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Protein

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Gene

PLOD3

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

Functioni

Multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen (PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Plays a redundant role in catalyzing the formation of hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens (PubMed:9582318, PubMed:9724729, PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Plays a redundant role in catalyzing the transfer of galactose onto hydroxylysine groups, giving rise to galactosyl 5-hydroxylysine (PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Has an essential role by catalyzing the subsequent transfer of glucose moieties, giving rise to 1,2-glucosylgalactosyl-5-hydroxylysine residues (PubMed:10934207, PubMed:11896059, PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Catalyzes hydroxylation and glycosylation of Lys residues in the MBL1 collagen-like domain, giving rise to hydroxylysine and 1,2-glucosylgalactosyl-5-hydroxylysine residues (PubMed:25419660). Essential for normal biosynthesis and secretion of type IV collagens (PubMed:18834968) (Probable). Essential for normal formation of basement membranes (By similarity).By similarityCurated10 Publications

Catalytic activityi

L-lysine-[procollagen] + 2-oxoglutarate + O2 = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO2.8 Publications
UDP-alpha-D-galactose + [procollagen]-(2S,5R)-5-hydroxy-L-lysine = UDP + [procollagen]-(2S,5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysine.4 Publications
UDP-alpha-D-glucose + [procollagen]-(2S,5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysine = UDP + [procollagen]-(2S,5R)-5-O-(alpha-D-glucosyl-(1->2)-beta-D-galactosyl)-5-hydroxy-L-lysine.7 Publications

Cofactori

Protein has several cofactor binding sites:

Activity regulationi

Lysyl hydroxylase activity is strongly inhibited by imidazole.1 Publication

Kineticsi

  1. KM=35 µM for UDP-galactose1 Publication
  2. KM=17 µM for UDP-glucose1 Publication
  3. KM=100 µM for 2-oxoglutarate2 Publications
  4. KM=300 µM for ascorbate1 Publication
  5. KM=350 µM for ascorbate1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi112ManganeseCombined sources1 Publication1
    Metal bindingi115ManganeseCombined sources1 Publication1
    Metal bindingi253ManganeseCombined sources1 Publication1
    Binding sitei5992-oxoglutarateCombined sources1 Publication1
    Binding sitei6562-oxoglutarateCombined sources1 Publication1
    Metal bindingi667IronPROSITE-ProRule annotationCombined sources1 Publication1
    Metal bindingi669IronPROSITE-ProRule annotationCombined sources1 Publication1
    Binding sitei6762-oxoglutarateCombined sources1 Publication1
    Metal bindingi719IronPROSITE-ProRule annotationCombined sources1 Publication1
    Binding sitei7292-oxoglutarateCombined sources1 Publication1

    GO - Molecular functioni

    • iron ion binding Source: InterPro
    • L-ascorbic acid binding Source: UniProtKB-KW
    • procollagen galactosyltransferase activity Source: UniProtKB
    • procollagen glucosyltransferase activity Source: UniProtKB
    • procollagen-lysine 5-dioxygenase activity Source: CAFA

    GO - Biological processi

    Keywordsi

    Molecular functionDioxygenase, Glycosyltransferase, Multifunctional enzyme, Oxidoreductase, Transferase
    LigandIron, Manganese, Metal-binding, Vitamin C

    Enzyme and pathway databases

    BRENDAi1.14.11.4 2681
    2.4.1.50 2681
    2.4.1.66 2681
    ReactomeiR-HSA-1650814 Collagen biosynthesis and modifying enzymes

    Protein family/group databases

    MoonDBiO60568 Curated
    MoonProtiO60568

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
    Including the following 2 domains:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (EC:1.14.11.46 Publications)
    Alternative name(s):
    Lysyl hydroxylase 32 Publications
    Short name:
    LH31 Publication
    Procollagen glycosyltransferase (EC:2.4.1.504 Publications, EC:2.4.1.667 Publications)
    Alternative name(s):
    Galactosylhydroxylysine-glucosyltransferase
    Procollagen galactosyltransferase
    Procollagen glucosyltransferase
    Gene namesi
    Name:PLOD3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 7

