Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q94517 (HDAC1_DROME) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 131. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone deacetylase Rpd3

Short name=HD
Short name=dRPD3
EC=3.5.1.98
Gene names
Name:Rpd3
Synonyms:HDAC1
ORF Names:CG7471
OrganismDrosophila melanogaster (Fruit fly) [Reference proteome]
Taxonomic identifier7227 [NCBI]
Taxonomic lineageEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora

Protein attributes

Sequence length521 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Subunit structure

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. Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12

Subcellular location

Nucleus Potential.

Sequence similarities

Belongs to the histone deacetylase family. HD type 1 subfamily.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Molecular functionChromatin regulator
Developmental protein
Hydrolase
Repressor
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processblastoderm segmentation

Inferred from mutant phenotype PubMed 10359792. Source: FlyBase

chromatin modification

Traceable author statement PubMed 12711221. Source: UniProtKB

chromatin silencing

Inferred from mutant phenotype PubMed 18454196. Source: FlyBase

dendrite guidance

Inferred from mutant phenotype PubMed 20660276. Source: FlyBase

dendrite morphogenesis

Inferred from mutant phenotype PubMed 16547170. Source: FlyBase

determination of adult lifespan

Inferred from mutant phenotype PubMed 12459580. Source: FlyBase

gene silencing

Inferred from mutant phenotype PubMed 11124122. Source: FlyBase

histone deacetylation

Inferred from mutant phenotype PubMed 12077326PubMed 20660276. Source: FlyBase

muscle organ development

Inferred from mutant phenotype PubMed 16547170. Source: FlyBase

negative regulation of axonogenesis

Inferred from mutant phenotype PubMed 20660276. Source: FlyBase

negative regulation of response to gamma radiation

Inferred from mutant phenotype PubMed 18410726. Source: FlyBase

negative regulation of transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 16391236. Source: FlyBase

negative regulation of transcription, DNA-templated

Inferred from genetic interaction PubMed 19129218. Source: FlyBase

neurogenesis

Inferred from mutant phenotype PubMed 21549331. Source: FlyBase

oogenesis

Traceable author statement PubMed 11691830. Source: FlyBase

regulation of transcription, DNA-templated

Inferred from direct assay PubMed 16137856. Source: FlyBase

respiratory electron transport chain

Inferred from direct assay PubMed 18042644. Source: FlyBase

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

tricarboxylic acid cycle

Inferred from direct assay PubMed 18042644. Source: FlyBase

   Cellular_componentESC/E(Z) complex

Inferred from direct assay Ref.9. Source: FlyBase

Myb complex

Inferred from direct assay Ref.11. Source: FlyBase

NuRD complex

Inferred from physical interaction PubMed 11743021. Source: FlyBase

Sin3 complex

Non-traceable author statement PubMed 11080159. Source: FlyBase

Sin3-type complex

Inferred from direct assay PubMed 20566628. Source: FlyBase

chromatin

Inferred from direct assay PubMed 11080159. Source: FlyBase

cytoplasm

Traceable author statement PubMed 12711221. Source: UniProtKB

histone deacetylase complex

Traceable author statement PubMed 12711221. Source: UniProtKB

nucleus

Traceable author statement PubMed 12711221. Source: UniProtKB

polytene chromosome

Inferred from direct assay PubMed 18535655. Source: FlyBase

polytene chromosome interband

Inferred from direct assay PubMed 18451879. Source: FlyBase

transcriptional repressor complex

Inferred from physical interaction Ref.12. Source: FlyBase

   Molecular_functionNAD-dependent histone deacetylase activity (H3-K14 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H3-K18 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H3-K9 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

NAD-dependent histone deacetylase activity (H4-K16 specific)

Inferred from electronic annotation. Source: UniProtKB-EC

histone deacetylase activity

Traceable author statement PubMed 12711221. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.10. Source: UniProtKB

transcription corepressor activity

Inferred from physical interaction PubMed 16391236. Source: FlyBase

transcription factor binding

Traceable author statement PubMed 12711221. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 521521Histone deacetylase Rpd3
PRO_0000114718

Regions

Region7 – 319313Histone deacetylase

Sites

Active site1391 By similarity

Amino acid modifications

Modified residue3911Phosphoserine Ref.13
Modified residue4191Phosphoserine Ref.13
Modified residue4211Phosphoserine Ref.13
Modified residue4551Phosphoserine Ref.13
Modified residue4571Phosphothreonine Ref.13

