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Q99P99

- HDAC4_RAT

UniProt

Q99P99 - HDAC4_RAT

Protein

Histone deacetylase 4

Gene

Hdac4

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 77 (01 Oct 2014)
      Sequence version 2 (20 Mar 2007)
      Previous versions | rss
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    Functioni

    Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D By similarity.By similarity

    Catalytic activityi

    Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi665 – 6651ZincBy similarity
    Metal bindingi667 – 6671ZincBy similarity
    Metal bindingi673 – 6731ZincBy similarity
    Metal bindingi744 – 7441ZincBy similarity
    Active sitei796 – 7961By similarity

    GO - Molecular functioni

    1. core promoter binding Source: RGD
    2. histone deacetylase activity Source: RGD
    3. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
    4. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
    5. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
    6. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC
    7. potassium ion binding Source: Ensembl
    8. protein binding Source: RGD
    9. sequence-specific DNA binding Source: Ensembl
    10. transcription corepressor activity Source: Ensembl
    11. zinc ion binding Source: Ensembl

    GO - Biological processi

    1. chromatin remodeling Source: Ensembl
    2. histone deacetylation Source: RGD
    3. negative regulation of cell proliferation Source: Ensembl
    4. negative regulation of glycolytic process Source: Ensembl
    5. negative regulation of myotube differentiation Source: Ensembl
    6. negative regulation of osteoblast differentiation Source: Ensembl
    7. negative regulation of sequence-specific DNA binding transcription factor activity Source: Ensembl
    8. negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
    9. osteoblast development Source: Ensembl
    10. peptidyl-lysine deacetylation Source: Ensembl
    11. positive regulation of cell proliferation Source: Ensembl
    12. positive regulation of protein sumoylation Source: Ensembl
    13. positive regulation of sequence-specific DNA binding transcription factor activity Source: Ensembl
    14. positive regulation of transcription from RNA polymerase II promoter Source: Ensembl
    15. regulation of cardiac muscle contraction by calcium ion signaling Source: Ensembl
    16. regulation of protein binding Source: Ensembl
    17. regulation of skeletal muscle fiber development Source: Ensembl
    18. response to denervation involved in regulation of muscle adaptation Source: Ensembl
    19. response to drug Source: RGD
    20. response to interleukin-1 Source: Ensembl
    21. skeletal system development Source: Ensembl
    22. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chromatin regulator, Hydrolase, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone deacetylase 4 (EC:3.5.1.98)
    Short name:
    HD4
    Gene namesi
    Name:Hdac4
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 9

    Organism-specific databases

    RGDi619979. Hdac4.

    Subcellular locationi

    Nucleus. Cytoplasm
    Note: Shuttles between the nucleus and the cytoplasm. Upon muscle cells differentiation, it accumulates in the nuclei of myotubes, suggesting a positive role of nuclear HDAC4 in muscle differentiation. The export to cytoplasm depends on the interaction with a 14-3-3 chaperone protein and is due to its phosphorylation at Ser-245, Ser-466 and Ser-630 by CaMK4 and SIK1. The nuclear localization probably depends on sumoylation By similarity.By similarity

    GO - Cellular componenti

    1. A band Source: MGI
    2. actomyosin Source: Ensembl
    3. cytoplasm Source: RGD
    4. cytosol Source: RGD
    5. histone deacetylase complex Source: Ensembl
    6. neuromuscular junction Source: Ensembl
    7. nucleus Source: RGD
    8. protein complex Source: RGD
    9. sarcomere Source: MGI
    10. transcriptional repressor complex Source: Ensembl
    11. Z disc Source: MGI

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 10771077Histone deacetylase 4PRO_0000281034Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei245 – 2451Phosphoserine; by CaMK4 and SIK1By similarity
    Modified residuei349 – 3491PhosphoserineBy similarity
    Modified residuei466 – 4661Phosphoserine; by CaMK4 and SIK1By similarity
    Cross-linki557 – 557Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
    Modified residuei563 – 5631PhosphoserineBy similarity
    Modified residuei630 – 6301Phosphoserine; by CaMK4By similarity
    Modified residuei631 – 6311PhosphoserineBy similarity

    Post-translational modificationi

    Phosphorylated by CaMK4 at Ser-245, Ser-466 and Ser-630. Phosphorylation at other residues by CaMK2D is required for the interaction with 14-3-3. Phosphorylation at Ser-349 impairs the binding of ANKRA2 but generates a high-affinity docking site for 14-3-3 By similarity.By similarity
    Sumoylation on Lys-557 is promoted by the E3 SUMO-protein ligase RANBP2, and prevented by phosphorylation by CaMK4.

