Q94517 (HDAC1_DROME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone deacetylase Rpd3
Short name=HD
Short name=dRPD3
EC=3.5.1.98

Gene names

Name:	Rpd3
Synonyms:	HDAC1
ORF Names:	CG7471

Organism

Drosophila melanogaster (Fruit fly)

Taxonomic identifier

7227 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Arthropoda › Hexapoda › Insecta › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Ephydroidea › Drosophilidae › Drosophila › Sophophora

Protein attributes

Sequence length	521 AA.
Sequence status	Complete.
Protein existence	Evidence 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.12
Subcellular location	Nucleus Potential.
Sequence similarities	Belongs to the histone deacetylase family. HD type 1 subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Chromatin regulator Developmental protein Hydrolase Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	blastoderm segmentation Inferred from mutant phenotype. Source: FlyBase chromatin silencing Inferred from mutant phenotype. Source: FlyBase dendrite guidance Inferred from mutant phenotype. Source: FlyBase determination of adult lifespan Inferred from mutant phenotype. Source: FlyBase muscle organ development Inferred from mutant phenotype. Source: FlyBase negative regulation of axonogenesis Inferred from mutant phenotype. Source: FlyBase oogenesis Traceable author statement. Source: FlyBase respiratory electron transport chain Inferred from direct assay. Source: FlyBase transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW tricarboxylic acid cycle Inferred from direct assay. Source: FlyBase
Cellular component	ESC/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. Source: FlyBase Sin3 complex Non-traceable author statement. Source: FlyBase cytoplasm Traceable author statement. Source: UniProtKB polytene chromosome interband Inferred from direct assay. Source: FlyBase
Molecular function	NAD-dependent histone deacetylase activity (H3-K14 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K9 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H4-K16 specific) Inferred from electronic annotation. Source: EC histone deacetylase activity (H3-K16 specific) Inferred from electronic annotation. Source: EC transcription corepressor activity Non-traceable author statement. Source: FlyBase transcription factor binding Traceable author statement. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Caf1	Q24572	4	EBI-302197,EBI-75924
E(z)	P42124	9	EBI-302197,EBI-112315
esc	Q24338	11	EBI-302197,EBI-88911
mip120	A1Z9E2	2	EBI-302197,EBI-75953
Pcl	Q24459	5	EBI-302197,EBI-430086
Su(var)3-9	P45975	2	EBI-302197,EBI-110378

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 521	521	Histone deacetylase Rpd3		PRO_0000114718
Regions
	Region	7 – 319	313	Histone deacetylase
Sites
	Active site	139	1	By similarity
Amino acid modifications
	Modified residue	391	1	Phosphoserine Ref.13
	Modified residue	419	1	Phosphoserine Ref.13
	Modified residue	421	1	Phosphoserine Ref.13
	Modified residue	455	1	Phosphoserine Ref.13
	Modified residue	457	1	Phosphothreonine Ref.13
Experimental info
	Sequence conflict	50 – 52	3	EIY → DI in CAA70455. Ref.1
	Sequence conflict	67	1	S → C in CAA70455. Ref.1
	Sequence conflict	97	1	D → N in AAC23917. Ref.3
	Sequence conflict	106	1	E → D in AAC23917. Ref.3
	Sequence conflict	296	1	V → VV in AAC23917. Ref.3
	Sequence conflict	305	1	N → K Ref.1
	Sequence conflict	305	1	N → K Ref.3
	Sequence conflict	371	1	L → V in AAC23917. Ref.3
	Sequence conflict	507	1	S → T Ref.2
	Sequence conflict	507	1	S → T Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q94517 [UniParc]. Last modified June 21, 2005. Version 2. Checksum: B0F6503D42A1BCE9	FASTA	521	58,331
	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

References

	« Hide 'large scale' referencesShow '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: 8955276] [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: 10655219] [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: 10731132] [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. , 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: 12537572] [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: 12537569] [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: 11571273] [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: 12533794] [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: 12408863] [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: 12697833] [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: 15545624] [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: 15306652] [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: 18327897] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-391; SER-419; SER-421; SER-455 AND THR-457, 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.
RefSeq	NP_647918.2. NM_139661.3.
UniGene	Dm.2976.
3D structure databases
ProteinModelPortal	Q94517.
SMR	Q94517. Positions 6-371.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-29512N.
IntAct	Q94517. 6 interactions.
MINT	MINT-1746418.
STRING	Q94517.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	FBtr0073317; FBpp0073173; FBgn0015805.
GeneID	38565.
KEGG	dme:Dmel_CG7471.
NMPDR	fig|7227.3.peg.8166.
Organism-specific databases
CTD	38565.
FlyBase	FBgn0015805. Rpd3.
Phylogenomic databases
eggNOG	inNOG09296.
GeneTree	EMGT00050000004694.
InParanoid	Q94517.
OMA	AYESIFV.
OrthoDB	EOG476HFG.
PhylomeDB	Q94517.
Gene expression databases
ArrayExpress	Q94517.
Bgee	Q94517.
GermOnline	CG7471. Drosophila melanogaster.
Family and domain databases
InterPro	IPR000286. His_deacetylse. IPR003084. His_deacetylse_1. IPR023801. His_deacetylse_dom. [Graphical view]
Gene3D	G3DSA:3.40.800.20. His_deacetylse. 1 hit.
KO	K06067.
PANTHER	PTHR10625. His_deacetylse. 1 hit.
Pfam	PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PIRSF	PIRSF037913. His_deacetylse_1. 1 hit.
PRINTS	PR01270. HDASUPER. PR01271. HISDACETLASE.
ProtoNet	Search...
Other
NextBio	809299.

Entry information

Entry name

HDAC1_DROME

Accession

Primary (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:	January 25, 2012
This is version 109 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Drosophila annotation project