity
Metal bindingi360 – 3601Calcium 1; catalyticBy similarity
Active sitei373 – 3731PROSITE-ProRule annotation
Metal bindingi407 – 4071Calcium 1; catalyticBy similarity
Binding sitei456 – 4561SubstrateBy similarity
Binding sitei458 – 4581SubstrateBy similarity
Binding sitei534 – 5341SubstrateBy similarity
Binding sitei561 – 5611SubstrateBy similarity
Metal bindingi664 – 6641Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi666 – 6661Calcium 2By similarity
Metal bindingi690 – 6901Calcium 2By similarity
Metal bindingi719 – 7191Calcium 3By similarity
Metal bindingi721 – 7211Calcium 3By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Calcium bindingi172 – 183121PROSITE-ProRule annotationAdd
BLAST
Calcium bindingi208 – 219122PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Transducer

Keywords - Biological processi

Lipid degradation, Lipid metabolism

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

ReactomeiREACT_323628. Synthesis of IP3 and IP4 in the cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3-A (EC:3.1.4.11)
Alternative name(s):
Phosphoinositide phospholipase C-delta-3-A
Phospholipase C-delta-3-A
Short name:
PLC-delta-3-A
Gene namesi
Name:plcd3a
ORF Names:zgc:158396
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Chromosome 3

Organism-specific databases

ZFINiZDB-GENE-070620-1. plcd3a.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7847841-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3-APRO_0000306823Add
BLAST

Keywords - PTMi

Phosphoprotein

Expressioni

Gene expression databases

BgeeiA5D6R3.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000093449.

Structurei

3D structure databases

ProteinModelPortaliA5D6R3.
SMRiA5D6R3. Positions 219-768.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini38 – 149112PHPROSITE-ProRule annotationAdd
BLAST
Domaini159 – 19436EF-hand 1PROSITE-ProRule annotationAdd
BLAST
Domaini195 – 23036EF-hand 2PROSITE-ProRule annotationAdd
BLAST
Domaini227 – 26236EF-hand 3PROSITE-ProRule annotationAdd
BLAST
Domaini313 – 458146PI-PLC X-boxPROSITE-ProRule annotationAdd
BLAST
Domaini506 – 621116PI-PLC Y-boxPROSITE-ProRule annotationAdd
BLAST
Domaini628 – 733106C2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni48 – 7831Substrate bindingBy similarityAdd
BLAST

Domaini

The C2 domain is a Ca2+-dependent membrane-targeting module.By similarity
The PH domain mediates interaction with the surface membrane by binding to PIP2.By similarity

Sequence similaritiesi

Contains 1 C2 domain.PROSITE-ProRule annotation
Contains 3 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

eggNOGiNOG149692.
GeneTreeiENSGT00760000118936.
HOGENOMiHOG000006871.
InParanoidiA5D6R3.
KOiK05857.
OMAiDARECSE.
OrthoDBiEOG7V49XT.
PhylomeDBiA5D6R3.
TreeFamiTF313216.

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-like_dom.
IPR001849. PH_domain.
IPR001192. PI-PLC_fam.
IPR028406. PLC-delta3.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
IPR015359. PLipase_C_EF-hand-like.
IPR000909. PLipase_C_PInositol-sp_X_dom.
IPR001711. PLipase_C_Pinositol-sp_Y.
[Graphical view]
PANTHERiPTHR10336. PTHR10336. 1 hit.
PTHR10336:SF33. PTHR10336:SF33. 1 hit.
PfamiPF00168. C2. 1 hit.
PF09279. EF-hand_like. 1 hit.
PF00169. PH. 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]
SUPFAMiSSF49562. SSF49562. 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.

