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Protein

Histone deacetylase RPD3

Gene

RPD3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic component of the RPD3 histone deacetylase (HDAC) complexes RPD3C(L) and RPD3C(S) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression, DNA damage response, osmotic stress response and developmental events. Is involved in rDNA and telomere silencing and in double strand breaks repair. Required for both full transcription repression and activation of many genes including cell type-specific genes (STE6, TY2 and HO), cell differentiation-specific genes (SPO13), genes that respond to external signals (PHO5) and TRK2. The RPD3 complexes regulate also chromosomal replication timing.19 Publications

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 sitei151 – 1511Curated

GO - Molecular functioni

  • histone deacetylase activity Source: SGD
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  • transcription coactivator activity Source: SGD
  • transcription corepressor activity Source: SGD

GO - Biological processi

  • histone H3 deacetylation Source: SGD
  • histone H4 deacetylation Source: SGD
  • negative regulation of chromatin silencing at rDNA Source: SGD
  • negative regulation of chromatin silencing at silent mating-type cassette Source: SGD
  • negative regulation of chromatin silencing at telomere Source: SGD
  • negative regulation of reciprocal meiotic recombination Source: SGD
  • negative regulation of transcription from RNA polymerase II promoter Source: SGD
  • negative regulation of transcription from RNA polymerase I promoter Source: SGD
  • negative regulation of transcription involved in meiotic cell cycle Source: SGD
  • positive regulation of macroautophagy Source: SGD
  • positive regulation of transcription from RNA polymerase II promoter Source: SGD
  • protein localization to nucleolar rDNA repeats Source: SGD
  • regulation of DNA-dependent DNA replication initiation Source: SGD
  • regulation of transcription involved in G1/S transition of mitotic cell cycle Source: SGD
  • regulation of transcription involved in G2/M transition of mitotic cell cycle Source: SGD
  • replicative cell aging Source: SGD
  • transcription elongation from RNA polymerase II promoter Source: SGD
  • transfer RNA gene-mediated silencing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-33314-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase RPD3 (EC:3.5.1.98)
Alternative name(s):
Transcriptional regulatory protein RPD3
Gene namesi
Name:RPD3
Synonyms:MOF6, REC3, SDI2, SDS6
Ordered Locus Names:YNL330C
ORF Names:N0305
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL330C.
SGDiS000005274. RPD3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • histone deacetylase complex Source: SGD
  • nuclear periphery Source: SGD
  • Rpd3L complex Source: SGD
  • Rpd3S complex Source: SGD
  • Sin3-type complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi150 – 1501H → A: Impairs histone deacetylase activity and transcription repression. 1 Publication
Mutagenesisi151 – 1511H → A: Impairs histone deacetylase activity and transcription repression. 1 Publication
Mutagenesisi188 – 1881H → A: Impairs histone deacetylase activity and transcription repression. 1 Publication
Mutagenesisi322 – 3221W → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi325 – 3251E → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi327 – 3271G → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi328 – 3281L → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi329 – 3291L → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi332 – 3321V → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi334 – 3341L → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi335 – 3351D → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi338 – 3381L → A: Reduces strongly HDAC activity. 1 Publication
Mutagenesisi339 – 3391P → A: Reduces strongly HDAC activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 433433Histone deacetylase RPD3PRO_0000114724Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei394 – 3941PhosphothreonineCombined sources
Modified residuei408 – 4081PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP32561.

PTM databases

iPTMnetiP32561.

Interactioni

Subunit structurei

Component of the RPD3C(L) complex composed of at least ASH1, CTI6, DEP1, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, UME1 and UME6. Component of the RPD3C(S) complex composed of at least EAF3, RCO1, RPD3, SIN3, and UME1. Interacts with cyclophilins CPR1, CPR6 and CPR7, with the kinase HOG1, and with ESS1, CYC8 and HAC1.10 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CPR6P536912EBI-15864,EBI-5429
CPR7P471032EBI-15864,EBI-5436
CYC8P149226EBI-15864,EBI-18215
HOT1Q032133EBI-15864,EBI-27376
RXT2P382556EBI-15864,EBI-21537
SIN3P2257912EBI-15864,EBI-17160
TUP1P166492EBI-15864,EBI-19654

Protein-protein interaction databases

BioGridi35511. 749 interactions.
DIPiDIP-681N.
IntActiP32561. 58 interactions.
MINTiMINT-614075.

