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Q9UPP1

- PHF8_HUMAN

UniProt

Q9UPP1 - PHF8_HUMAN

Protein

Histone lysine demethylase PHF8

Gene

PHF8

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 3 (16 Aug 2005)
      Previous versions | rss
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    Functioni

    Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20' residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3.10 Publications

    Catalytic activityi

    Protein N6,N(6)-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO2.
    Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2.

    Cofactori

    Binds 1 Fe2+ ion per subunit.2 Publications

    Kineticsi

    1. KM=134 µM for histone H3 H3K9Me21 Publication
    2. KM=8 µM for histone H3 H3K4me3 and H3K9Me21 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei280 – 2801Substrate
    Metal bindingi283 – 2831Iron; catalytic2 PublicationsPROSITE-ProRule annotation
    Metal bindingi285 – 2851Iron; catalytic2 PublicationsPROSITE-ProRule annotation
    Binding sitei300 – 3001Substrate
    Metal bindingi355 – 3551Iron; catalytic2 PublicationsPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri41 – 9252PHD-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. chromatin binding Source: UniProtKB
    2. histone demethylase activity Source: UniProtKB
    3. histone demethylase activity (H3-K27 specific) Source: UniProtKB
    4. histone demethylase activity (H3-K36 specific) Source: UniProtKB
    5. histone demethylase activity (H3-K9 specific) Source: UniProtKB
    6. histone demethylase activity (H4-K20 specific) Source: UniProtKB
    7. iron ion binding Source: UniProtKB
    8. methylated histone binding Source: UniProtKB
    9. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Source: UniProtKB
    10. protein binding Source: IntAct
    11. zinc ion binding Source: UniProtKB

    GO - Biological processi

    1. brain development Source: UniProtKB
    2. G1/S transition of mitotic cell cycle Source: UniProtKB
    3. histone H3-K27 demethylation Source: UniProtKB
    4. histone H3-K36 demethylation Source: UniProtKB
    5. histone H3-K9 demethylation Source: UniProtKB
    6. histone H4-K20 demethylation Source: UniProtKB
    7. mitotic cell cycle Source: Reactome
    8. negative regulation of chromatin silencing at rDNA Source: UniProtKB
    9. positive regulation of transcription, DNA-templated Source: UniProtKB
    10. positive regulation of transcription from RNA polymerase I promoter Source: UniProtKB
    11. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Activator, Chromatin regulator, Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Cell cycle, Transcription, Transcription regulation

    Keywords - Ligandi

    Iron, Metal-binding, Zinc

    Enzyme and pathway databases

    ReactomeiREACT_172744. Condensation of Prophase Chromosomes.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone lysine demethylase PHF8 (EC:1.14.11.27)
    Alternative name(s):
    PHD finger protein 8
    Gene namesi
    Name:PHF8
    Synonyms:KIAA1111, ZNF422
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome X

    Organism-specific databases

    HGNCiHGNC:20672. PHF8.

    Subcellular locationi

    Nucleus. Nucleusnucleolus
    Note: Recruited to H3K4me3 sites on chromatin during interphase. Dissociates from chromatin when cells enter mitosis.

    GO - Cellular componenti

    1. microtubule cytoskeleton Source: HPA
    2. nucleolus Source: UniProtKB
    3. nucleoplasm Source: Reactome
    4. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Involvement in diseasei

    Mental retardation, X-linked, syndromic, Siderius type (MRXSSD) [MIM:300263]: A syndrome characterized by mild to borderline mental retardation with or without cleft lip/cleft palate.2 Publications
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti315 – 3151F → S in MRXSSD; abolishes histone methyltransferase activity. 1 Publication
    VAR_062250

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi43 – 431Y → A: Abolishes binding to H3K4me3; when associated with A-50. 2 Publications
    Mutagenesisi50 – 501Y → A: Abolishes binding to H3K4me3; when associated with A-43. Abolishes binding to H3K4me3; when associated with A-65. 1 Publication
    Mutagenesisi65 – 651W → A: Abolishes binding to H3K4me3; when associated with A-50. 1 Publication
    Mutagenesisi69 – 691S → A: Impairs phosphorylation by CDK1 and dissociation from chromatin when cells enter mitosis; when associated with A-120. 1 Publication
    Mutagenesisi120 – 1201S → A: Impairs phosphorylation by CDK1 and dissociation from chromatin when cells enter mitosis; when associated with A-69. 1 Publication
    Mutagenesisi283 – 2853HID → AAA: Abolishes histone methyltransferase activity. 3 Publications
    Mutagenesisi283 – 2831H → A: Abolishes histone methyltransferase activity. 3 Publications