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000106397.11
    HGNCiHGNC:9083 PLOD3
    MIMi603066 gene
    neXtProtiNX_O60568

    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

    Endoplasmic reticulum, Membrane, Secreted

    Pathology & Biotechi

    Involvement in diseasei

    Lysyl hydroxylase 3 deficiency (LH3 deficiency)2 Publications
    The disease is caused by mutations affecting the gene represented in this entry.
    Disease descriptionConnective tissue disorder. The syndrome is characterized by congenital malformations severely affecting many tissues and organs and revealing features of several collagen disorders, most of them involving COL2A1 (type II collagen). The findings suggest that the failure of lysyl hydroxylation and hydroxylysyl carbohydrate addition, which affects many collagens, is the molecular basis of this syndrome.
    See also OMIM:612394
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_054913223N → S in LH3 deficiency; generates a new glycosylation site; decreases protein stability; strongly decreases lysyl hydroxylase activity and nearly abolishes glycosyltransferase activity. 2 PublicationsCorresponds to variant dbSNP:rs121434414EnsemblClinVar.1

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi75W → A: Decreased lysyl hydroxylase activity and loss of glycosyltransferase activity. 1 Publication1
    Mutagenesisi114Y → A: Decreased lysyl hydroxylase and glycosyltransferase activity. 1 Publication1
    Mutagenesisi144C → I: Strongly reduced glucosyltransferase activity. Strongly reduced galactosyltransferase activity. 2 Publications1
    Mutagenesisi187 – 191DDDDD → ADAAA: Loss of glucosyltransferase activity. Loss of galactosyltransferase activity. 3 Publications5
    Mutagenesisi187 – 189DDD → ADA: Nearly abolishes glucosyltransferase activity. Nearly abolishes galactosyltransferase activity. 2 Publications3
    Mutagenesisi208L → I: Reduced glucosyltransferase activity. 1 Publication1
    Mutagenesisi669D → A: Strongly decreased lysyl hydroxylase activity. No effect on glycosyltransferase activity. 2 Publications1
    Mutagenesisi672T → N: Loss of dimerization. Loss of lysyl hydroxylase activity and decreased glycosyltransferase activity. 1 Publication1
    Mutagenesisi714R → N: Loss of dimerization. Loss of lysyl hydroxylase activity and no effect on glycosyltransferase activity. 1 Publication1
    Mutagenesisi715L → D: No effect on dimerization, lysyl hydroxylase and glycosyltransferase activity. 1 Publication1
    Mutagenesisi715L → R: Loss of lysyl hydroxylase activity and decreased glycosyltransferase activity. 1 Publication1

    Keywords - Diseasei

    Disease mutation

    Organism-specific databases

    DisGeNETi8985
    MalaCardsiPLOD3
    MIMi612394 phenotype
    OpenTargetsiENSG00000106397
    Orphaneti300284 Connective tissue disorder due to lysyl hydroxylase-3 deficiency
    PharmGKBiPA33413

    Chemistry databases

    DrugBankiDB00139 Succinic acid
    DB00126 Vitamin C

    Polymorphism and mutation databases

    BioMutaiPLOD3

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 24Sequence analysisAdd BLAST24
    ChainiPRO_000002468625 – 738Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3Add BLAST714

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Glycosylationi63N-linked (GlcNAc...) asparagineCombined sources1 Publication1
    Disulfide bondi279 ↔ 282Combined sources1 Publication
    Disulfide bondi379 ↔ 385Combined sources1 Publication
    Glycosylationi548N-linked (GlcNAc...) asparagineCombined sources1 Publication1
    Disulfide bondi563 ↔ 698Combined sources1 Publication

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    EPDiO60568
    MaxQBiO60568
    PaxDbiO60568
    PeptideAtlasiO60568
    PRIDEiO60568
    ProteomicsDBi49474

