UniProtKB - Q5FVH2 (PLD3_RAT)
Protein
5'-3' exonuclease PLD3
Gene
Pld3
Organism
Rattus norvegicus (Rat)
Status
Functioni
5'->3' DNA exonuclease which digests single-stranded DNA (ssDNA) (By similarity). Regulates inflammatory cytokine responses via the degradation of nucleic acids, by reducing the concentration of ssDNA able to stimulate TLR9, a nucleotide-sensing receptor in collaboration with PLD4 (By similarity). May be important in myotube formation. Plays a role in lysosomal homeostasis. Involved in the regulation of endosomal protein sorting (By similarity).By similarity
Caution
It was initially thought that PDL3 has phospholipase D activity due to its HKD motifs. The second HKD motif contains Glu instead of the canonical Asp. Its enzyme activity is therefore unsure. Catalytic phospholipase D activity is still controversial (By similarity). Its closest homolog PLD4, exhibits no phospholipase activity (By similarity).By similarity
Catalytic activityi
- Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.By similarity EC:3.1.16.1
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 199 | PROSITE-ProRule annotation | 1 | |
Active sitei | 201 | PROSITE-ProRule annotation | 1 | |
Active sitei | 206 | PROSITE-ProRule annotation | 1 |
GO - Molecular functioni
- single-stranded DNA 5'-3' exodeoxyribonuclease activity Source: UniProtKB
GO - Biological processi
- immune system process Source: UniProtKB-KW
- inflammatory response Source: UniProtKB-KW
- myotube differentiation Source: UniProtKB
- regulation of cytokine production involved in inflammatory response Source: UniProtKB
Keywordsi
Molecular function | Exonuclease, Hydrolase, Nuclease |
Biological process | Immunity, Inflammatory response |
Enzyme and pathway databases
Reactomei | R-RNO-2029485, Role of phospholipids in phagocytosis |
Names & Taxonomyi
Protein namesi | Recommended name: 5'-3' exonuclease PLD3 (EC:3.1.16.1By similarity)Alternative name(s): Choline phosphatase 3 Phosphatidylcholine-hydrolyzing phospholipase D3 Phospholipase D3 Short name: PLD 3 |
Gene namesi | Name:Pld3 |
Organismi | Rattus norvegicus (Rat) |
Taxonomic identifieri | 10116 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus |
Proteomesi |
|
Organism-specific databases
RGDi | 1308248, Pld3 |
Subcellular locationi
Golgi apparatus
- Golgi apparatus membrane By similarity; Single-pass type II membrane protein By similarity
Lysosome
- Lysosome lumen By similarity
Endosome
- Early endosome membrane By similarity; Single-pass type II membrane protein By similarity
- Late endosome membrane By similarity; Single-pass type II membrane protein By similarity
- Endosome membrane By similarity; Single-pass type II membrane protein By similarity
Endoplasmic reticulum
- Endoplasmic reticulum membrane By similarity; Single-pass type II membrane protein By similarity
Note: Localizes to ER-associated vesicles in differentiating myotubes. The soluble form in lysosome arises by proteolytic processing of the membrane-bound form.By similarity
Endoplasmic reticulum
- endoplasmic reticulum membrane Source: UniProtKB
Endosome
