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Protein

Histone-lysine N-methyltransferase SETMAR

Gene

SETMAR

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Protein derived from the fusion of a methylase with the transposase of an Hsmar1 transposon that plays a role in DNA double-strand break repair, stalled replication fork restart and DNA integration. DNA-binding protein, it is indirectly recruited to sites of DNA damage through protein-protein interactions. Has also kept a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity (PubMed:16332963, PubMed:16672366, PubMed:17877369, PubMed:17403897, PubMed:18263876, PubMed:22231448, PubMed:24573677, PubMed:20521842). In parallel, has a histone methyltransferase activity and methylates 'Lys-4' and 'Lys-36' of histone H3. Specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining (PubMed:16332963, PubMed:21187428, PubMed:22231448). Also regulates replication fork processing, promoting replication fork restart and regulating DNA decatenation through stimulation of the topoisomerase activity of TOP2A (PubMed:18790802, PubMed:20457750).1 Publication10 Publications

Miscellaneous

The mariner transposase region in only present in primates and appeared 40-58 million years ago, after the insertion of a transposon downstream of a preexisting SET gene, followed by the de novo exonization of previously non-coding sequence and the creation of a new intron.

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N6-methyl-L-lysine-[histone].1 Publication

Cofactori

Mg2+Note: Binds 1 Mg2+ ion per subunit.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi75Zinc 11
Metal bindingi75Zinc 21
Metal bindingi77Zinc 11
Metal bindingi82Zinc 11
Metal bindingi82Zinc 31
Metal bindingi87Zinc 11
Metal bindingi89Zinc 21
Metal bindingi118Zinc 21
Metal bindingi118Zinc 31
Metal bindingi122Zinc 21
Metal bindingi124Zinc 31
Metal bindingi128Zinc 31
Binding sitei192S-adenosyl-L-methionine1
Binding sitei220S-adenosyl-L-methioninePROSITE-ProRule annotation1
Metal bindingi226Zinc 41
Metal bindingi287Zinc 41
Metal bindingi289Zinc 41
Metal bindingi294Zinc 41
Metal bindingi496Magnesium1
Metal bindingi588Magnesium1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi364 – 395H-T-H motifBy similarityAdd BLAST32
DNA bindingi428 – 448H-T-H motifAdd BLAST21

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, DNA-binding, Endonuclease, Hydrolase, Methyltransferase, Multifunctional enzyme, Nuclease, Transferase
Biological processDNA damage, DNA repair
LigandMagnesium, Metal-binding, S-adenosyl-L-methionine, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase SETMARCurated
Alternative name(s):
SET domain and mariner transposase fusion proteinCurated
Short name:
Metnase1 Publication
Including the following 2 domains:
Histone-lysine N-methyltransferaseCurated (EC:2.1.1.431 Publication)
Transposon Hsmar1 transposase1 Publication (EC:3.1.-.-1 Publication)
Gene namesi
Name:SETMARImported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000170364.12
HGNCiHGNC:10762 SETMAR
MIMi609834 gene
neXtProtiNX_Q53H47

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi223N → S: Reduces activity in double-strand break repair. 1 Publication1
Mutagenesisi261D → S: Reduces activity in double-strand break repair. 1 Publication1
Mutagenesisi445R → A: Abolishes TIR-specific DNA-binding. 1 Publication1
Mutagenesisi473F → K: Abolishes homodimerization and DNA-binding and reduces cleavage of single-stranded DNA. 1 Publication1
Mutagenesisi496D → A: Abolishes DNA cleavage. 1 Publication1
Mutagenesisi503D → S: Reduces activity in double-strand break repair. 1 Publication1
Mutagenesisi508S → A: Prevents phosphorylation. Impairs recruitment to damaged DNA and double-strand break repair. Impairs interaction with histone H3 and its methylation. Allows replication fork restart. 1 Publication1
Mutagenesisi623N → D or E: Loss of function in DNA repair. Altered DNA-binding properties. 1 Publication1

Organism-specific databases

DisGeNETi6419
OpenTargetsiENSG00000170364
PharmGKBiPA35680

Chemistry databases

ChEMBLiCHEMBL2189111

Polymorphism and mutation databases

DMDMi74740552

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002595261 – 684Histone-lysine N-methyltransferase SETMARAdd BLAST684

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei498N6-methyllysine1 Publication1
Modified residuei508Phosphoserine; by CHEK1Combined sources1 Publication1

