Protein Overview: RPD3

General Information:
Name(s) found:	RPD3 / YNL330C [SGD]
Description(s) found: SHOW ONLY BEST	pir\|\|S22284 transcription regulator RPD3 - yeast (Saccharomyces cerevisiae) [NCBI NR] gi\|642338\|emb\|CAA58228.1\| global transcriptional regulator [Saccharomyces cerevisiae] [NCBI NR] gi\|6323999\|ref\|NP_014069.1\| Histone deacetylase; regulates transcription and silencing; Rpd3p [Saccharomyces cerevisiae] [NCBI NR] gi\|51013077\|gb\|AAT92832.1\| YNL330C [Saccharomyces cerevisiae] [NCBI NR] gi\|417699\|sp\|P32561.1\|RPD3_YEAST RecName: Full=Histone deacetylase RPD3; AltName: Full=Transcriptional regulatory protein RPD3 [NCBI NR] gi\|238962\|gb\|AAB20328.1\| RPD3 [Saccharomyces cerevisiae] [NCBI NR] gi\|1302451\|emb\|CAA96263.1\| RPD3 [Saccharomyces cerevisiae] [NCBI NR] Histone deacetylase RPD3 OS=Saccharomyces cerevisiae GN=RPD3 PE=1 SV=1 [Swiss-Prot] RPD3 Histone deacetylase B [mips] Histone deacetylase; regulates transcription and silencing; plays a role in regulating Ty1 transposition [SGD] Chr XIV from 19302-18001, reverse complement [yeastorf5.fasta] (P32561) Histone deacetylase RPD3 (Transcriptional regulatory protein RPD3) [4932.FASTACCERV.txt] Chr XIV from 18001-19302, reverse complement [yeastorf3.fasta] RPD3, Chr XIV from 18001-19302, reverse complement [yeast_orfs2] RPD3 SGDID:S0005274, Chr XIV from 19302-18001, reverse complement, Verified ORF [yeastflysequest.fasta] Histone deacetylase; regulates transcription and silencing [Saccharomyces cerevisiae]gi\|51013077\|gb\|AAT92832.1\| YNL330C [Saccharomyces cerevisiae]gi\|1302451\|emb\|CAA96263.1\| RPD3 [Saccharomyces cerevisiae]gi\|642338\|emb\|CAA58228.1\| global transcriptional [nrdb_11152004_Chlamydomonas] RPD3 SGDID:S000005274, Chr XIV from 19302-18001, reverse complement, Verified ORF, "Histone deacetylase; regulates transcription and silencing" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] RPD3 SGDID:S000005274, Chr XIV from 19302-18001, reverse complement, Verified ORF, "Histone deacetylase; regulates transcription and silencing; plays a role in regulating Ty1 transposition" [SGD_S-cerevisiae_na_08-19-2008_con_reversed.fasta] global transcriptional regulator [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Histone deacetylase; regulates transcription and silencing; Rpd3p [Saccharomyces cerevisiae] [nr-271106-contam.fasta] YNL330C [Saccharomyces cerevisiae] [nr-271106-contam.fasta] RPD3 [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Histone deacetylase RPD3 (Transcriptional regulatory protein RPD3) [nr-271106-contam.fasta] [chemostatdb.fasta] Histone deacetylase RPD3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPD3 PE=1 SV=1 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] RPD3 SGDID:S000005274, Chr XIV from 19302-18001, Genome Release 64-1-1, reverse complement, Verified ORF, "Histone deacetylase; regulates transcription, silencing, and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members" [yeast-030211-contam.fasta] RPD3 SGDID:S000005274, Chr XIV from 19302-18001, Genome Release 64-2-1, reverse complement, Verified ORF, "Histone deacetylase, component of both the Rpd3S and Rpd3L complexes; regulates transcription, silencing, autophagy and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members; Rpd3(L) recruitment to the subtelomeric region is regulated by interaction with the arginine methyltransferase, Hmt1p" [20141208_orf_trans.fasta] YNL330C SGDID:S000005274, Chr XIV from 19302-18001, Genome Release 64-1-1, reverse complement, Verified ORF, "Histone deacetylase; regulates transcription, silencing, and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta]
Organism:	Saccharomyces cerevisiae
Length:	433 amino acids
Gene Ontology:
Cellular Component:	histone deacetylase complex [IDA]
Biological Process:	negative regulation of transcription from RNA polymerase II promoter [IMP] chromatin silencing at rDNA [IMP] loss of chromatin silencing involved in replicative cell aging [IMP] protein amino acid deacetylation [IDA ] chromatin silencing [IDA] double-strand break repair via nonhomologous end joining [IMP] chromatin organization [TAS ] histone deacetylation [IMP] chromatin silencing at silent mating-type cassette [IMP] positive regulation of transcription from RNA polymerase II promoter [IMP] chromatin silencing at telomere [IMP] mitotic recombination [IMP]
Molecular Function:	transcription coactivator activity [IMP] histone deacetylase activity [IDA][IMP ][TAS] transcription corepressor activity [IMP]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK  60
   61 MEIYRAKPAT KQEMCQFHTD EYIDFLSRVT PDNLEMFKRE SVKFNVGDDC PVFDGLYEYC 120
  121 SISGGGSMEG AARLNRGKCD VAVNYAGGLH HAKKSEASGF CYLNDIVLGI IELLRYHPRV 180
  181 LYIDIDVHHG DGVEEAFYTT DRVMTCSFHK YGEFFPGTGE LRDIGVGAGK NYAVNVPLRD 240
  241 GIDDATYRSV FEPVIKKIME WYQPSAVVLQ CGGDSLSGDR LGCFNLSMEG HANCVNYVKS 300
  301 FGIPMMVVGG GGYTMRNVAR TWCFETGLLN NVVLDKDLPY NEYYEYYGPD YKLSVRPSNM 360
  361 FNVNTPEYLD KVMTNIFANL ENTKYAPSVQ LNHTPRDAED LGDVEEDSAE AKDTKGGSQY 420
  421 ARDLHVEHDN EFY