    Keywords - Diseasei

    Disease mutation, Mental retardation

    Organism-specific databases

    MIMi300263. phenotype.
    Orphaneti85287. intellectual disability, X-linked, Siderius type.
    PharmGKBiPA134889361.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 10601060Histone lysine demethylase PHF8PRO_0000059295Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei69 – 691Phosphoserine; by CDK11 Publication
    Modified residuei120 – 1201Phosphoserine; by CDK11 Publication
    Modified residuei651 – 6511Phosphoserine1 Publication
    Modified residuei705 – 7051Phosphothreonine2 Publications
    Modified residuei706 – 7061Phosphothreonine2 Publications
    Modified residuei804 – 8041Phosphoserine1 Publication
    Modified residuei854 – 8541Phosphoserine3 Publications
    Modified residuei857 – 8571Phosphoserine5 Publications
    Modified residuei880 – 8801Phosphoserine3 Publications

    Post-translational modificationi

    Phosphorylation at Ser-69 and Ser-120 are required for dissociation from chromatin and accumulation of H4K20Me1 levels during prophase.6 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ9UPP1.
    PaxDbiQ9UPP1.
    PRIDEiQ9UPP1.

    PTM databases

    PhosphoSiteiQ9UPP1.

    Expressioni

    Gene expression databases

    ArrayExpressiQ9UPP1.
    BgeeiQ9UPP1.
    CleanExiHS_PHF8.
    GenevestigatoriQ9UPP1.

    Organism-specific databases

    HPAiHPA038779.

    Interactioni

    Subunit structurei

    Interacts with POLR1B, UBTF, SETD1A, HCFC1, E2F1 and ZNF711.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PML-RARQ151566EBI-6601215,EBI-867256
    RARAP102762EBI-6601215,EBI-413374

    Protein-protein interaction databases

    BioGridi116751. 32 interactions.
    DIPiDIP-38913N.
    IntActiQ9UPP1. 3 interactions.
    MINTiMINT-4651164.
    STRINGi9606.ENSP00000338868.

    Structurei

    Secondary structure

    1
    1060
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni44 – 474
    Beta strandi56 – 583
    Turni60 – 623
    Beta strandi65 – 673
    Helixi68 – 714
    Helixi75 – 784
    Beta strandi81 – 833
    Helixi87 – 937
    Helixi121 – 1299
    Turni136 – 1383
    Turni144 – 1463
    Helixi149 – 1557
    Beta strandi161 – 1655
    Turni167 – 1704
    Helixi180 – 1878
    Beta strandi192 – 1976
    Turni198 – 2014
    Beta strandi202 – 2076
    Helixi208 – 2158
    Beta strandi224 – 2307
    Helixi235 – 2384
    Helixi244 – 2496
    Helixi251 – 2555
    Beta strandi270 – 2745
    Beta strandi278 – 2836
    Helixi286 – 2883
    Beta strandi290 – 30516
    Helixi309 – 31911
    Helixi324 – 3263
    Helixi329 – 3313
    Beta strandi332 – 3343
    Beta strandi337 – 3426
    Beta strandi346 – 3494
    Beta strandi354 – 37017
    Beta strandi373 – 3753
    Helixi376 – 38914
    Helixi393 – 3953
    Helixi400 – 42021
    Helixi427 – 44418
    Turni446 – 4483
    Helixi449 – 4513
    Helixi453 – 4553
    Helixi462 – 47716

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2WWUX-ray2.15A115-483[»]
    3K3NX-ray2.40A122-483[»]
    3K3OX-ray2.10A122-483[»]
    3KV4X-ray2.19A37-483[»]
    4DO0X-ray2.55A115-483[»]
    ProteinModelPortaliQ9UPP1.
    SMRiQ9UPP1. Positions 39-483.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9UPP1.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini231 – 387157JmjCPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni101 – 11515LinkerAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi769 – 80739Ser-richAdd
    BLAST

    Domaini

    The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 promotes its access to H3K9me2.
    The linker region is a critical determinant of demethylase specificity. It enables the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3.

