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Q94517

- HDAC1_DROME

UniProt

Q94517 - HDAC1_DROME

Protein

Histone deacetylase Rpd3

Gene

Rpd3

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 133 (01 Oct 2014)
      Sequence version 2 (21 Jun 2005)
      Previous versions | rss
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    Functioni

    Catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation may constitute a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. For instance, deacetylation of histone H3 may be a prerequisite for the subsequent recruitment of the histone methyltransferase Su(var)3-9 to histones. Involved in position-effect variegation (PEV).

    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
    Active sitei139 – 1391By similarity

    GO - Molecular functioni

    1. histone deacetylase activity Source: UniProtKB
    2. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
    3. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
    4. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
    5. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC
    6. protein binding Source: UniProtKB
    7. transcription corepressor activity Source: FlyBase
    8. transcription factor binding Source: UniProtKB

    GO - Biological processi

    1. blastoderm segmentation Source: FlyBase
    2. chromatin modification Source: UniProtKB
    3. chromatin silencing Source: FlyBase
    4. dendrite guidance Source: FlyBase
    5. dendrite morphogenesis Source: FlyBase
    6. determination of adult lifespan Source: FlyBase
    7. gene silencing Source: FlyBase
    8. histone deacetylation Source: FlyBase
    9. muscle organ development Source: FlyBase
    10. negative regulation of axonogenesis Source: FlyBase
    11. negative regulation of response to gamma radiation Source: FlyBase
    12. negative regulation of transcription, DNA-templated Source: FlyBase
    13. negative regulation of transcription from RNA polymerase II promoter Source: FlyBase
    14. neurogenesis Source: FlyBase
    15. oogenesis Source: FlyBase
    16. regulation of transcription, DNA-templated Source: FlyBase
    17. respiratory electron transport chain Source: FlyBase
    18. transcription, DNA-templated Source: UniProtKB-KW
    19. tricarboxylic acid cycle Source: FlyBase

    Keywords - Molecular functioni

    Chromatin regulator, Developmental protein, Hydrolase, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Enzyme and pathway databases

    ReactomeiREACT_180658. G0 and Early G1.
    REACT_181669. Downregulation of SMAD2/3:SMAD4 transcriptional activity.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone deacetylase Rpd3 (EC:3.5.1.98)
    Short name:
    HD
    Short name:
    dRPD3
    Gene namesi
    Name:Rpd3
    Synonyms:HDAC1
    ORF Names:CG7471
    OrganismiDrosophila melanogaster (Fruit fly)
    Taxonomic identifieri7227 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
    ProteomesiUP000000803: Chromosome 3L

    Organism-specific databases

    FlyBaseiFBgn0015805. Rpd3.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. chromatin Source: FlyBase
    2. cytoplasm Source: UniProtKB
    3. ESC/E(Z) complex Source: FlyBase
    4. histone deacetylase complex Source: UniProtKB
    5. Myb complex Source: FlyBase
    6. nucleus Source: UniProtKB
    7. NuRD complex Source: FlyBase
    8. polytene chromosome Source: FlyBase
    9. polytene chromosome interband Source: FlyBase
    10. Sin3 complex Source: FlyBase
    11. Sin3-type complex Source: FlyBase
    12. transcriptional repressor complex Source: FlyBase

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 521521Histone deacetylase Rpd3PRO_0000114718Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei391 – 3911Phosphoserine1 Publication
    Modified residuei419 – 4191Phosphoserine1 Publication
    Modified residuei421 – 4211Phosphoserine1 Publication
    Modified residuei455 – 4551Phosphoserine1 Publication
    Modified residuei457 – 4571Phosphothreonine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ94517.

    Expressioni

    Gene expression databases

    BgeeiQ94517.

    Interactioni

    Subunit structurei

    Interacts with Su(var)3-9. Component of a form of the Esc/E(z) complex present specifically during early embryogenesis which is composed of Caf1, esc, E(z), Su(z)12, Pcl and Rpd3. The Esc/E(z) complex may also associate with Pcl and Rpd3 during early embryogenesis. This complex is distinct from the PRC1 complex, which contains many other PcG proteins like Pc, Ph, Psc, Su(z)2. The 2 complexes however cooperate and interact together during the first 3 hours of development to establish PcG silencing. Interacts with the histone methyltransferase Su(var)3-9. Component of a complex that contains at least Rpd3, CoRest and Su(var)3-3/Hdm. Component of the DREAM complex at least composed of Myb, Caf1, mip40, mip120, mip130, E2f2, Dp, Rbf, Rbf2, lin-52, Rpd3 and l3mbt. Interacts with neuronal repressor Ttk88.6 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    Caf1Q245724EBI-302197,EBI-75924
    E(z)P421249EBI-302197,EBI-112315
    escQ2433811EBI-302197,EBI-88911
    mip120A1Z9E22EBI-302197,EBI-75953
    PclQ244595EBI-302197,EBI-430086

    Protein-protein interaction databases

    BioGridi64037. 30 interactions.
    DIPiDIP-29512N.
    IntActiQ94517. 15 interactions.
    MINTiMINT-1746418.
    STRINGi7227.FBpp0073173.

