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UniProtKB - Q5FVH2 (PLD3_RAT)

Entry version 116 (07 Apr 2021)
Sequence version 1 (01 Mar 2005)
Previous versions | rss
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Protein

5'-3' exonuclease PLD3

Gene

Pld3

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

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

  • Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.By similarity EC:3.1.16.1

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei199PROSITE-ProRule annotation1
Active sitei201PROSITE-ProRule annotation1
Active sitei206PROSITE-ProRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease
Biological processImmunity, Inflammatory response

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-RNO-2029485, Role of phospholipids in phagocytosis

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Pld3
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiRattus norvegicus (Rat)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10116 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002494 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 1

Organism-specific databases

Rat genome database

More...RGDi		1308248, Pld3

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini1 – 38CytoplasmicBy similarityAdd BLAST38
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei39 – 59Helical; Signal-anchor for type II membrane proteinBy similarityAdd BLAST21
Topological domaini60 – 488LumenalBy similarityAdd BLAST429

Keywords - Cellular componenti

Endoplasmic reticulum, Endosome, Golgi apparatus, Lysosome, Membrane

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002803301 – 4885'-3' exonuclease PLD3Add BLAST488

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section specifies the position and type of each covalently attached glycan group (mono-, di-, or polysaccharide).<p><a href='/help/carbohyd' target='_top'>More...</a></p>Glycosylationi132N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi385N-linked (GlcNAc...) asparagineCombined sources1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>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 conjugation

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		Q5FVH2

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		Q5FVH2

PRoteomics IDEntifications database

More...PRIDEi		Q5FVH2

PTM databases

GlyGen: Computational and Informatics Resources for Glycoscience

More...GlyGeni		Q5FVH2, 2 sites, 2 N-linked glycans (1 site)

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		Q5FVH2

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...PhosphoSitePlusi		Q5FVH2

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSRNOG00000018390, Expressed in frontal cortex and 20 other tissues

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		Q5FVH2, RN

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts with APP.

By similarity

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		262748, 1 interactor

Protein interaction database and analysis system

More...IntActi		Q5FVH2, 2 interactors

STRING: functional protein association networks

More...STRINGi		10116.ENSRNOP00000054004

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini194 – 221PLD phosphodiesterase 1PROSITE-ProRule annotationAdd BLAST28
Domaini409 – 435PLD phosphodiesterase 2PROSITE-ProRule annotationAdd BLAST27

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the phospholipase D family.Curated

Keywords - Domaini

Repeat, Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG3603, Eukaryota

Ensembl GeneTree

More...GeneTreei		ENSGT00950000183059

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_027021_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q5FVH2

Identification of Orthologs from Complete Genome Data

More...OMAi		QTHFYIG

Database of Orthologous Groups

More...OrthoDBi		1057467at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q5FVH2

TreeFam database of animal gene trees

More...TreeFami		TF313378

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR032803, PLDc_3
IPR001736, PLipase_D/transphosphatidylase

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00614, PLDc, 1 hit
PF13918, PLDc_3, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00155, PLDc, 2 hits

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50035, PLD, 2 hits

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q5FVH2-1 [UniParc]FASTAAdd to basket
« Hide
        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
Length:488
Mass (Da):54,399
Last modified:March 1, 2005 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i081AA487F575747A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
BC089987 mRNA Translation: AAH89987.1

NCBI Reference Sequences

More...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

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSRNOT00000057177; ENSRNOP00000054004; ENSRNOG00000018390

Database of genes from NCBI RefSeq genomes

More...GeneIDi		361527

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		rno:361527

UCSC genome browser

More...UCSCi		RGD:1308248, rat

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC089987 mRNA Translation: AAH89987.1
RefSeqiNP_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

Database of comparative protein structure models

More...ModBasei		Search...

SWISS-MODEL Interactive Workspace

More...SWISS-MODEL-Workspacei		Submit a new modelling project...

Protein-protein interaction databases

BioGRIDi262748, 1 interactor
IntActiQ5FVH2, 2 interactors
STRINGi10116.ENSRNOP00000054004

PTM databases

GlyGeniQ5FVH2, 2 sites, 2 N-linked glycans (1 site)
iPTMnetiQ5FVH2
PhosphoSitePlusiQ5FVH2

Proteomic databases

jPOSTiQ5FVH2
PaxDbiQ5FVH2
PRIDEiQ5FVH2

Genome annotation databases

EnsembliENSRNOT00000057177; ENSRNOP00000054004; ENSRNOG00000018390
GeneIDi361527
KEGGirno:361527
UCSCiRGD:1308248, rat

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		23646
RGDi1308248, Pld3

Phylogenomic databases

eggNOGiKOG3603, Eukaryota
GeneTreeiENSGT00950000183059
HOGENOMiCLU_027021_0_0_1
InParanoidiQ5FVH2
OMAiQTHFYIG
OrthoDBi1057467at2759
PhylomeDBiQ5FVH2
TreeFamiTF313378

Enzyme and pathway databases

ReactomeiR-RNO-2029485, Role of phospholipids in phagocytosis

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q5FVH2

Gene expression databases

BgeeiENSRNOG00000018390, Expressed in frontal cortex and 20 other tissues
GenevisibleiQ5FVH2, RN

Family and domain databases

InterProiView protein in InterPro
IPR032803, PLDc_3
IPR001736, PLipase_D/transphosphatidylase
PfamiView protein in Pfam
PF00614, PLDc, 1 hit
PF13918, PLDc_3, 1 hit
SMARTiView protein in SMART
SM00155, PLDc, 2 hits
PROSITEiView protein in PROSITE
PS50035, PLD, 2 hits

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPLD3_RAT
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q5FVH2
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated 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.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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