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Q94517

- HDAC1_DROME

UniProt

Q94517 - HDAC1_DROME

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Protein
Histone deacetylase Rpd3
Gene
Rpd3, HDAC1, CG7471
Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 – 1391 By similarity

GO - Molecular functioni

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

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 from RNA polymerase II promoter Source: FlyBase
  13. negative regulation of transcription, DNA-templated 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
Complete GO annotation...

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 Reviewed prediction

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 521521Histone deacetylase Rpd3
PRO_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.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni7 – 319313Histone deacetylase
Add
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

Sequence conflict

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

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...

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 132 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

Similar proteinsi