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Riffle et al. (2010) (Unpublished Data)		CTI6 DEP1 EAF3 PHO23 RCO1 RPD3 RXT2 RXT3 SAP30 SDS3 SIN3 UME1
View Details	(MIPS) Mewes HW, et al. (2004)		RPD3 SAP30 SIN3 STB1 STB2
View Details	Krogan NJ, et al. (2006)		ASH1 COQ6 CTI6 DEP1 EAF3 GRX5 PHO23 RCO1 RPD3 RXT2 RXT3 SAP30 SAY1 SDS3 SIN3 UME1
View Details	Gavin AC, et al. (2006)		CTI6 RCO1 RPD3 RXT3 SAP30 SDS3 SIN3 UME1
View Details	Gavin AC, et al. (2002)		ABF2 CDC45 CKA1 CKA2 CKB1 CKB2 CTI6 DEP1 DOT6 EAF3 ECM16 ERG26 GLT1 HAT1 HSP42 HTA2 IOC3 ISW1 LYS12 MCM2 MCM5 MCM6 MCM7 MED4 NHP10 NRD1 ORC1 ORC2 ORC3 ORC4 ORC5 ORC6 PHO23 RCO1 RPD3 RPN9 RSC8 RXT2 RXT3 SAP30 SDS3 SIN3 STO1 TFP1 TOP1 TUP1 UME1 UME6 VPS1
View Details	Ho Y, et al. (2002)		CTI6 RPD3 SIN3 UME1
View Details	Qiu et al. (2008)		ASH1 HDA1 HDA2 HDA3 HOS1 HOS4 PHO23 RPD3 RXT2 SAP30 SDS3 SIF2 SNT1 STB2 TFB5

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	CEP3	sample cbf3 from feb 2005	Sandall S, et all (2006)
View Run	ZDS1	Sample 2- cpn2 from june 2005	McCusker D, et al (2007)
View Run	ZDS1	Sample 3 - cpn + atp, from june 2005	McCusker D, et al (2007)
View Run	MLP2	#31 Asynchronous Prep (Protease cleavage)	Keck JM, et al. (2011)
View Run	MLP2	#03 Alpha Factor Prep1-TiO2 Flowthrough	Keck JM, et al. (2011)

Yeast Two-Hybrid Data

The following interactions contain this protein:

SHOWING SINGLE HITS. [ Hide Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	AIM7	RPD3	1	Unpublished Fields Lab Data
View Screen	IST3	RPD3	1	Unpublished Fields Lab Data
View Screen	UBC7	RPD3	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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	PROTEIN(S)	PUBLICATION
View Data	RPD3	Huh WK, et al. (2003)
View Data	RPD3 and NOP56	Huh WK, et al. (2003)

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..177]	PSI-BLAST	507.40824	HDAC homologue
2	View Details	[178..347]	PSI-BLAST	507.40824	HDAC homologue
3	View Details	[348..433]	deduced	N/A	No confident structure predictions are available.

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.99

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2