    Sequence similaritiesi

    Contains 1 JmjC domain.PROSITE-ProRule annotation
    Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri41 – 9252PHD-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG290496.
    HOGENOMiHOG000231232.
    HOVERGENiHBG045631.
    InParanoidiQ9UPP1.
    KOiK11445.
    OMAiEIDLYHC.
    PhylomeDBiQ9UPP1.
    TreeFamiTF106480.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR003347. JmjC_dom.
    IPR019786. Zinc_finger_PHD-type_CS.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF02373. JmjC. 1 hit.
    PF00628. PHD. 1 hit.
    [Graphical view]
    SMARTiSM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.
    PROSITEiPS51184. JMJC. 1 hit.
    PS01359. ZF_PHD_1. 1 hit.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view]

    Sequences (5)i

    Sequence statusi: Complete.

    This entry describes 5 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9UPP1-1) [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

    MNRSRAIVQR GRVLPPPAPL DTTNLAGRRT LQGRAKMASV PVYCLCRLPY     50
    DVTRFMIECD MCQDWFHGSC VGVEEEKAAD IDLYHCPNCE VLHGPSIMKK 100
    RRGSSKGHDT HKGKPVKTGS PTFVRELRSR TFDSSDEVIL KPTGNQLTVE 150
    FLEENSFSVP ILVLKKDGLG MTLPSPSFTV RDVEHYVGSD KEIDVIDVTR 200
    QADCKMKLGD FVKYYYSGKR EKVLNVISLE FSDTRLSNLV ETPKIVRKLS 250
    WVENLWPEEC VFERPNVQKY CLMSVRDSYT DFHIDFGGTS VWYHVLKGEK 300
    IFYLIRPTNA NLTLFECWSS SSNQNEMFFG DQVDKCYKCS VKQGQTLFIP 350
    TGWIHAVLTP VDCLAFGGNF LHSLNIEMQL KAYEIEKRLS TADLFRFPNF 400
    ETICWYVGKH ILDIFRGLRE NRRHPASYLV HGGKALNLAF RAWTRKEALP 450
    DHEDEIPETV RTVQLIKDLA REIRLVEDIF QQNVGKTSNI FGLQRIFPAG 500
    SIPLTRPAHS TSVSMSRLSL PSKNGSKKKG LKPKELFKKA ERKGKESSAL 550
    GPAGQLSYNL MDTYSHQALK TGSFQKAKFN ITGACLNDSD DDSPDLDLDG 600
    NESPLALLMS NGSTKRVKSL SKSRRTKIAK KVDKARLMAE QVMEDEFDLD 650
    SDDELQIDER LGKEKATLII RPKFPRKLPR AKPCSDPNRV REPGEVEFDI 700
    EEDYTTDEDM VEGVEGKLGN GSGAGGILDL LKASRQVGGP DYAALTEAPA 750
    SPSTQEAIQG MLCMANLQSS SSSPATSSLQ AWWTGGQDRS SGSSSSGLGT 800
    VSNSPASQRT PGKRPIKRPA YWRTESEEEE ENASLDEQDS LGACFKDAEY 850
    IYPSLESDDD DPALKSRPKK KKNSDDAPWS PKARVTPTLP KQDRPVREGT 900
    RVASIETGLA AAAAKLAQQE LQKAQKKKYI KKKPLLKEVE QPRPQDSNLS 950
    LTVPAPTVAA TPQLVTSSSP LPPPEPKQEA LSGSLADHEY TARPNAFGMA 1000
    QANRSTTPMA PGVFLTQRRP SVGSQSNQAG QGKRPKKGLA TAKQRLGRIL 1050
    KIHRNGKLLL 1060
    Length:1,060
    Mass (Da):117,864
    Last modified:August 16, 2005 - v3
    Checksum:i04C83D7C5E9E56B8
    GO
    Isoform 2 (identifier: Q9UPP1-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-36: Missing.

    Show »
    Length:1,024
    Mass (Da):113,913
    Checksum:i75773C0918578FB0
    GO
    Isoform 3 (identifier: Q9UPP1-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         478-578: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:959
    Mass (Da):106,902
    Checksum:iF54BE8A814BF1701
    GO
    Isoform 4 (identifier: Q9UPP1-4) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-36: Missing.
         478-578: Missing.
         1060-1060: L → LRQVIVQAECRQAIHEPKLKRRDAHP

    Note: No experimental confirmation available.

    Show »
    Length:948
    Mass (Da):105,913
    Checksum:iF32740CB7A2CE3F6
    GO
    Isoform 5 (identifier: Q9UPP1-5) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-36: Missing.
         717-746: KLGNGSGAGGILDLLKASRQVGGPDYAALT → YQTATPAPAQGAS
         920-931: ELQKAQKKKYIK → VKKMKLSLTDSG
         932-1060: Missing.