Experimental info

Sequence conflict50 – 523EIY → DI in CAA70455. Ref.1
Sequence conflict671S → C in CAA70455. Ref.1
Sequence conflict971D → N in AAC23917. Ref.3
Sequence conflict1061E → D in AAC23917. Ref.3
Sequence conflict2961V → VV in AAC23917. Ref.3
Sequence conflict3051N → K Ref.1
Sequence conflict3051N → K Ref.3
Sequence conflict3711L → V in AAC23917. Ref.3
Sequence conflict5071S → T Ref.2
Sequence conflict5071S → T Ref.3

Sequences

Sequence LengthMass (Da)Tools
Q94517 [UniParc].

Last modified June 21, 2005. Version 2.
Checksum: B0F6503D42A1BCE9

FASTA52158,331
        10         20         30         40         50         60 
MQSHSKKRVC YYYDSDIGNY YYGQGHPMKP HRIRMTHNLL LNYGLYRKME IYRPHKATAD 

        70         80         90        100        110        120 
EMTKFHSDEY VRFLRSIRPD NMSEYNKQMQ RFNVGEDCPV FDGLYEFCQL SAGGSVAAAV 

       130        140        150        160        170        180 
KLNKQASEIC INWGGGLHHA KKSEASGFCY VNDIVLGILE LLKYHQRVLY IDIDVHHGDG 

       190        200        210        220        230        240 
VEEAFYTTDR VMTVSFHKYG EYFPGTGDLR DIGAGKGKYY AVNIPLRDGM DDDAYESIFV 

       250        260        270        280        290        300 
PIISKVMETF QPAAVVLQCG ADSLTGDRLG CFNLTVKGHG KCVEFVKKYN LPFLMVGGGG 

       310        320        330        340        350        360 
YTIRNVSRCW TYETSVALAV EIANELPYND YFEYFGPDFK LHISPSNMTN QNTSEYLEKI 

       370        380        390        400        410        420 
KNRLFENLRM LPHAPGVQIQ AIPEDAINDE SDDEDKVDKD DRLPQSDKDK RIVPENEYSD 

       430        440        450        460        470        480 
SEDEGEGGRR DNRSYKGQRK RPRLDKDTNS NKASSETSSE IKDEKEKGDG ADGEESTASN 

       490        500        510        520 
TNSNNNSNNK SDNDAGATAN AGSGSGSGSG AGAKGAKENN I 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review."
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S., Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E., Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P., Bettencourt B.R., Celniker S.E., de Grey A.D.N.J. expand/collapse author list , Drysdale R.A., Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: Berkeley.
[6]"A Drosophila full-length cDNA resource."
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M., Celniker S.E.
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_647918.2. NM_139661.4.
UniGeneDm.2976.

3D structure databases

ProteinModelPortalQ94517.
SMRQ94517. Positions 6-373.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid64037. 30 interactions.
DIPDIP-29512N.
IntActQ94517. 15 interactions.
MINTMINT-1746418.
STRING7227.FBpp0073173.

Proteomic databases

PaxDbQ94517.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaFBtr0073317; FBpp0073173; FBgn0015805.
GeneID38565.
KEGGdme:Dmel_CG7471.

Organism-specific databases

CTD38565.
FlyBaseFBgn0015805. Rpd3.

Phylogenomic databases

eggNOGCOG0123.
GeneTreeENSGT00530000062889.
InParanoidQ94517.
KOK06067.
OMAASWCRCH.
OrthoDBEOG7DNNTW.
PhylomeDBQ94517.

Gene expression databases

BgeeQ94517.

Family and domain databases

Gene3D3.40.800.20. 1 hit.
InterProIPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
IPR023801. His_deacetylse_dom.
[Graphical view]
PANTHERPTHR10625. PTHR10625. 1 hit.
PfamPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFPIRSF037913. His_deacetylse_1. 1 hit.
PRINTSPR01270. HDASUPER.
PR01271. HISDACETLASE.
ProtoNetSearch...

Other

GenomeRNAi38565.
NextBio809299.

Entry information

Entry nameHDAC1_DROME
AccessionPrimary (citable) accession number: Q94517
Secondary accession number(s): O17429, O77213, Q9VZA1
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: June 21, 2005
Last modified: July 9, 2014
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Relevant documents

SIMILARITY comments

Index of protein domains and families

Drosophila

Drosophila: entries, gene names and cross-references to FlyBase