ID PLD3_XENTR Reviewed; 494 AA.
AC Q640B3;
DT 20-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2004, sequence version 1.
DT 27-MAR-2024, entry version 109.
DE RecName: Full=5'-3' exonuclease PLD3;
DE EC=3.1.16.1 {ECO:0000250|UniProtKB:Q8IV08};
DE AltName: Full=Choline phosphatase 3;
DE AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D3;
DE AltName: Full=Phospholipase D3;
DE Short=PLD 3;
GN Name=pld3;
OS Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX NCBI_TaxID=8364;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: 5'->3' DNA exonuclease which digests single-stranded DNA
CC (ssDNA) (By similarity). Regulates inflammatory cytokine responses via
CC the degradation of nucleic acids, by reducing the concentration of
CC ssDNA able to stimulate TLR9, a nucleotide-sensing receptor in
CC collaboration with PLD4 (By similarity). May be important in myotube
CC formation. Plays a role in lysosomal homeostasis. Involved in the
CC regulation of endosomal protein sorting (By similarity).
CC {ECO:0000250|UniProtKB:O35405, ECO:0000250|UniProtKB:Q8IV08}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 5'- to 3'-direction to yield
CC nucleoside 3'-phosphates.; EC=3.1.16.1;
CC Evidence={ECO:0000250|UniProtKB:Q8IV08};
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000250|UniProtKB:Q8IV08}; Single-pass type II membrane protein
CC {ECO:0000250|UniProtKB:Q8IV08}. Lysosome lumen
CC {ECO:0000250|UniProtKB:Q8IV08}. Early endosome membrane
CC {ECO:0000250|UniProtKB:Q8IV08}; Single-pass type II membrane protein
CC {ECO:0000250|UniProtKB:Q8IV08}. Late endosome membrane
CC {ECO:0000250|UniProtKB:Q8IV08}; Single-pass type II membrane protein
CC {ECO:0000250|UniProtKB:Q8IV08}. Golgi apparatus membrane
CC {ECO:0000250|UniProtKB:Q8IV08}; Single-pass type II membrane protein
CC {ECO:0000250|UniProtKB:Q8IV08}. Endosome membrane
CC {ECO:0000250|UniProtKB:Q8IV08}; Single-pass type II membrane protein
CC {ECO:0000250|UniProtKB:Q8IV08}. Note=Localizes to ER-associated
CC vesicles in differentiating myotubes. The soluble form in lysosome
CC arises by proteolytic processing of the membrane-bound form.
CC {ECO:0000250|UniProtKB:Q8IV08}.
CC -!- PTM: N-glycosylated. {ECO:0000250|UniProtKB:Q8IV08}.
CC -!- PTM: Proteolytically processed to a soluble form that is stable within
CC endosomes and lysosomes. During transport through the secretory pathway
CC becomes proteolysed by cysteine proteases, thereby releasing a stable
CC soluble lysosomal lumenal polypeptide, whereas the transmembrane-bound
CC fragment is rapidly degraded. Its transport route to lysosomes involves
CC ubiquitination and the ESCRT complex. {ECO:0000250|UniProtKB:Q8IV08}.
CC -!- PTM: Ubiquitinated. Ubiquitination mediates sorting into lysosomes.
CC {ECO:0000250|UniProtKB:Q8IV08}.
CC -!- SIMILARITY: Belongs to the phospholipase D family. {ECO:0000305}.
CC -!- CAUTION: It was initially thought that PDL3 has phospholipase D
CC activity due to its HKD motifs. The second HKD motif contains Glu
CC instead of the canonical Asp. Its enzyme activity is therefore unsure.
CC Catalytic phospholipase D activity is still controversial (By
CC similarity). Its closest homolog PLD4, exhibits no phospholipase
CC activity (By similarity). {ECO:0000250|UniProtKB:O35405,
CC ECO:0000250|UniProtKB:Q8BG07}.
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DR EMBL; BC082717; AAH82717.1; -; mRNA.
DR RefSeq; NP_001011023.1; NM_001011023.1.
DR AlphaFoldDB; Q640B3; -.
DR SMR; Q640B3; -.
DR STRING; 8364.ENSXETP00000009562; -.
DR GlyCosmos; Q640B3; 9 sites, No reported glycans.
DR PaxDb; 8364-ENSXETP00000036949; -.
DR DNASU; 496432; -.
DR GeneID; 496432; -.
DR KEGG; xtr:496432; -.
DR AGR; Xenbase:XB-GENE-1006824; -.
