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Protein

DNA polymerase/3'-5' exonuclease PolX

Gene

polX

Organism
Bacillus subtilis (strain 168)
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

Strictly DNA-template-directed DNA polymerase, preferentially acting on DNA structures containing gaps from one to a few nucleotides and bearing a phosphate group at the 5' end of the downstream DNA. The fact that PolX is able to conduct filling of a single-nucleotide gap, allowing further sealing of the resulting nick by a DNA ligase, points to a putative role in base excision repair (BER) during the B.subtilis life cycle. Moreover, also possesses a 3'-5' exonuclease activity able to edit unpaired 3'-termini in a gapped DNA substrate and likely involved in resecting unannealed 3'-termini during DNA repair. The same PolX molecule could perform the subsequent gap-filling step. Does not display 5'-deoxyribose 5'-phosphate (dRP) lyase activity, as predicted by the lack of the lysine and tyrosine residues responsible for the dRP lyase activity in some other PolX members.2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 3'- to 5'-direction to yield nucleoside 5'-phosphates. EC:3.1.11.1

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:
  • Mn2+Curated, Mg2+CuratedNote: Probably binds 2 divalent metal cations per N-terminal polymerase domain. Mn2+ is more effective than Mg2+ for DNA polymerase activity.Curated
  • Mn2+CuratedNote: Probably binds 3 Mn2+ ions per C-terminal exonuclease domain. Mg2+ cannot replace Mn2+ for 3'-5' exonuclease activity.Curated

<p>This subsection of the ‘Function’ section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

The polymerization activity is inhibited in the presence of 2'-3'-dideoxynucleoside 5'-triphosphate (ddNTP).1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi193Divalent metal cation 1Curated1
Metal bindingi193Divalent metal cation 2Curated1
Metal bindingi195Divalent metal cation 1Curated1
Metal bindingi195Divalent metal cation 2Curated1
Metal bindingi240Divalent metal cation 2By similarity1
Metal bindingi339Manganese 1Curated1
Metal bindingi341Manganese 1Curated1
Metal bindingi371Manganese 2By similarity1
Metal bindingi410Manganese 1By similarity1
Metal bindingi410Manganese 3By similarity1
Metal bindingi437Manganese 3By similarity1
Metal bindingi465Manganese 3By similarity1
Metal bindingi526Manganese 1By similarity1
Metal bindingi528Manganese 2By similarity1

<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

GO - Biological processi

<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 functionDNA-binding, DNA-directed DNA polymerase, Hydrolase, Multifunctional enzyme, Nucleotidyltransferase, Transferase
Biological processDNA damage, DNA repair, DNA replication, DNA synthesis
LigandMagnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU28590-MONOMER

<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_and_taxonomy_section">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:
DNA polymerase/3'-5' exonuclease PolX
Including the following 2 domains:
DNA polymerase type-X (EC:2.7.7.7)
3'-5' exodeoxyribonuclease (EC:3.1.11.1)
Short name:
3'-5' exonuclease
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:polX
Synonyms:yshC
Ordered Locus Names:BSU28590
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi193 – 195DLD → ALA: Abolishes DNA polymerase activity. 1 Publication3
Mutagenesisi339 – 341HMH → AMA: Abolishes 3'-5' exonuclease activity. Still possesses DNA polymerase activity. 1 Publication3

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003607711 – 570DNA polymerase/3'-5' exonuclease PolXAdd BLAST570

Proteomic databases

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

More...
PaxDbi
P94544

PRoteomics IDEntifications database

More...
PRIDEi
P94544

<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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.Bsubs1_010100015606

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P94544

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P94544

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 315DNA polymerase type-XAdd BLAST315
Regioni333 – 5703'-5' exonucleaseAdd BLAST238

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi33 – 36Poly-Ala4

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The 3'-5' exonuclease activity resides in the C-terminal PHP domain.1 Publication

<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

In the N-terminal section; belongs to the DNA polymerase type-X family.Curated
In the C-terminal section; belongs to the PHP family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105DCG Bacteria
COG1387 LUCA
COG1796 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000292866

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P94544

KEGG Orthology (KO)

More...
KOi
K02347

Identification of Orthologs from Complete Genome Data

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OMAi
IIAHPTG

Database for complete collections of gene phylogenies

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PhylomeDBi
P94544

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00141 NT_POLXc, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
1.10.150.110, 1 hit
3.30.210.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002054 DNA-dir_DNA_pol_X
IPR010996 DNA_pol_b-like_N
IPR027421 DNA_pol_lamdba_lyase_dom_sf
IPR037160 DNA_Pol_thumb_sf
IPR003583 Hlx-hairpin-Hlx_DNA-bd_motif
IPR004013 PHP_dom
IPR003141 Pol/His_phosphatase_N
IPR016195 Pol/histidinol_Pase-like
IPR029398 PolB_thumb
IPR022311 UCP005047_YshC