    PTM databases

    GlyConnecti1635
    iPTMnetiO60568
    PhosphoSitePlusiO60568

    Expressioni

    Tissue specificityi

    Ubiquitous (PubMed:9724729). Detected in heart, placenta and pancreas, and at lower levels in lung, liver and skeletal muscle (PubMed:9582318, PubMed:9724729).2 Publications

    Gene expression databases

    BgeeiENSG00000106397 Expressed in 220 organ(s), highest expression level in placenta
    CleanExiHS_PLOD3
    ExpressionAtlasiO60568 baseline and differential
    GenevisibleiO60568 HS

    Organism-specific databases

    HPAiHPA001236

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Binary interactionsi

    Protein-protein interaction databases

    BioGridi114467, 58 interactors
    IntActiO60568, 34 interactors
    MINTiO60568
    STRINGi9606.ENSP00000223127

    Structurei

    Secondary structure

    1738
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliO60568
    SMRiO60568
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini647 – 738Fe2OG dioxygenasePROSITE-ProRule annotationAdd BLAST92

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni25 – 290Required for glycosyltransferase activity2 PublicationsAdd BLAST266
    Regioni44 – 46UDP-sugar bindingCombined sources1 Publication3
    Regioni112 – 114UDP-sugar bindingCombined sources1 Publication3
    Regioni256 – 259UDP-sugar bindingCombined sources1 Publication4
    Regioni295 – 520Accessory region1 PublicationAdd BLAST226
    Regioni672 – 715Important for dimerization1 PublicationAdd BLAST44

    Domaini

    The N-terminal domain mediates glycosyltransferase activity.1 Publication
    The C-terminal domain that mediates lysyl hydroxylase activity is also important for homodimerization.1 Publication

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiKOG1971 Eukaryota
    ENOG410Y4QU LUCA
    GeneTreeiENSGT00550000074427
    HOGENOMiHOG000231099
    HOVERGENiHBG053618
    InParanoidiO60568
    KOiK13646
    OMAiCIVSSPR
    OrthoDBiEOG091G02DK
    PhylomeDBiO60568
    TreeFamiTF313826

    Family and domain databases

    InterProiView protein in InterPro
    IPR029044 Nucleotide-diphossugar_trans
    IPR005123 Oxoglu/Fe-dep_dioxygenase
    IPR006620 Pro_4_hyd_alph
    IPR001006 Procol_lys_dOase
    PfamiView protein in Pfam
    PF03171 2OG-FeII_Oxy, 1 hit
    SMARTiView protein in SMART
    SM00702 P4Hc, 1 hit
    SUPFAMiSSF53448 SSF53448, 1 hit
    PROSITEiView protein in PROSITE
    PS51471 FE2OG_OXY, 1 hit
    PS01325 LYS_HYDROXYLASE, 1 hit

    Sequence (1+)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry has 1 described isoform and 6 potential isoforms that are computationally mapped.Show allAlign All