    Show »
    Length:878
    Mass (Da):98,290
    Checksum:i690CE764C0C28D28
    GO

    Sequence cautioni

    The sequence BAA83063.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.
    The sequence BAB13877.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence CAI45929.1 differs from that shown. Reason: Erroneous termination at position 419. Translated as Arg.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti232 – 2321S → P in BAB13877. (PubMed:12168954)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti315 – 3151F → S in MRXSSD; abolishes histone methyltransferase activity. 1 Publication
    VAR_062250

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 3636Missing in isoform 2, isoform 4 and isoform 5. 3 PublicationsVSP_014964Add
    BLAST
    Alternative sequencei478 – 578101Missing in isoform 3 and isoform 4. 1 PublicationVSP_014965Add
    BLAST
    Alternative sequencei717 – 74630KLGNG…YAALT → YQTATPAPAQGAS in isoform 5. 1 PublicationVSP_054019Add
    BLAST
    Alternative sequencei920 – 93112ELQKA…KKYIK → VKKMKLSLTDSG in isoform 5. 1 PublicationVSP_054020Add
    BLAST
    Alternative sequencei932 – 1060129Missing in isoform 5. 1 PublicationVSP_054021Add
    BLAST
    Alternative sequencei1060 – 10601L → LRQVIVQAECRQAIHEPKLK RRDAHP in isoform 4. 1 PublicationVSP_043640

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB029034 mRNA. Translation: BAA83063.1. Different initiation.
    CR933612 mRNA. Translation: CAI45929.1. Sequence problems.
    AK021696 mRNA. Translation: BAB13877.1. Different initiation.
    AK022788 mRNA. Translation: BAG51116.1.
    AK304272 mRNA. Translation: BAH14147.1.
    AL589872 Genomic DNA. No translation available.
    AL732374 Genomic DNA. No translation available.
    Z98051 Genomic DNA. No translation available.
    BC042108 mRNA. No translation available.
    BC053861 mRNA. Translation: AAH53861.1.
    CCDSiCCDS14355.1. [Q9UPP1-2]
    CCDS55418.1. [Q9UPP1-4]
    CCDS55419.1. [Q9UPP1-5]
    CCDS55420.1. [Q9UPP1-1]
    RefSeqiNP_001171825.1. NM_001184896.1. [Q9UPP1-1]
    NP_001171826.1. NM_001184897.1. [Q9UPP1-4]
    NP_055922.1. NM_015107.2. [Q9UPP1-2]
    UniGeneiHs.133352.

    Genome annotation databases

    EnsembliENST00000322659; ENSP00000319473; ENSG00000172943. [Q9UPP1-5]
    ENST00000338154; ENSP00000338868; ENSG00000172943. [Q9UPP1-2]
    ENST00000338946; ENSP00000340051; ENSG00000172943. [Q9UPP1-4]
    ENST00000357988; ENSP00000350676; ENSG00000172943. [Q9UPP1-1]
    GeneIDi23133.
    KEGGihsa:23133.
    UCSCiuc004dst.3. human. [Q9UPP1-1]
    uc004dsw.3. human. [Q9UPP1-4]

    Polymorphism databases

    DMDMi73620986.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB029034 mRNA. Translation: BAA83063.1 . Different initiation.
    CR933612 mRNA. Translation: CAI45929.1 . Sequence problems.
    AK021696 mRNA. Translation: BAB13877.1 . Different initiation.
    AK022788 mRNA. Translation: BAG51116.1 .
    AK304272 mRNA. Translation: BAH14147.1 .
    AL589872 Genomic DNA. No translation available.
    AL732374 Genomic DNA. No translation available.
    Z98051 Genomic DNA. No translation available.
    BC042108 mRNA. No translation available.
    BC053861 mRNA. Translation: AAH53861.1 .
    CCDSi CCDS14355.1. [Q9UPP1-2 ]
    CCDS55418.1. [Q9UPP1-4 ]
    CCDS55419.1. [Q9UPP1-5 ]
    CCDS55420.1. [Q9UPP1-1 ]
    RefSeqi NP_001171825.1. NM_001184896.1. [Q9UPP1-1 ]
    NP_001171826.1. NM_001184897.1. [Q9UPP1-4 ]
    NP_055922.1. NM_015107.2. [Q9UPP1-2 ]
    UniGenei Hs.133352.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2WWU X-ray 2.15 A 115-483 [» ]
    3K3N X-ray 2.40 A 122-483 [» ]
    3K3O X-ray 2.10 A 122-483 [» ]
    3KV4 X-ray 2.19 A 37-483 [» ]
    4DO0 X-ray 2.55 A 115-483 [» ]
    ProteinModelPortali Q9UPP1.
    SMRi Q9UPP1. Positions 39-483.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116751. 32 interactions.
    DIPi DIP-38913N.
    IntActi Q9UPP1. 3 interactions.
    MINTi MINT-4651164.
    STRINGi 9606.ENSP00000338868.