    Structurei

    3D structure databases

    ProteinModelPortaliQ94517.
    SMRiQ94517. Positions 6-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni7 – 319313Histone deacetylaseAdd
    BLAST

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0123.
    GeneTreeiENSGT00530000062889.
    InParanoidiQ94517.
    KOiK06067.
    OMAiASWCRCH.
    OrthoDBiEOG7DNNTW.
    PhylomeDBiQ94517.

    Family and domain databases

    Gene3Di3.40.800.20. 1 hit.
    InterProiIPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view]
    PANTHERiPTHR10625. PTHR10625. 1 hit.
    PfamiPF00850. Hist_deacetyl. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSiPR01270. HDASUPER.
    PR01271. HISDACETLASE.

    Sequencei

    Sequence statusi: Complete.

    Q94517-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQSHSKKRVC YYYDSDIGNY YYGQGHPMKP HRIRMTHNLL LNYGLYRKME    50
    IYRPHKATAD EMTKFHSDEY VRFLRSIRPD NMSEYNKQMQ RFNVGEDCPV 100
    FDGLYEFCQL SAGGSVAAAV KLNKQASEIC INWGGGLHHA KKSEASGFCY 150
    VNDIVLGILE LLKYHQRVLY IDIDVHHGDG VEEAFYTTDR VMTVSFHKYG 200
    EYFPGTGDLR DIGAGKGKYY AVNIPLRDGM DDDAYESIFV PIISKVMETF 250
    QPAAVVLQCG ADSLTGDRLG CFNLTVKGHG KCVEFVKKYN LPFLMVGGGG 300
    YTIRNVSRCW TYETSVALAV EIANELPYND YFEYFGPDFK LHISPSNMTN 350
    QNTSEYLEKI KNRLFENLRM LPHAPGVQIQ AIPEDAINDE SDDEDKVDKD 400
    DRLPQSDKDK RIVPENEYSD SEDEGEGGRR DNRSYKGQRK RPRLDKDTNS 450
    NKASSETSSE IKDEKEKGDG ADGEESTASN TNSNNNSNNK SDNDAGATAN 500
    AGSGSGSGSG AGAKGAKENN I 521
    Length:521
    Mass (Da):58,331
    Last modified:June 21, 2005 - v2
    Checksum:iB0F6503D42A1BCE9
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti50 – 523EIY → DI in CAA70455. (PubMed:8955276)Curated
    Sequence conflicti67 – 671S → C in CAA70455. (PubMed:8955276)Curated
    Sequence conflicti97 – 971D → N in AAC23917. 1 PublicationCurated
    Sequence conflicti106 – 1061E → D in AAC23917. 1 PublicationCurated
    Sequence conflicti296 – 2961V → VV in AAC23917. 1 PublicationCurated
    Sequence conflicti305 – 3051N → K(PubMed:8955276)Curated
    Sequence conflicti305 – 3051N → K1 PublicationCurated
    Sequence conflicti371 – 3711L → V in AAC23917. 1 PublicationCurated
    Sequence conflicti507 – 5071S → T(PubMed:10655219)Curated
    Sequence conflicti507 – 5071S → T1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y09258 mRNA. Translation: CAA70455.1.
    AF086715 Genomic DNA. Translation: AAC61494.1.
    AF026949 mRNA. Translation: AAC23917.1.
    AE014296 Genomic DNA. Translation: AAF47924.1.
    AY058487 mRNA. Translation: AAL13716.1.
    RefSeqiNP_647918.2. NM_139661.4.
    UniGeneiDm.2976.

    Genome annotation databases

    EnsemblMetazoaiFBtr0073317; FBpp0073173; FBgn0015805.
    GeneIDi38565.
    KEGGidme:Dmel_CG7471.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y09258 mRNA. Translation: CAA70455.1 .
    AF086715 Genomic DNA. Translation: AAC61494.1 .
    AF026949 mRNA. Translation: AAC23917.1 .
    AE014296 Genomic DNA. Translation: AAF47924.1 .
    AY058487 mRNA. Translation: AAL13716.1 .
    RefSeqi NP_647918.2. NM_139661.4.
    UniGenei Dm.2976.

    3D structure databases

    ProteinModelPortali Q94517.
    SMRi Q94517. Positions 6-373.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 64037. 30 interactions.
    DIPi DIP-29512N.
    IntActi Q94517. 15 interactions.
    MINTi MINT-1746418.
    STRINGi 7227.FBpp0073173.