Post-translational modificationi

Methylated. Methylation regulates activity in DNA decatenation.1 Publication
Phosphorylated at Ser-508 by CHEK1 and dephosphorylated by protein phosphatase 2A/PP2A. Phosphorylation at Ser-508 is enhanced by DNA damage and promotes recruitment to damaged DNA. It stimulates DNA repair and impairs replication fork restart.1 Publication

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ53H47
MaxQBiQ53H47
PaxDbiQ53H47
PeptideAtlasiQ53H47
PRIDEiQ53H47
ProteomicsDBi62493
62494 [Q53H47-2]

PTM databases

iPTMnetiQ53H47
PhosphoSitePlusiQ53H47

Expressioni

Tissue specificityi

Widely expressed, with highest expression in placenta and ovary and lowest expression in skeletal muscle.1 Publication

Gene expression databases

BgeeiENSG00000170364 Expressed in 201 organ(s), highest expression level in body of uterus
CleanExiHS_SETMAR
ExpressionAtlasiQ53H47 baseline and differential
GenevisibleiQ53H47 HS

Organism-specific databases

HPAiHPA057999

Interactioni

Subunit structurei

Homodimer (PubMed:20521842). Interacts with PRPF19; required for SETMAR recruitment to damaged DNA sites (PubMed:18263876). Interacts with PCNA (PubMed:20457750). Interacts with TOP2A; stimulates TOP2A topoisomerase activity (PubMed:18790802, PubMed:20457750). May interact with RAD9A and/or RAD9B (PubMed:20457750).4 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi112317, 18 interactors
IntActiQ53H47, 3 interactors
MINTiQ53H47
STRINGi9606.ENSP00000373354

Chemistry databases

BindingDBiQ53H47

Structurei

Secondary structure

1684
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ53H47
SMRiQ53H47
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53H47

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini73 – 136Pre-SETPROSITE-ProRule annotationAdd BLAST64
Domaini139 – 263SETPROSITE-ProRule annotationAdd BLAST125
Domaini283 – 299Post-SETPROSITE-ProRule annotationAdd BLAST17

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 345Histone-lysine N-methyltransferaseAdd BLAST345
Regioni149 – 151S-adenosyl-L-methionine binding3
Regioni223 – 224S-adenosyl-L-methionine binding2
Regioni346 – 684Mariner transposase Hsmar1Add BLAST339

Domaini

The mariner transposase Hsmar1 region mediates DNA-binding. It has retained some of the nucleases activity but has lost its transposase activity because the active site contains an Asn in position 610 instead of an Asp residue.1 Publication
In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.

Sequence similaritiesi

In the N-terminal section; belongs to the class V-like SAM-binding methyltransferase superfamily.Curated
In the C-terminal section; belongs to the mariner transposase family.Curated

Phylogenomic databases

eggNOGiKOG1082 Eukaryota
COG2940 LUCA
GeneTreeiENSGT00440000033232
HOGENOMiHOG000154295
HOVERGENiHBG093941
InParanoidiQ53H47
KOiK11433
OMAiMHQKLQR
OrthoDBiEOG091G0Y4N
PhylomeDBiQ53H47
TreeFamiTF352220

