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Protein

Histone deacetylase Rpd3

Gene

Rpd3

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: -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 N6-acetyl-lysine residue of a histone to yield a deacetylated histone.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei139By similarity1

GO - Molecular functioni

  • histone deacetylase activity Source: FlyBase
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  • transcription corepressor activity Source: FlyBase
  • transcription factor binding Source: UniProtKB

GO - Biological processi

  • blastoderm segmentation Source: FlyBase
  • chromatin organization Source: UniProtKB
  • chromatin silencing Source: FlyBase
  • chromosome condensation Source: FlyBase
  • dendrite guidance Source: FlyBase
  • determination of adult lifespan Source: FlyBase
  • gene silencing Source: FlyBase
  • histone deacetylation Source: FlyBase
  • negative regulation of axonogenesis Source: FlyBase
  • negative regulation of gene expression Source: UniProtKB
  • negative regulation of histone H3-K27 methylation Source: UniProtKB
  • negative regulation of histone methylation Source: UniProtKB
  • negative regulation of response to gamma radiation Source: FlyBase
  • negative regulation of smoothened signaling pathway Source: FlyBase
  • negative regulation of transcription, DNA-templated Source: FlyBase
  • negative regulation of transcription by RNA polymerase II Source: FlyBase
  • oogenesis Source: FlyBase
  • regulation of histone acetylation Source: FlyBase
  • regulation of neuroblast proliferation Source: UniProtKB
  • regulation of neuron differentiation Source: UniProtKB
  • regulation of transcription, DNA-templated Source: FlyBase
  • respiratory electron transport chain Source: FlyBase
  • transcription, DNA-templated Source: UniProtKB-KW
  • tricarboxylic acid cycle Source: FlyBase

Keywordsi

Molecular functionChromatin regulator, Developmental protein, Hydrolase, Repressor
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-DME-1538133 G0 and Early G1
R-DME-201722 Formation of the beta-catenin:TCF transactivating complex
R-DME-209394 Transcriptional activtion and repression of REL-68 target genes
R-DME-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-DME-3769402 Deactivation of the beta-catenin transactivating complex
R-DME-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-DME-8943724 Regulation of PTEN gene transcription
R-DME-983231 Factors involved in megakaryocyte development and platelet production

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 lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraHolometabolaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 3L

Organism-specific databases

FlyBaseiFBgn0015805 Rpd3

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

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001147181 – 521Histone deacetylase Rpd3Add BLAST521

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei391Phosphoserine1 Publication1
Modified residuei419Phosphoserine1 Publication1
Modified residuei421Phosphoserine1 Publication1
Modified residuei455Phosphoserine1 Publication1
Modified residuei457Phosphothreonine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ94517
PRIDEiQ94517

PTM databases

iPTMnetiQ94517

Expressioni

Gene expression databases

BgeeiFBgn0015805
ExpressionAtlasiQ94517 differential
GenevisibleiQ94517 DM

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

Show more details

GO - Molecular functioni

  • transcription factor binding Source: UniProtKB

Protein-protein interaction databases

BioGridi64037, 62 interactors
DIPiDIP-29512N
IntActiQ94517, 23 interactors
MINTiQ94517
STRINGi7227.FBpp0073173

Structurei

3D structure databases

ProteinModelPortaliQ94517
SMRiQ94517
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni7 – 319Histone deacetylaseAdd BLAST313

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1342 Eukaryota
COG0123 LUCA
GeneTreeiENSGT00910000144047
InParanoidiQ94517
KOiK06067
OMAiKRVCYFF
OrthoDBiEOG091G067J
PhylomeDBiQ94517

Family and domain databases

Gene3Di3.40.800.20, 1 hit
InterProiView protein in InterPro
IPR000286 His_deacetylse
IPR003084 His_deacetylse_1
IPR023801 His_deacetylse_dom
IPR037138 His_deacetylse_dom_sf
IPR023696 Ureohydrolase_dom_sf
PANTHERiPTHR10625 PTHR10625, 1 hit
PfamiView protein in Pfam
PF00850 Hist_deacetyl, 1 hit
PIRSFiPIRSF037913 His_deacetylse_1, 1 hit
PRINTSiPR01270 HDASUPER
PR01271 HISDACETLASE
SUPFAMiSSF52768 SSF52768, 1 hit

Sequencei

Sequence statusi: Complete.

Q94517-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQSHSKKRVC YYYDSDIGNY YYGQGHPMKP HRIRMTHNLL LNYGLYRKME
60 70 80 90 100
IYRPHKATAD EMTKFHSDEY VRFLRSIRPD NMSEYNKQMQ RFNVGEDCPV
110 120 130 140 150
FDGLYEFCQL SAGGSVAAAV KLNKQASEIC INWGGGLHHA KKSEASGFCY
160 170 180 190 200
VNDIVLGILE LLKYHQRVLY IDIDVHHGDG VEEAFYTTDR VMTVSFHKYG
210 220 230 240 250
EYFPGTGDLR DIGAGKGKYY AVNIPLRDGM DDDAYESIFV PIISKVMETF
260 270 280 290 300
QPAAVVLQCG ADSLTGDRLG CFNLTVKGHG KCVEFVKKYN LPFLMVGGGG
310 320 330 340 350
YTIRNVSRCW TYETSVALAV EIANELPYND YFEYFGPDFK LHISPSNMTN
360 370 380 390 400
QNTSEYLEKI KNRLFENLRM LPHAPGVQIQ AIPEDAINDE SDDEDKVDKD
410 420 430 440 450
DRLPQSDKDK RIVPENEYSD SEDEGEGGRR DNRSYKGQRK RPRLDKDTNS
460 470 480 490 500
NKASSETSSE IKDEKEKGDG ADGEESTASN TNSNNNSNNK SDNDAGATAN
510 520
AGSGSGSGSG AGAKGAKENN I
Length:521
Mass (Da):58,331
Last modified:June 21, 2005 - v2
Checksum:iB0F6503D42A1BCE9
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti50 – 52EIY → DI in CAA70455 (PubMed:8955276).Curated3
Sequence conflicti67S → C in CAA70455 (PubMed:8955276).Curated1
Sequence conflicti97D → N in AAC23917 (Ref. 3) Curated1
Sequence conflicti106E → D in AAC23917 (Ref. 3) Curated1
Sequence conflicti296V → VV in AAC23917 (Ref. 3) Curated1
Sequence conflicti305N → K (PubMed:8955276).Curated1
Sequence conflicti305N → K (Ref. 3) Curated1
Sequence conflicti371L → V in AAC23917 (Ref. 3) Curated1
Sequence conflicti507S → T (PubMed:10655219).Curated1
Sequence conflicti507S → T (Ref. 3) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

Similar proteinsi

Entry informationi

Entry nameiHDAC1_DROME
AccessioniPrimary (citable) accession number: Q94517
Secondary accession number(s): O17429, O77213, Q9VZA1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: June 21, 2005
Last modified: March 28, 2018
This is version 168 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health