    Proteomic databases

    PaxDbi Q94517.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblMetazoai FBtr0073317 ; FBpp0073173 ; FBgn0015805 .
    GeneIDi 38565.
    KEGGi dme:Dmel_CG7471.

    Organism-specific databases

    CTDi 38565.
    FlyBasei FBgn0015805. Rpd3.

    Phylogenomic databases

    eggNOGi COG0123.
    GeneTreei ENSGT00530000062889.
    InParanoidi Q94517.
    KOi K06067.
    OMAi ASWCRCH.
    OrthoDBi EOG7DNNTW.
    PhylomeDBi Q94517.

    Enzyme and pathway databases

    Reactomei REACT_180658. G0 and Early G1.
    REACT_181669. Downregulation of SMAD2/3:SMAD4 transcriptional activity.

    Miscellaneous databases

    GenomeRNAii 38565.
    NextBioi 809299.

    Gene expression databases

    Bgeei Q94517.

    Family and domain databases

    Gene3Di 3.40.800.20. 1 hit.
    InterProi IPR000286. His_deacetylse.
    IPR003084. His_deacetylse_1.
    IPR023801. His_deacetylse_dom.
    [Graphical view ]
    PANTHERi PTHR10625. PTHR10625. 1 hit.
    Pfami PF00850. Hist_deacetyl. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037913. His_deacetylse_1. 1 hit.
    PRINTSi PR01270. HDASUPER.
    PR01271. HISDACETLASE.
    ProtoNeti Search...

    Publicationsi

    1. "The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast."
      de Rubertis F., Kadosh D., Henchoz S., Pauli D., Reuter G., Struhl K., Spierer P.
      Nature 384:589-591(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Tissue: Embryo.
    2. "Mutational analysis of a histone deacetylase in Drosophila melanogaster: missense mutations suppress gene silencing associated with position effect variegation."
      Mottus R., Sobel R.E., Grigliatti T.A.
      Genetics 154:657-668(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. Johnson C.A., White D., O'Neill L.P., Turner B.M.
      Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    4. "The genome sequence of Drosophila melanogaster."
      Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D.
      , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.
      Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Berkeley.
    5. Cited for: GENOME REANNOTATION.
      Strain: Berkeley.
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: Berkeley.
      Tissue: Ovary.
    7. "Physical and functional association of SU(VAR)3-9 and HDAC1 in Drosophila."
      Czermin B., Schotta G., Huelsmann B.B., Brehm A., Becker P.B., Reuter G., Imhof A.
      EMBO Rep. 2:915-919(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SU(VAR)3-9.
    8. "Polycomb group proteins ESC and E(Z) are present in multiple distinct complexes that undergo dynamic changes during development."
      Furuyama T., Tie F., Harte P.J.
      Genesis 35:114-124(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN AN ESC/E(Z) COMPLEX WITH CAF1; ESC AND E(Z).
    9. "Drosophila Enhancer of zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites."
      Czermin B., Melfi R., McCabe D., Seitz V., Imhof A., Pirrotta V.
      Cell 111:185-196(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN AN ESC/E(Z) COMPLEX WITH CAF1; ESC; E(Z) AND SU(Z)12, METHYLTRANSFERASE ACTIVITY OF THE COMPLEX.
    10. "A 1-megadalton ESC/E(Z) complex from Drosophila that contains polycomblike and RPD3."
      Tie F., Prasad-Sinha J., Birve A., Rasmuson-Lestander A., Harte P.J.
      Mol. Cell. Biol. 23:3352-3362(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN AN ESC/E(Z) COMPLEX WITH CAF1; ESC; E(Z); PCL AND SU(Z)12.
    11. "Identification of a Drosophila Myb-E2F2/RBF transcriptional repressor complex."
      Lewis P.W., Beall E.L., Fleischer T.C., Georlette D., Link A.J., Botchan M.R.
      Genes Dev. 18:2929-2940(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE DREAM COMPLEX.
    12. "A conserved role but different partners for the transcriptional corepressor CoREST in fly and mammalian nervous system formation."
      Dallman J.E., Allopenna J., Bassett A., Travers A., Mandel G.
      J. Neurosci. 24:7186-7193(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH COREST.
    13. "Phosphoproteome analysis of Drosophila melanogaster embryos."
      Zhai B., Villen J., Beausoleil S.A., Mintseris J., Gygi S.P.
      J. Proteome Res. 7:1675-1682(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-391; SER-419; SER-421; SER-455 AND THR-457, IDENTIFICATION BY MASS SPECTROMETRY.
      Tissue: Embryo.

    Entry informationi

    Entry nameiHDAC1_DROME
    AccessioniPrimary (citable) accession number: Q94517
    Secondary accession number(s): O17429, O77213, Q9VZA1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: June 21, 2005
    Last modified: October 1, 2014
    This is version 133 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programDrosophila annotation project

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Drosophila
      Drosophila: entries, gene names and cross-references to FlyBase
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3