    O60568-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE
    60 70 80 90 100
    GYLRFLRSAE FFNYTVRTLG LGEEWRGGDV ARTVGGGQKV RWLKKEMEKY
    110 120 130 140 150
    ADREDMIIMF VDSYDVILAG SPTELLKKFV QSGSRLLFSA ESFCWPEWGL
    160 170 180 190 200
    AEQYPEVGTG KRFLNSGGFI GFATTIHQIV RQWKYKDDDD DQLFYTRLYL
    210 220 230 240 250
    DPGLREKLSL NLDHKSRIFQ NLNGALDEVV LKFDRNRVRI RNVAYDTLPI
    260 270 280 290 300
    VVHGNGPTKL QLNYLGNYVP NGWTPEGGCG FCNQDRRTLP GGQPPPRVFL
    310 320 330 340 350
    AVFVEQPTPF LPRFLQRLLL LDYPPDRVTL FLHNNEVFHE PHIADSWPQL
    360 370 380 390 400
    QDHFSAVKLV GPEEALSPGE ARDMAMDLCR QDPECEFYFS LDADAVLTNL
    410 420 430 440 450
    QTLRILIEEN RKVIAPMLSR HGKLWSNFWG ALSPDEYYAR SEDYVELVQR
    460 470 480 490 500
    KRVGVWNVPY ISQAYVIRGD TLRMELPQRD VFSGSDTDPD MAFCKSFRDK
    510 520 530 540 550
    GIFLHLSNQH EFGRLLATSR YDTEHLHPDL WQIFDNPVDW KEQYIHENYS
    560 570 580 590 600
    RALEGEGIVE QPCPDVYWFP LLSEQMCDEL VAEMEHYGQW SGGRHEDSRL
    610 620 630 640 650
    AGGYENVPTV DIHMKQVGYE DQWLQLLRTY VGPMTESLFP GYHTKARAVM
    660 670 680 690 700
    NFVVRYRPDE QPSLRPHHDS STFTLNVALN HKGLDYEGGG CRFLRYDCVI
    710 720 730
    SSPRKGWALL HPGRLTHYHE GLPTTWGTRY IMVSFVDP
    Length:738
    Mass (Da):84,785
    Last modified:August 1, 1998 - v1
    Checksum:i08424B46985941F9
    GO

    Computationally mapped potential isoform sequencesi

    There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
    EntryEntry nameProtein names
    Gene namesLengthAnnotation
    H7C2S8H7C2S8_HUMAN
    Procollagen-lysine,2-oxoglutarate 5...
    PLOD3
    264Annotation score:
    C9JIX5C9JIX5_HUMAN
    Procollagen-lysine,2-oxoglutarate 5...
    PLOD3
    75Annotation score:
    C9JU11C9JU11_HUMAN
    Procollagen-lysine,2-oxoglutarate 5...
    PLOD3
    171Annotation score:
    H7C2A8H7C2A8_HUMAN
    Procollagen-lysine,2-oxoglutarate 5...
    PLOD3
    125Annotation score:
    H7C0B8H7C0B8_HUMAN
    Procollagen-lysine,2-oxoglutarate 5...
    PLOD3
    66Annotation score:
    H7C2V1H7C2V1_HUMAN
    Procollagen-lysine,2-oxoglutarate 5...
    PLOD3
    270Annotation score:

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_051708151A → V. Corresponds to variant dbSNP:rs35627324Ensembl.1
    Natural variantiVAR_054913223N → S in LH3 deficiency; generates a new glycosylation site; decreases protein stability; strongly decreases lysyl hydroxylase activity and nearly abolishes glycosyltransferase activity. 2 PublicationsCorresponds to variant dbSNP:rs121434414EnsemblClinVar.1
    Natural variantiVAR_012075286R → W. Corresponds to variant dbSNP:rs1134907Ensembl.1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF046889 mRNA Translation: AAC39753.1
    AF068229 mRNA Translation: AAC34808.1
    AF207069 Genomic DNA Translation: AAF63701.1
    AY220458 mRNA Translation: AAO61775.1
    AK312743 mRNA Translation: BAG35613.1
    AC004876 Genomic DNA Translation: AAD45831.1
    CH471197 Genomic DNA Translation: EAW50205.1
    BC011674 mRNA Translation: AAH11674.1
    CCDSiCCDS5715.1
    RefSeqiNP_001075.1, NM_001084.4
    UniGeneiHs.153357

    Genome annotation databases

    EnsembliENST00000223127; ENSP00000223127; ENSG00000106397
    GeneIDi8985
    KEGGihsa:8985
    UCSCiuc003uyd.4 human

    Keywords - Coding sequence diversityi

    Polymorphism

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF046889 mRNA Translation: AAC39753.1
    AF068229 mRNA Translation: AAC34808.1
    AF207069 Genomic DNA Translation: AAF63701.1
    AY220458 mRNA Translation: AAO61775.1
    AK312743 mRNA Translation: BAG35613.1
    AC004876 Genomic DNA Translation: AAD45831.1
    CH471197 Genomic DNA Translation: EAW50205.1
    BC011674 mRNA Translation: AAH11674.1
    CCDSiCCDS5715.1
    RefSeqiNP_001075.1, NM_001084.4
    UniGeneiHs.153357