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR003616 Post-SET_dom
IPR007728 Pre-SET_dom
IPR001214 SET_dom
IPR001888 Transposase_1
IPR036388 WH-like_DNA-bd_sf
PfamiView protein in Pfam
PF05033 Pre-SET, 1 hit
PF00856 SET, 1 hit
PF01359 Transposase_1, 1 hit
SMARTiView protein in SMART
SM00468 PreSET, 1 hit
SM00317 SET, 1 hit
PROSITEiView protein in PROSITE
PS50868 POST_SET, 1 hit
PS50867 PRE_SET, 1 hit
PS50280 SET, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q53H47-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MFAEAAKTTR PCGMAEFKEK PEAPTEQLDV ACGQENLPVG AWPPGAAPAP
60 70 80 90 100
FQYTPDHVVG PGADIDPTQI TFPGCICVKT PCLPGTCSCL RHGENYDDNS
110 120 130 140 150
CLRDIGSGGK YAEPVFECNV LCRCSDHCRN RVVQKGLQFH FQVFKTHKKG
160 170 180 190 200
WGLRTLEFIP KGRFVCEYAG EVLGFSEVQR RIHLQTKSDS NYIIAIREHV
210 220 230 240 250
YNGQVMETFV DPTYIGNIGR FLNHSCEPNL LMIPVRIDSM VPKLALFAAK
260 270 280 290 300
DIVPEEELSY DYSGRYLNLT VSEDKERLDH GKLRKPCYCG AKSCTAFLPF
310 320 330 340 350
DSSLYCPVEK SNISCGNEKE PSMCGSAPSV FPSCKRLTLE TMKMMLDKKQ
360 370 380 390 400
IRAIFLFEFK MGRKAAETTR NINNAFGPGT ANERTVQWWF KKFCKGDESL
410 420 430 440 450
EDEERSGRPS EVDNDQLRAI IEADPLTTTR EVAEELNVNH STVVRHLKQI
460 470 480 490 500
GKVKKLDKWV PHELTENQKN RRFEVSSSLI LRNHNEPFLD RIVTCDEKWI
510 520 530 540 550
LYDNRRRSAQ WLDQEEAPKH FPKPILHPKK VMVTIWWSAA GLIHYSFLNP
560 570 580 590 600
GETITSEKYA QEIDEMNQKL QRLQLALVNR KGPILLHDNA RPHVAQPTLQ
610 620 630 640 650
KLNELGYEVL PHPPYSPDLL PTNYHVFKHL NNFLQGKRFH NQQDAENAFQ
660 670 680
EFVESQSTDF YATGINQLIS RWQKCVDCNG SYFD
Length:684
Mass (Da):78,034
Last modified:April 16, 2014 - v2
Checksum:iBB9460455C0BDBFA
GO
Isoform 2 (identifier: Q53H47-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     341-365: TMKMMLDKKQIRAIFLFEFKMGRKA → VSLFSDKQLAPPYSGRQWLASFTSA
     366-684: Missing.

Note: No experimental confirmation available.
Show »
Length:365
Mass (Da):40,510
Checksum:iE1FFA86B6E63F8E4
GO
Isoform 3 (identifier: Q53H47-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     163-301: Missing.

Show »
Length:545
Mass (Da):62,124
Checksum:i8F570F8A67A495C7
GO

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8WEU1F8WEU1_HUMAN
Histone-lysine N-methyltransferase ...
SETMAR
171Annotation score:
B9ZVV8B9ZVV8_HUMAN
Histone-lysine N-methyltransferase ...
SETMAR
212Annotation score:
F8WB33F8WB33_HUMAN
Histone-lysine N-methyltransferase ...
SETMAR
67Annotation score:

Sequence cautioni

The sequence AAH11635 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAY29570 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAD96454 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti91R → H in BAG63636 (PubMed:14702039).Curated1
Sequence conflicti343K → E in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti439N → D in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti465T → S in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti484H → N in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti508S → P in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti514Q → R in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti525I → N in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti528P → Q in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti535I → V in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti562E → Q in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti567 – 568NQ → HR in AAC52010 (PubMed:9461395).Curated2
Sequence conflicti575L → P in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti620L → S in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti623N → D in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti626V → F in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti631N → D in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti656Q → R in AAC52010 (PubMed:9461395).Curated1
Sequence conflicti667Q → K in AAC52010 (PubMed:9461395).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_054089163 – 301Missing in isoform 3. CuratedAdd BLAST139
Alternative sequenceiVSP_021440341 – 365TMKMM…MGRKA → VSLFSDKQLAPPYSGRQWLA SFTSA in isoform 2. 2 PublicationsAdd BLAST25
Alternative sequenceiVSP_021441366 – 684Missing in isoform 2. 2 PublicationsAdd BLAST319

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK222734 mRNA Translation: BAD96454.1 Different initiation.
AK302296 mRNA Translation: BAG63636.1
AC023483 Genomic DNA No translation available.
AC034191 Genomic DNA No translation available.
BC011635 mRNA Translation: AAH11635.1 Different initiation.
AY952295 mRNA Translation: AAY29570.1 Different initiation.
DQ341316 Genomic DNA Translation: ABC72087.1
U52077 Genomic DNA Translation: AAC52010.1
CCDSiCCDS2563.2 [Q53H47-1]
CCDS58814.1 [Q53H47-3]
CCDS63528.1 [Q53H47-2]
RefSeqiNP_001230652.1, NM_001243723.1 [Q53H47-3]
NP_001263254.1, NM_001276325.1 [Q53H47-2]
NP_001307606.1, NM_001320677.1
NP_001307607.1, NM_001320678.1
NP_006506.3, NM_006515.3 [Q53H47-1]
UniGeneiHs.475300