Structurei

3D structure databases

ProteinModelPortaliP32561.
SMRiP32561. Positions 18-380.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni19 – 331313Histone deacetylaseAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi320 – 34021ESA1-RPD3 motifAdd
BLAST

Domaini

The ESA1-RPD3 (ER) motif is common to ESA1 and RPD3 and is required for ESA1 histone acetyl-transferase (HAT) activity and RPD3 histone deacetylase (HDAC) activity.1 Publication

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00530000062889.
HOGENOMiHOG000225180.
InParanoidiP32561.
KOiK06067.
OMAiMENANSK.
OrthoDBiEOG092C1END.

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.

P32561-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS
60 70 80 90 100
LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRVT PDNLEMFKRE
110 120 130 140 150
SVKFNVGDDC PVFDGLYEYC SISGGGSMEG AARLNRGKCD VAVNYAGGLH
160 170 180 190 200
HAKKSEASGF CYLNDIVLGI IELLRYHPRV LYIDIDVHHG DGVEEAFYTT
210 220 230 240 250
DRVMTCSFHK YGEFFPGTGE LRDIGVGAGK NYAVNVPLRD GIDDATYRSV
260 270 280 290 300
FEPVIKKIME WYQPSAVVLQ CGGDSLSGDR LGCFNLSMEG HANCVNYVKS
310 320 330 340 350
FGIPMMVVGG GGYTMRNVAR TWCFETGLLN NVVLDKDLPY NEYYEYYGPD
360 370 380 390 400
YKLSVRPSNM FNVNTPEYLD KVMTNIFANL ENTKYAPSVQ LNHTPRDAED
410 420 430
LGDVEEDSAE AKDTKGGSQY ARDLHVEHDN EFY
Length:433
Mass (Da):48,904
Last modified:October 1, 1993 - v1
Checksum:i34FFD72A7E7425DB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S66438 Genomic DNA. Translation: AAB20328.1.
X83226 Genomic DNA. Translation: CAA58228.1.
Z46259 Genomic DNA. Translation: CAA86368.1.
Z71605 Genomic DNA. Translation: CAA96262.1.
Z71606 Genomic DNA. Translation: CAA96263.1.
AY692813 Genomic DNA. Translation: AAT92832.1.
BK006947 Genomic DNA. Translation: DAA10233.1.
PIRiS22284.
RefSeqiNP_014069.1. NM_001183168.1.

Genome annotation databases

EnsemblFungiiYNL330C; YNL330C; YNL330C.
GeneIDi855386.
KEGGisce:YNL330C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S66438 Genomic DNA. Translation: AAB20328.1.
X83226 Genomic DNA. Translation: CAA58228.1.
Z46259 Genomic DNA. Translation: CAA86368.1.
Z71605 Genomic DNA. Translation: CAA96262.1.
Z71606 Genomic DNA. Translation: CAA96263.1.
AY692813 Genomic DNA. Translation: AAT92832.1.
BK006947 Genomic DNA. Translation: DAA10233.1.
PIRiS22284.
RefSeqiNP_014069.1. NM_001183168.1.

3D structure databases

ProteinModelPortaliP32561.
SMRiP32561. Positions 18-380.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35511. 749 interactions.
DIPiDIP-681N.
IntActiP32561. 58 interactions.
MINTiMINT-614075.

PTM databases

iPTMnetiP32561.

Proteomic databases

MaxQBiP32561.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL330C; YNL330C; YNL330C.
GeneIDi855386.
KEGGisce:YNL330C.

Organism-specific databases

EuPathDBiFungiDB:YNL330C.
SGDiS000005274. RPD3.

Phylogenomic databases

GeneTreeiENSGT00530000062889.
HOGENOMiHOG000225180.
InParanoidiP32561.
KOiK06067.
OMAiMENANSK.
OrthoDBiEOG092C1END.

Enzyme and pathway databases

BioCyciYEAST:G3O-33314-MONOMER.

Miscellaneous databases

PROiP32561.

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.
ProtoNetiSearch...

Entry informationi

Entry nameiRPD3_YEAST
AccessioniPrimary (citable) accession number: P32561
Secondary accession number(s): D6W0L7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: September 7, 2016
This is version 166 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 3850 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.