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    6FXKX-ray2.70A25-738[»]
    6FXMX-ray2.10A25-738[»]
    6FXRX-ray2.10A25-738[»]
    6FXTX-ray2.50A25-738[»]
    6FXXX-ray3.00A25-738[»]
    6FXYX-ray2.14A25-738[»]
    ProteinModelPortaliO60568
    SMRiO60568
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi114467, 58 interactors
    IntActiO60568, 34 interactors
    MINTiO60568
    STRINGi9606.ENSP00000223127

    Chemistry databases

    DrugBankiDB00139 Succinic acid
    DB00126 Vitamin C

    Protein family/group databases

    MoonDBiO60568 Curated
    MoonProtiO60568

    PTM databases

    GlyConnecti1635
    iPTMnetiO60568
    PhosphoSitePlusiO60568

    Polymorphism and mutation databases

    BioMutaiPLOD3

    Proteomic databases

    EPDiO60568
    MaxQBiO60568
    PaxDbiO60568
    PeptideAtlasiO60568
    PRIDEiO60568
    ProteomicsDBi49474

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000223127; ENSP00000223127; ENSG00000106397
    GeneIDi8985
    KEGGihsa:8985
    UCSCiuc003uyd.4 human

    Organism-specific databases

    CTDi8985
    DisGeNETi8985
    EuPathDBiHostDB:ENSG00000106397.11
    GeneCardsiPLOD3
    HGNCiHGNC:9083 PLOD3
    HPAiHPA001236
    MalaCardsiPLOD3
    MIMi603066 gene
    612394 phenotype
    neXtProtiNX_O60568
    OpenTargetsiENSG00000106397
    Orphaneti300284 Connective tissue disorder due to lysyl hydroxylase-3 deficiency
    PharmGKBiPA33413
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG1971 Eukaryota
    ENOG410Y4QU LUCA
    GeneTreeiENSGT00550000074427
    HOGENOMiHOG000231099
    HOVERGENiHBG053618
    InParanoidiO60568
    KOiK13646
    OMAiCIVSSPR
    OrthoDBiEOG091G02DK
    PhylomeDBiO60568
    TreeFamiTF313826

    Enzyme and pathway databases

    BRENDAi1.14.11.4 2681
    2.4.1.50 2681
    2.4.1.66 2681
    ReactomeiR-HSA-1650814 Collagen biosynthesis and modifying enzymes

    Miscellaneous databases

    ChiTaRSiPLOD3 human
    GeneWikiiPLOD3
    GenomeRNAii8985
    PROiPR:O60568
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000106397 Expressed in 220 organ(s), highest expression level in placenta
    CleanExiHS_PLOD3
    ExpressionAtlasiO60568 baseline and differential
    GenevisibleiO60568 HS

    Family and domain databases

    InterProiView protein in InterPro
    IPR029044 Nucleotide-diphossugar_trans
    IPR005123 Oxoglu/Fe-dep_dioxygenase
    IPR006620 Pro_4_hyd_alph
    IPR001006 Procol_lys_dOase
    PfamiView protein in Pfam
    PF03171 2OG-FeII_Oxy, 1 hit
    SMARTiView protein in SMART
    SM00702 P4Hc, 1 hit
    SUPFAMiSSF53448 SSF53448, 1 hit
    PROSITEiView protein in PROSITE
    PS51471 FE2OG_OXY, 1 hit
    PS01325 LYS_HYDROXYLASE, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPLOD3_HUMAN
    AccessioniPrimary (citable) accession number: O60568
    Secondary accession number(s): B2R6W6, Q540C3
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: August 1, 1998
    Last modified: November 7, 2018
    This is version 172 of the entry and version 1 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. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    2. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    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. Human chromosome 7
      Human chromosome 7: entries, gene names and cross-references to MIM
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