Genome annotation databases

EnsembliENST00000358065; ENSP00000373354; ENSG00000170364 [Q53H47-1]
ENST00000425863; ENSP00000403145; ENSG00000170364 [Q53H47-3]
ENST00000430981; ENSP00000403000; ENSG00000170364 [Q53H47-2]
GeneIDi6419
KEGGihsa:6419
UCSCiuc003bpw.6 human [Q53H47-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Web resourcesi

Protein Spotlight

Taming genes - Issue 167 of February 2015

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK222734 mRNA Translation: BAD96454.1 Different initiation.
AK302296 mRNA Translation: BAG63636.1
AC023483 Genomic DNA No translation available.
AC034191 Genomic DNA No translation available.
BC011635 mRNA Translation: AAH11635.1 Different initiation.
AY952295 mRNA Translation: AAY29570.1 Different initiation.
DQ341316 Genomic DNA Translation: ABC72087.1
U52077 Genomic DNA Translation: AAC52010.1
CCDSiCCDS2563.2 [Q53H47-1]
CCDS58814.1 [Q53H47-3]
CCDS63528.1 [Q53H47-2]
RefSeqiNP_001230652.1, NM_001243723.1 [Q53H47-3]
NP_001263254.1, NM_001276325.1 [Q53H47-2]
NP_001307606.1, NM_001320677.1
NP_001307607.1, NM_001320678.1
NP_006506.3, NM_006515.3 [Q53H47-1]
UniGeneiHs.475300

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BO5X-ray1.59A15-303[»]
3F2KX-ray1.85A/B459-684[»]
3K9JX-ray1.90A/B446-684[»]
3K9KX-ray2.55A/B446-684[»]
ProteinModelPortaliQ53H47
SMRiQ53H47
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112317, 18 interactors
IntActiQ53H47, 3 interactors
MINTiQ53H47
STRINGi9606.ENSP00000373354

Chemistry databases

BindingDBiQ53H47
ChEMBLiCHEMBL2189111

PTM databases

iPTMnetiQ53H47
PhosphoSitePlusiQ53H47

Polymorphism and mutation databases

DMDMi74740552

Proteomic databases

EPDiQ53H47
MaxQBiQ53H47
PaxDbiQ53H47
PeptideAtlasiQ53H47
PRIDEiQ53H47
ProteomicsDBi62493
62494 [Q53H47-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000358065; ENSP00000373354; ENSG00000170364 [Q53H47-1]
ENST00000425863; ENSP00000403145; ENSG00000170364 [Q53H47-3]
ENST00000430981; ENSP00000403000; ENSG00000170364 [Q53H47-2]
GeneIDi6419
KEGGihsa:6419
UCSCiuc003bpw.6 human [Q53H47-1]

Organism-specific databases

CTDi6419
DisGeNETi6419
EuPathDBiHostDB:ENSG00000170364.12
GeneCardsiSETMAR
HGNCiHGNC:10762 SETMAR
HPAiHPA057999
MIMi609834 gene
neXtProtiNX_Q53H47
OpenTargetsiENSG00000170364
PharmGKBiPA35680
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1082 Eukaryota
COG2940 LUCA
GeneTreeiENSGT00440000033232
HOGENOMiHOG000154295
HOVERGENiHBG093941
InParanoidiQ53H47
KOiK11433
OMAiMHQKLQR
OrthoDBiEOG091G0Y4N
PhylomeDBiQ53H47
TreeFamiTF352220

Miscellaneous databases

EvolutionaryTraceiQ53H47
GeneWikiiSETMAR
GenomeRNAii6419
PROiPR:Q53H47
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000170364 Expressed in 201 organ(s), highest expression level in body of uterus
CleanExiHS_SETMAR
ExpressionAtlasiQ53H47 baseline and differential
GenevisibleiQ53H47 HS

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR003616 Post-SET_dom
IPR007728 Pre-SET_dom
IPR001214 SET_dom
IPR001888 Transposase_1
IPR036388 WH-like_DNA-bd_sf
PfamiView protein in Pfam
PF05033 Pre-SET, 1 hit
PF00856 SET, 1 hit
PF01359 Transposase_1, 1 hit
SMARTiView protein in SMART
SM00468 PreSET, 1 hit
SM00317 SET, 1 hit
PROSITEiView protein in PROSITE
PS50868 POST_SET, 1 hit
PS50867 PRE_SET, 1 hit
PS50280 SET, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSETMR_HUMAN
AccessioniPrimary (citable) accession number: Q53H47
Secondary accession number(s): B4DY74
, E7EN68, Q13579, Q1G668, Q96F41
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: April 16, 2014
Last modified: November 7, 2018
This is version 124 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
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