    Chemistry

    BindingDBi Q9UPP1.
    ChEMBLi CHEMBL1938212.
    GuidetoPHARMACOLOGYi 2698.

    PTM databases

    PhosphoSitei Q9UPP1.

    Polymorphism databases

    DMDMi 73620986.

    Proteomic databases

    MaxQBi Q9UPP1.
    PaxDbi Q9UPP1.
    PRIDEi Q9UPP1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000322659 ; ENSP00000319473 ; ENSG00000172943 . [Q9UPP1-5 ]
    ENST00000338154 ; ENSP00000338868 ; ENSG00000172943 . [Q9UPP1-2 ]
    ENST00000338946 ; ENSP00000340051 ; ENSG00000172943 . [Q9UPP1-4 ]
    ENST00000357988 ; ENSP00000350676 ; ENSG00000172943 . [Q9UPP1-1 ]
    GeneIDi 23133.
    KEGGi hsa:23133.
    UCSCi uc004dst.3. human. [Q9UPP1-1 ]
    uc004dsw.3. human. [Q9UPP1-4 ]

    Organism-specific databases

    CTDi 23133.
    GeneCardsi GC0XM053979.
    HGNCi HGNC:20672. PHF8.
    HPAi HPA038779.
    MIMi 300263. phenotype.
    300560. gene.
    neXtProti NX_Q9UPP1.
    Orphaneti 85287. intellectual disability, X-linked, Siderius type.
    PharmGKBi PA134889361.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG290496.
    HOGENOMi HOG000231232.
    HOVERGENi HBG045631.
    InParanoidi Q9UPP1.
    KOi K11445.
    OMAi EIDLYHC.
    PhylomeDBi Q9UPP1.
    TreeFami TF106480.

    Enzyme and pathway databases

    Reactomei REACT_172744. Condensation of Prophase Chromosomes.