Pfam protein domain database

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Pfami
View protein in Pfam
PF14791 DNA_pol_B_thumb, 1 hit
PF14716 HHH_8, 1 hit
PF02811 PHP, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF005047 UCP005047_YshC, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

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SMARTi
View protein in SMART
SM00278 HhH1, 3 hits
SM00481 POLIIIAc, 1 hit
SM00483 POLXc, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47802 SSF47802, 1 hit
SSF89550 SSF89550, 1 hit

<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_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

P94544-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MHKKDIIRLL ETIAVYMELK GDNPFKVSAF RKAAAALEQD DRSLSEMDDM
60 70 80 90 100
MSLSGIGKGT YSVIKEYIDE GKSSTLESLQ KEVPEGLVPL LKLPGLGGKK
110 120 130 140 150
IAKLYKELGV HDAESLKEAC EQQKVQGLAG FGKKSEEKIL QALGEAGKQP
160 170 180 190 200
ERFPIGYALR IAREIEEHLS QFTHIIKFSR AGSLRRARET VKDLDYIIAT
210 220 230 240 250
DHPAEVREQL LELPNIKSVI ASGDTKVSVI LSFEYETSVD FRLVTEEQFP
260 270 280 290 300
TTLHHFTGSK DHNIKMRQIA KERGERISEY GVETVETGEI KTFPSEREFY
310 320 330 340 350
AHFGLPLIPP EIRESGQEVE TYSDSIELIE LGQIKGDLHM HSTWSDGAFS
360 370 380 390 400
IREMAEACIK KGYQYMAITD HSQYLKVANG LTAERLKQQA KEIDALNAEF
410 420 430 440 450
ENFRILKGVE MDILPDGTLD YDDDVLAEMD IVIASIHSSF NQPEHVIMKR
460 470 480 490 500
LETALTNKHV DIIAHPTGRL IGRRAGYEID IDQLIELARK TNTALELNAN
510 520 530 540 550
PARLDLRTEH LMKANEQGVT LVINTDAHNI EMLDDMKTGV TAARKGWTET
560 570
KNVLNARSLK DVEAFLKRND
Length:570
Mass (Da):64,120
Last modified:May 1, 1997 - 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:i06AEA028BFA3D3F5
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
Z75208 Genomic DNA Translation: CAA99568.1
AL009126 Genomic DNA Translation: CAB14819.1

Protein sequence database of the Protein Information Resource

More...
PIRi
C69985

NCBI Reference Sequences

More...
RefSeqi
NP_390737.1, NC_000964.3
WP_003229538.1, NZ_JNCM01000036.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB14819; CAB14819; BSU28590

Database of genes from NCBI RefSeq genomes

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GeneIDi
937426

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU28590

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.3106

<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
Z75208 Genomic DNA Translation: CAA99568.1
AL009126 Genomic DNA Translation: CAB14819.1
PIRiC69985
RefSeqiNP_390737.1, NC_000964.3
WP_003229538.1, NZ_JNCM01000036.1

3D structure databases

ProteinModelPortaliP94544
SMRiP94544
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100015606

Proteomic databases

PaxDbiP94544
PRIDEiP94544

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
937426
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14819; CAB14819; BSU28590
GeneIDi937426
KEGGibsu:BSU28590
PATRICifig|224308.179.peg.3106

Phylogenomic databases

eggNOGiENOG4105DCG Bacteria
COG1387 LUCA
COG1796 LUCA
HOGENOMiHOG000292866
InParanoidiP94544
KOiK02347
OMAiIIAHPTG
PhylomeDBiP94544

Enzyme and pathway databases

BioCyciBSUB:BSU28590-MONOMER

Family and domain databases

CDDicd00141 NT_POLXc, 1 hit
Gene3Di1.10.150.110, 1 hit
3.30.210.10, 1 hit
InterProiView protein in InterPro
IPR002054 DNA-dir_DNA_pol_X
IPR010996 DNA_pol_b-like_N
IPR027421 DNA_pol_lamdba_lyase_dom_sf
IPR037160 DNA_Pol_thumb_sf
IPR003583 Hlx-hairpin-Hlx_DNA-bd_motif
IPR004013 PHP_dom
IPR003141 Pol/His_phosphatase_N
IPR016195 Pol/histidinol_Pase-like
IPR029398 PolB_thumb
IPR022311 UCP005047_YshC
PfamiView protein in Pfam
PF14791 DNA_pol_B_thumb, 1 hit
PF14716 HHH_8, 1 hit
PF02811 PHP, 1 hit
PIRSFiPIRSF005047 UCP005047_YshC, 1 hit
SMARTiView protein in SMART
SM00278 HhH1, 3 hits
SM00481 POLIIIAc, 1 hit
SM00483 POLXc, 1 hit
SUPFAMiSSF47802 SSF47802, 1 hit
SSF89550 SSF89550, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
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 nameiPOLX_BACSU
<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: P94544
Secondary accession number(s): Q795X4
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: May 1, 1997
Last modified: December 5, 2018
This is version 115 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 programProkaryotic 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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