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    PaxDbiQ99P99.
    PRIDEiQ99P99.

    PTM databases

    PhosphoSiteiQ99P99.

    Expressioni

    Gene expression databases

    GenevestigatoriQ99P99.

    Interactioni

    Subunit structurei

    Interacts with HDAC7. Homodimer By similarity. Homodimerization via its N-terminal domain. Interacts with MEF2C and NR2C1. Interacts with a 14-3-3 chaperone protein in a phosphorylation dependent manner. Interacts with KDM5B and AHRR By similarity. Interacts with BTBD14B. Interacts with MYOCD. Interacts with ANKRA2. Interacts with EP300 in the presence of TFAP2C By similarity.By similarity

    Protein-protein interaction databases

    BioGridi264106. 4 interactions.

    Structurei

    3D structure databases

    ProteinModelPortaliQ99P99.
    SMRiQ99P99. Positions 62-128, 648-1044.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni117 – 312196Interaction with MEF2ABy similarityAdd
    BLAST
    Regioni653 – 1077425Histone deacetylaseBy similarityAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili66 – 169104Sequence AnalysisAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi1044 – 107734Nuclear export signalBy similarityAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi465 – 50036Gln-richAdd
    BLAST
    Compositional biasi562 – 5698Poly-Glu

    Domaini

    The nuclear export sequence mediates the shuttling between the nucleus and the cytoplasm.By similarity

    Sequence similaritiesi

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiCOG0123.
    GeneTreeiENSGT00530000062809.
    HOGENOMiHOG000232065.
    HOVERGENiHBG057100.
    InParanoidiQ99P99.
    KOiK11406.
    OMAiVSFGGHR.
    OrthoDBiEOG7RFTH5.
    PhylomeDBiQ99P99.
    TreeFamiTF106174.

    Family and domain databases

    Gene3Di3.40.800.20. 1 hit.
    InterProiIPR000286. His_deacetylse.
    IPR023801. His_deacetylse_dom.
    IPR024643. Hist_deacetylase_Gln_rich_N.
    IPR017320. Histone_deAcase_II_euk.
    [Graphical view]
    PANTHERiPTHR10625. PTHR10625. 1 hit.
    PfamiPF12203. HDAC4_Gln. 1 hit.
    PF00850. Hist_deacetyl. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037911. HDAC_II_euk. 1 hit.
    PRINTSiPR01270. HDASUPER.

    Sequencei

    Sequence statusi: Complete.

    Q99P99-1 [UniParc]FASTAAdd to Basket

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    MSSQSHPDGL SGRDQPVELL NPARVNHMPS TVDVATALPL QVAPAAVPMD     50
    LRLDHQFSLP LEPALREQQL QQELLALKQK QQIQRQILIA EFQRQHEQLS 100
    RQHEAQLHEH IKQQQEMLAM KHQQELLEHQ RKLERHRQEQ ELEKQHREQK 150
    LQQLKNKEKG KESAVASTEV KMKLQEFVLN KKKALAHRNL NHCMSSDPRY 200
    WYGKTQHSSL DQSSPPQSGV SASYNHPVLG MYDAKDDFPL RKTASEPNLK 250
    LRSRLKQKVA ERRSSPLLRR KDGPVATALK KRPLDVTDSA CSSAPGSGPS 300
    SPNSSSGNVS TENGIAPTVP STPAETSLAH RLVTREGSVA PLPLYTSPSL 350
    PNITLGLPAT GPAAGAAGQQ DAERLALPAL QQRISLFPGT HLTPYLSTSP 400
    LERDGGAAHN PLLQHMVLLE QPPTQTPLVT GLGALPLHTQ SLVGADRVSP 450
    SIHKLRQHRP LGRTQSAPLP QNAQALQHLV IQQQHQQFLE KHKQQFQQQQ 500
    LHLSKMISKP SEPPRQPESH PEETEEELRE HQALLDEPYL DRLPGQKEPS 550
    LAGVQVKQEP IESEEEEVEA TREAEPSQRP ATEQELLFRQ QALLLEQQRI 600
    HQLRNYQASM EAAGIPVSFG SHRPLSRAQS SPASATFPMS VQEPPTKPRF 650
    TTGLVYDTLM LKHQCTCGNT NSHPEHAGRI QSIWSRLQET GLRGKCECIR 700
    GRKATLEELQ TVHSEAHTLL YGTNPLNRQK LDSSLTSVFV RLPCGGVGVD 750
    SDTIWNEVHS SGAARLAVGC VVELVFKVAT GELKNGFAVV RPPGHHAEES 800
    TPMGFCYFNS VAIAAKLLQQ RLNVSKILIV DWDVHHGNGT QQAFYNDPNV 850
    LYMSLHRYDD GNFFPGSGAP DEVGTGPGVG FNVNMAFTGG LDPPMGDAEY 900
    LAAFRTVVMP IANEFAPDVV LVSSGFDAVE GHPTPLGGYN LSAKCFGYLT 950
    KQLMGLAGGR IVLALEGGHD LTAICDASEA CVSALLGNEL EPLPEKVLHQ 1000
    RPNANAVHSM EKVMGIHSEY WRCLQRLSPT VGHSLIEAQK CENEEAETVT 1050
    AMASLSVGVK PAEKRSEEEP MEEEPPL 1077
    Length:1,077
    Mass (Da):118,652
    Last modified:March 20, 2007 - v2
    Checksum:i88127299D9962DBA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AABR03067902 Genomic DNA. No translation available.
    AABR03068091 Genomic DNA. No translation available.
    AABR03070452 Genomic DNA. No translation available.
    AF321132 mRNA. Translation: AAK11185.1.
    RefSeqiNP_445901.1. NM_053449.1.
    UniGeneiRn.23483.