    Miscellaneous databases

    ChiTaRSi PHF8. human.
    EvolutionaryTracei Q9UPP1.
    GeneWikii PHF8.
    GenomeRNAii 23133.
    NextBioi 35468941.
    PROi Q9UPP1.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9UPP1.
    Bgeei Q9UPP1.
    CleanExi HS_PHF8.
    Genevestigatori Q9UPP1.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR003347. JmjC_dom.
    IPR019786. Zinc_finger_PHD-type_CS.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view ]
    Pfami PF02373. JmjC. 1 hit.
    PF00628. PHD. 1 hit.
    [Graphical view ]
    SMARTi SM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view ]
    SUPFAMi SSF57903. SSF57903. 1 hit.
    PROSITEi PS51184. JMJC. 1 hit.
    PS01359. ZF_PHD_1. 1 hit.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
      Kikuno R., Nagase T., Ishikawa K., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
      DNA Res. 6:197-205(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Brain.
    2. "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
      Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
      DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: SEQUENCE REVISION.
    3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 34-927 (ISOFORM 3), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 515-1060 (ISOFORM 1).
      Tissue: Embryo, Teratocarcinoma and Trachea.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Endometrial tumor.
    5. "The DNA sequence of the human X chromosome."
      Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
      , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
      Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 5).
      Tissue: Brain and Cervix.
    7. Cited for: INVOLVEMENT IN MRXSSD.
    8. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
      Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
      Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-857, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    9. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-705; THR-706; SER-854; SER-857 AND SER-880, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    10. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
      Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
      Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-651; THR-705; THR-706; SER-854 AND SER-857, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Leukemic T-cell.
    12. "PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis."
      Zhu Z., Wang Y., Li X., Wang Y., Xu L., Wang X., Sun T., Dong X., Chen L., Mao H., Yu Y., Li J., Chen P.A., Chen C.D.
      Cell Res. 20:794-801(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF HIS-283.
    13. "The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation."
      Qiu J., Shi G., Jia Y., Li J., Wu M., Li J., Dong S., Wong J.
      Cell Res. 20:908-918(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CHARACTERIZATION OF VARIANT MRXSSD SER-315.
    14. "PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase."
      Loenarz C., Ge W., Coleman M.L., Rose N.R., Cooper C.D.O., Klose R.J., Ratcliffe P.J., Schofield C.J.
      Hum. Mol. Genet. 19:217-222(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBCELLULAR LOCATION.
    15. "A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation."
      Kleine-Kohlbrecher D., Christensen J., Vandamme J., Abarrategui I., Bak M., Tommerup N., Shi X., Gozani O., Rappsilber J., Salcini A.E., Helin K.
      Mol. Cell 38:165-178(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DOMAIN PHD-FINGER, INTERACTION WITH ZNF711, CHARACTERIZATION OF VARIANT MRXSSD SER-315, MUTAGENESIS OF HIS-283.
    16. "PHF8 targets histone methylation and RNA polymerase II to activate transcription."
      Fortschegger K., de Graaf P., Outchkourov N.S., van Schaik F.M., Timmers H.T., Shiekhattar R.
      Mol. Cell. Biol. 30:3286-3298(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DOMAIN PHD-FINGER, CHARACTERIZATION OF VARIANT MRXSSD SER-315.
    17. "PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation."
      Feng W., Yonezawa M., Ye J., Jenuwein T., Grummt I.
      Nat. Struct. Mol. Biol. 17:445-450(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH POLR1B AND UBTF, CHARACTERIZATION OF VARIANT MRXSSD SER-315, MUTAGENESIS OF TYR-43 AND 283-HIS--ASP-285.
    18. Cited for: FUNCTION, DOMAIN PHD-FINGER, CHARACTERIZATION OF VARIANT MRXSSD SER-315, MUTAGENESIS OF TYR-43; TYR-50 AND TRP-65.
    19. Cited for: FUNCTION, SUBCELLULAR LOCATION, DOMAIN PHD-FINGER, INTERACTION WITH SETD1A; HCFC1 AND E2F1, CHARACTERIZATION OF VARIANT MRXSSD SER-315, PHOSPHORYLATION AT SER-69 AND SER-120, MUTAGENESIS OF SER-69; SER-120 AND HIS-283.
    20. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-804; SER-857 AND SER-880, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    21. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    22. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
      Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
      Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-854; SER-857 AND SER-880, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    23. "Structural insights into a novel histone demethylase PHF8."
      Yu L., Wang Y., Huang S., Wang J., Deng Z., Zhang Q., Wu W., Zhang X., Liu Z., Gong W., Chen Z.
      Cell Res. 20:166-173(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 122-483 IN COMPLEX WITH IRON AND ALPHA-KETOGLUTARATE, FUNCTION, CHARACTERIZATION OF VARIANT MRXSSD SER-315.
    24. "Crystal structure of the PHF8 Jumonji domain, an N(epsilon)-methyl lysine demethylase."
      Yue W.W., Hozjan V., Ge W., Loenarz C., Cooper C.D., Schofield C.J., Kavanagh K.L., Oppermann U., McDonough M.A.
      FEBS Lett. 584:825-830(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 115-483.
    25. "Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases."
      Horton J.R., Upadhyay A.K., Qi H.H., Zhang X., Shi Y., Cheng X.
      Nat. Struct. Mol. Biol. 17:38-43(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-447 IN COMPLEX WITH IRON AND N-OXALYLGLYCINE, ZINC-BINDING, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, DOMAIN LINKER AND PHD-FINGER.
    26. "Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate."
      Koivisto A.M., Ala-Mello S., Lemmelae S., Komu H.A., Rautio J., Jaervelae I.
      Clin. Genet. 72:145-149(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT MRXSSD SER-315.

    Entry informationi

    Entry nameiPHF8_HUMAN
    AccessioniPrimary (citable) accession number: Q9UPP1
    Secondary accession number(s): B3KMV4
    , B7Z911, Q5H9U5, Q5JPR9, Q5JPS0, Q5JPS2, Q5JPS3, Q5VUJ4, Q7Z6D4, Q9HAH2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 19, 2004
    Last sequence update: August 16, 2005
    Last modified: October 1, 2014
    This is version 119 of the entry and version 3 of the sequence. [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 chromosome X
      Human chromosome X: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3