A5D6R3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLGRKKNPET VQTESKSVES KTHDPLRRLG VLDDEDVLLM LQGSKMMKVR
60 70 80 90 100
SQRWRKDRRL KLLEDCVTVW CESSKTSRKS NRQQTFSVTE VECVREGCQS
110 120 130 140 150
ECLRRMTDLV PEKNCFTVVF RGGRKSLDLC CHTQEEAERW VRGIRTLKDR
160 170 180 190 200
VSNMSQKEKL DHWIRGYLRR ADQNQDGKMS YDEVKHLLQL INIDLNEQYA
210 220 230 240 250
RTLFKKCDRS CDGRLDHVEI EEFCREMMRR PELDAVFRHY SGNGCVLTTL
260 270 280 290 300
ELRDFLGDQG EDASLVHAKS LIQTFELNDW AQKNLFMTQN GFTMYMLSKE
310 320 330 340 350
NDVFNPDHTH VYQDMSKPLA HYYISSSHNT YLTKDQVTSA SSTEPYIRAL
360 370 380 390 400
NQGCRCVELD CWDGDKGEPI IYHGHTLTSK VLFKEVIETI AQYAFKASPY
410 420 430 440 450
PLILSLENHC SVEQQAIMAQ QLQSILGKKL LAKPLSDLPL KQLPSPEELK
460 470 480 490 500
GRILLKGKKL NGLLGKTESW TSFTNSSDEE SVAGGNKKES KKDLARSAST
510 520 530 540 550
KLSPELSDLV VYCQSVPFSG FETANQRPPS VITSFSENEA LKLIKDSGKL
560 570 580 590 600
FVRNNSRQLS RIYPSAQRLQ SSNFDPQDMW NAGCQMVALN FQTPGEQMDL
610 620 630 640 650
NQGRFLPNGR CGYVLKPEFL CDPKSDFDPE NTGGGPGHIP TQLTIRVISA
660 670 680 690 700
QQLPKINTDK PNSIVDPQVW VEIHGVSIDK ARAKTQRIDN NGFNPRWDCT
710 720 730 740 750
VSFQLQLPEL ALVRFMVEDH DHKSKNDFIG QFTLPFTSLR TGYRHVHLLK
760 770 780
ADGSTLSPAT LFIHVKVVRR GVHIKTVSER IGKA
Length:784
Mass (Da):89,381
Last modified:June 12, 2007 - v1
Checksum:i4078823F379343C6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC139849 mRNA. Translation: AAI39850.1.
RefSeqiNP_001092893.1. NM_001099423.1.
UniGeneiDr.50929.

Genome annotation databases

EnsembliENSDART00000102674; ENSDARP00000093449; ENSDARG00000052957.
GeneIDi569040.
KEGGidre:569040.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC139849 mRNA. Translation: AAI39850.1.
RefSeqiNP_001092893.1. NM_001099423.1.
UniGeneiDr.50929.

3D structure databases

ProteinModelPortaliA5D6R3.
SMRiA5D6R3. Positions 219-768.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000093449.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000102674; ENSDARP00000093449; ENSDARG00000052957.
GeneIDi569040.
KEGGidre:569040.

Organism-specific databases

CTDi569040.
ZFINiZDB-GENE-070620-1. plcd3a.

Phylogenomic databases

eggNOGiNOG149692.
GeneTreeiENSGT00760000118936.
HOGENOMiHOG000006871.
InParanoidiA5D6R3.
KOiK05857.
OMAiDARECSE.
OrthoDBiEOG7V49XT.
PhylomeDBiA5D6R3.
TreeFamiTF313216.

Enzyme and pathway databases

ReactomeiREACT_323628. Synthesis of IP3 and IP4 in the cytosol.

Miscellaneous databases

NextBioi20889471.
PROiA5D6R3.

Gene expression databases

BgeeiA5D6R3.

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-like_dom.
IPR001849. PH_domain.
IPR001192. PI-PLC_fam.
IPR028406. PLC-delta3.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
IPR015359. PLipase_C_EF-hand-like.
IPR000909. PLipase_C_PInositol-sp_X_dom.
IPR001711. PLipase_C_Pinositol-sp_Y.
[Graphical view]
PANTHERiPTHR10336. PTHR10336. 1 hit.
PTHR10336:SF33. PTHR10336:SF33. 1 hit.
PfamiPF00168. C2. 1 hit.
PF09279. EF-hand_like. 1 hit.
PF00169. PH. 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]
SUPFAMiSSF49562. SSF49562. 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...

Publicationsi

« Hide 'large scale' publications
  1. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Kidney.
  2. "Duplication of phospholipase C-delta gene family in fish genomes."
    Kim M.S., Seo J.S., Ahn S.J., Kim N.Y., Je J.E., Sung J.H., Lee H.H., Chung J.K.
    Genomics 92:366-371(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE DUPLICATION.

Entry informationi

Entry nameiPLD3A_DANRE
AccessioniPrimary (citable) accession number: A5D6R3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 2, 2007
Last sequence update: June 12, 2007
Last modified: July 22, 2015
This is version 75 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.