DR CTD; 23646; -.
DR Xenbase; XB-GENE-1006824; pld3.
DR eggNOG; KOG3603; Eukaryota.
DR HOGENOM; CLU_027021_0_0_1; -.
DR InParanoid; Q640B3; -.
DR OrthoDB; 1203524at2759; -.
DR TreeFam; TF313378; -.
DR Proteomes; UP000008143; Chromosome 8.
DR GO; GO:0031901; C:early endosome membrane; ISS:UniProtKB.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; ISS:UniProtKB.
DR GO; GO:0000139; C:Golgi membrane; ISS:UniProtKB.
DR GO; GO:0031902; C:late endosome membrane; ISS:UniProtKB.
DR GO; GO:0043202; C:lysosomal lumen; ISS:UniProtKB.
DR GO; GO:0045145; F:single-stranded DNA 5'-3' DNA exonuclease activity; ISS:UniProtKB.
DR GO; GO:0002376; P:immune system process; IEA:UniProtKB-KW.
DR GO; GO:0006954; P:inflammatory response; IEA:UniProtKB-KW.
DR GO; GO:0014902; P:myotube differentiation; ISS:UniProtKB.
DR GO; GO:1900015; P:regulation of cytokine production involved in inflammatory response; ISS:UniProtKB.
DR CDD; cd09144; PLDc_vPLD3_1; 1.
DR Gene3D; 3.30.870.10; Endonuclease Chain A; 2.
DR InterPro; IPR032803; PLDc_3.
DR InterPro; IPR001736; PLipase_D/transphosphatidylase.
DR PANTHER; PTHR10185:SF16; 5'-3' EXONUCLEASE PLD3; 1.
DR PANTHER; PTHR10185; PHOSPHOLIPASE D - RELATED; 1.
DR Pfam; PF13918; PLDc_3; 1.
DR SMART; SM00155; PLDc; 2.
DR SUPFAM; SSF56024; Phospholipase D/nuclease; 2.
DR PROSITE; PS50035; PLD; 2.
PE 2: Evidence at transcript level;
KW Endoplasmic reticulum; Endosome; Exonuclease; Glycoprotein;
KW Golgi apparatus; Hydrolase; Immunity; Inflammatory response; Lysosome;
KW Membrane; Nuclease; Reference proteome; Repeat; Signal-anchor;
KW Transmembrane; Transmembrane helix; Ubl conjugation.
FT CHAIN 1..494
FT /note="5'-3' exonuclease PLD3"
FT /id="PRO_0000280332"
FT TOPO_DOM 1..37
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 38..58
FT /note="Helical; Signal-anchor for type II membrane protein"
FT /evidence="ECO:0000255"
FT TOPO_DOM 59..494
FT /note="Lumenal"
FT /evidence="ECO:0000255"
FT DOMAIN 198..225
FT /note="PLD phosphodiesterase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT DOMAIN 413..439
FT /note="PLD phosphodiesterase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 203
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 205
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 210
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 418
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 420
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT ACT_SITE 425
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00153"
FT CARBOHYD 100
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 238
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 260
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 270
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 286
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 389
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 434
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 451
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 477
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
SQ SEQUENCE 494 AA; 56213 MW; EACEA360F7437F18 CRC64;
MNPKVEYKQI QSHDEAENQV LQHECHQAKA RKYYRCAVVI AIIITLLFCV LASQLLLFPL
FSITSQTTTE IVLNKDIQCD DQCRFVLVES IPEGLVYDAN ATINPSIFQS WLNILTSAKS
SVDIASFYWT LTNEDTQTQE PSAHQGELIL QELLNLKQRG VSVRVAVNPP DSPLRAKDIS
ALKDSGADVR VVDLPKLTDG VLHTKFWVVD SEHFYIGSAN MDWRSLTQVK ELGATIYNCS
CLAEDLKKIF EAYWILGLPN ATLPSPWPVN YSTPYNKDTP MQVMLNSTAS QVYISSSPPP
LSATGRTDDL QSIINIIDDA KKFVYISVMD YSPTEEFSHP RRYWPYIDNH LRKAVYERNV
NVRLLISCWQ NSRPSMFTFL RSLAALHSNK SHYNIEVKIF VVPATEVQKK IPYARVNHNK
YMVTDRVAYI GTSNWSGDYF IHTAGSALIV NQTQSVGTSD TIQMQLQAVF ERDWNSNYSR
TFNTLSSWKE KCIF
//