    Genome annotation databases

    EnsembliENSRNOT00000027622; ENSRNOP00000027622; ENSRNOG00000020372.
    GeneIDi363287.
    KEGGirno:363287.
    UCSCiRGD:619979. rat.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AABR03067902 Genomic DNA. No translation available.
    AABR03068091 Genomic DNA. No translation available.
    AABR03070452 Genomic DNA. No translation available.
    AF321132 mRNA. Translation: AAK11185.1 .
    RefSeqi NP_445901.1. NM_053449.1.
    UniGenei Rn.23483.

    3D structure databases

    ProteinModelPortali Q99P99.
    SMRi Q99P99. Positions 62-128, 648-1044.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 264106. 4 interactions.

    Chemistry

    BindingDBi Q99P99.
    ChEMBLi CHEMBL2095943.

    PTM databases

    PhosphoSitei Q99P99.

    Proteomic databases

    PaxDbi Q99P99.
    PRIDEi Q99P99.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000027622 ; ENSRNOP00000027622 ; ENSRNOG00000020372 .
    GeneIDi 363287.
    KEGGi rno:363287.
    UCSCi RGD:619979. rat.

    Organism-specific databases

    CTDi 9759.
    RGDi 619979. Hdac4.

    Phylogenomic databases

    eggNOGi COG0123.
    GeneTreei ENSGT00530000062809.
    HOGENOMi HOG000232065.
    HOVERGENi HBG057100.
    InParanoidi Q99P99.
    KOi K11406.
    OMAi VSFGGHR.
    OrthoDBi EOG7RFTH5.
    PhylomeDBi Q99P99.
    TreeFami TF106174.

    Miscellaneous databases

    NextBioi 683134.
    PROi Q99P99.

    Gene expression databases

    Genevestigatori Q99P99.

    Family and domain databases

    Gene3Di 3.40.800.20. 1 hit.
    InterProi IPR000286. His_deacetylse.
    IPR023801. His_deacetylse_dom.
    IPR024643. Hist_deacetylase_Gln_rich_N.
    IPR017320. Histone_deAcase_II_euk.
    [Graphical view ]
    PANTHERi PTHR10625. PTHR10625. 1 hit.
    Pfami PF12203. HDAC4_Gln. 1 hit.
    PF00850. Hist_deacetyl. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037911. HDAC_II_euk. 1 hit.
    PRINTSi PR01270. HDASUPER.
    ProtoNeti Search...

    Publicationsi

    1. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
      Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M.
      , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
      Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Brown Norway.
    2. "Expression pattern of rat histone deacetylases."
      Wilquet V., Chavez M., Korbers R., Geerts A.
      Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 55-208.
      Strain: Wistar.
      Tissue: Testis.
    3. "The POZ/BTB protein NAC1 interacts with two different histone deacetylases in neuronal-like cultures."
      Korutla L., Wang P.J., Mackler S.A.
      J. Neurochem. 94:786-793(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH BTBD14B.

    Entry informationi

    Entry nameiHDAC4_RAT
    AccessioniPrimary (citable) accession number: Q99P99
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 20, 2007
    Last sequence update: March 20, 2007
    Last modified: October 1, 2014
    This is version 77 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3