- early endosome membrane Source: UniProtKB
- late endosome membrane Source: UniProtKB
Golgi apparatus
- Golgi membrane Source: UniProtKB
Lysosome
- lysosomal lumen Source: UniProtKB
- lysosomal membrane Source: RGD
Other locations
- integral component of membrane Source: UniProtKB-KW
Topology
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Topological domaini | 1 – 38 | CytoplasmicBy similarityAdd BLAST | 38 | |
Transmembranei | 39 – 59 | Helical; Signal-anchor for type II membrane proteinBy similarityAdd BLAST | 21 | |
Topological domaini | 60 – 488 | LumenalBy similarityAdd BLAST | 429 |
Keywords - Cellular componenti
Endoplasmic reticulum, Endosome, Golgi apparatus, Lysosome, MembranePTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000280330 | 1 – 488 | 5'-3' exonuclease PLD3Add BLAST | 488 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Glycosylationi | 132 | N-linked (GlcNAc...) asparagineSequence analysis | 1 | |
Glycosylationi | 385 | N-linked (GlcNAc...) asparagineCombined sources | 1 |
Post-translational modificationi
N-glycosylated.By similarity
Proteolytically processed to a soluble form that is stable within endosomes and lysosomes. During transport through the secretory pathway becomes proteolysed by cysteine proteases, thereby releasing a stable soluble lysosomal lumenal polypeptide, whereas the transmembrane-bound fragment is rapidly degraded. Its transport route to lysosomes involves ubiquitination and the ESCRT complex.By similarity
Ubiquitinated. Ubiquitination mediates sorting into lysosomes.By similarity
Keywords - PTMi
Glycoprotein, Ubl conjugationProteomic databases
jPOSTi | Q5FVH2 |
PaxDbi | Q5FVH2 |
PRIDEi | Q5FVH2 |
PTM databases
GlyGeni | Q5FVH2, 2 sites, 2 N-linked glycans (1 site) |
iPTMneti | Q5FVH2 |
PhosphoSitePlusi | Q5FVH2 |
Expressioni
Gene expression databases
Bgeei | ENSRNOG00000018390, Expressed in frontal cortex and 20 other tissues |
Genevisiblei | Q5FVH2, RN |
Interactioni
Subunit structurei
Interacts with APP.
By similarityProtein-protein interaction databases
BioGRIDi | 262748, 1 interactor |
IntActi | Q5FVH2, 2 interactors |
STRINGi | 10116.ENSRNOP00000054004 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 194 – 221 | PLD phosphodiesterase 1PROSITE-ProRule annotationAdd BLAST | 28 | |
Domaini | 409 – 435 | PLD phosphodiesterase 2PROSITE-ProRule annotationAdd BLAST | 27 |
Sequence similaritiesi
Belongs to the phospholipase D family.Curated
Keywords - Domaini
Repeat, Signal-anchor, Transmembrane, Transmembrane helixPhylogenomic databases
eggNOGi | KOG3603, Eukaryota |
GeneTreei | ENSGT00950000183059 |
HOGENOMi | CLU_027021_0_0_1 |
InParanoidi | Q5FVH2 |
OMAi | QTHFYIG |
OrthoDBi | 1057467at2759 |
PhylomeDBi | Q5FVH2 |
TreeFami | TF313378 |
Family and domain databases
InterProi | View protein in InterPro IPR032803, PLDc_3 IPR001736, PLipase_D/transphosphatidylase |
Pfami | View protein in Pfam PF00614, PLDc, 1 hit PF13918, PLDc_3, 1 hit |
SMARTi | View protein in SMART SM00155, PLDc, 2 hits |
PROSITEi | View protein in PROSITE PS50035, PLD, 2 hits |
i Sequence
Sequence statusi: Complete.
Q5FVH2-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MKPKLMYQEL KVPVEEPAGE LPMNEIEAWK AAEKKARWVL LVLILAVVGF
60 70 80 90 100
GALMTQLFLW EYGDLHLFGP NQHPAPCYDP CEAVLVESIP EGLEFPNATT
110 120 130 140 150
SNPSTSQAWL GLLAGAHSSL DIASFYWTLT NNDTHTQEPS AQQGEEVLQQ
160 170 180 190 200
LQALAPRGVK VRIAVSKPNG PLADLQSLLQ SGAQVRMVDM QKLTHGVLHT
210 220 230 240 250
KFWVVDQTHF YLGSANMDWR SLTQVKELGV VMYNCSCLAR DLTKIFEAYW
260 270 280 290 300
FLGQAGSSIP STWPRPFDTR YNQETPMEIC LNGTPALAYL ASAPPPLCPG
310 320 330 340 350
GRTPDLKALL SVVDNARSFI YIAVMNYLPT MEFSHPRRFW PAIDDGLRRA
360 370 380 390 400
AYERGVKVRL LISCWGHSEP SMRSFLLSLA ALRDNHTHSD IQVKLFVVPA
410 420 430 440 450
DEAQARIPYA RVNHNKYMVT ERTTYIGTSN WSGSYFTETA GTSLLVTQNG
460 470 480
HGGLRSQLEA VFLRDWESPY SHNLDTSADS VGNACRLL
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | BC089987 mRNA Translation: AAH89987.1 |
RefSeqi | NP_001012167.1, NM_001012167.1 XP_006228640.1, XM_006228578.3 XP_006228641.1, XM_006228579.3 XP_006228642.1, XM_006228580.2 XP_006228643.1, XM_006228581.3 |
Genome annotation databases
Ensembli | ENSRNOT00000057177; ENSRNOP00000054004; ENSRNOG00000018390 |
GeneIDi | 361527 |
KEGGi | rno:361527 |
UCSCi | RGD:1308248, rat |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | BC089987 mRNA Translation: AAH89987.1 |
RefSeqi | NP_001012167.1, NM_001012167.1 XP_006228640.1, XM_006228578.3 XP_006228641.1, XM_006228579.3 XP_006228642.1, XM_006228580.2 XP_006228643.1, XM_006228581.3 |
3D structure databases
ModBasei | Search... |
SWISS-MODEL-Workspacei | Submit a new modelling project... |
Protein-protein interaction databases
BioGRIDi | 262748, 1 interactor |
IntActi | Q5FVH2, 2 interactors |
STRINGi | 10116.ENSRNOP00000054004 |
PTM databases
GlyGeni | Q5FVH2, 2 sites, 2 N-linked glycans (1 site) |
iPTMneti | Q5FVH2 |
PhosphoSitePlusi | Q5FVH2 |
Proteomic databases
jPOSTi | Q5FVH2 |
PaxDbi | Q5FVH2 |
PRIDEi | Q5FVH2 |
Genome annotation databases
Ensembli | ENSRNOT00000057177; ENSRNOP00000054004; ENSRNOG00000018390 |
GeneIDi | 361527 |
KEGGi | rno:361527 |
UCSCi | RGD:1308248, rat |
Organism-specific databases
CTDi | 23646 |
RGDi | 1308248, Pld3 |
Phylogenomic databases
eggNOGi | KOG3603, Eukaryota |
GeneTreei | ENSGT00950000183059 |
HOGENOMi | CLU_027021_0_0_1 |
InParanoidi | Q5FVH2 |
OMAi | QTHFYIG |
OrthoDBi | 1057467at2759 |
PhylomeDBi | Q5FVH2 |
TreeFami | TF313378 |
Enzyme and pathway databases
Reactomei | R-RNO-2029485, Role of phospholipids in phagocytosis |
Miscellaneous databases
PROi | PR:Q5FVH2 |
Gene expression databases
Bgeei | ENSRNOG00000018390, Expressed in frontal cortex and 20 other tissues |
Genevisiblei | Q5FVH2, RN |
Family and domain databases
InterProi | View protein in InterPro IPR032803, PLDc_3 IPR001736, PLipase_D/transphosphatidylase |
Pfami | View protein in Pfam PF00614, PLDc, 1 hit PF13918, PLDc_3, 1 hit |
SMARTi | View protein in SMART SM00155, PLDc, 2 hits |
PROSITEi | View protein in PROSITE PS50035, PLD, 2 hits |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | PLD3_RAT | |
Accessioni | Q5FVH2Primary (citable) accession number: Q5FVH2 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | March 20, 2007 |
Last sequence update: | March 1, 2005 | |
Last modified: | April 7, 2021 | |
This is version 116 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families