CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-006165
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone deacetylase RPD3 
Protein Synonyms/Alias
 Transcriptional regulatory protein RPD3 
Gene Name
 RPD3 
Gene Synonyms/Alias
 MOF6; REC3; SDI2; SDS6; YNL330C; N0305 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
412EEDSAEAKDTKGGSQubiquitination[1]
Reference
 [1] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301] 
Functional Description
 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. 
Sequence Annotation
 REGION 19 331 Histone deacetylase.
 MOTIF 320 340 ESA1-RPD3 motif.
 ACT_SITE 151 151 Probable.
 MOD_RES 394 394 Phosphothreonine.
 MOD_RES 408 408 Phosphoserine.  
Keyword
 Chromatin regulator; Complete proteome; Cytoplasm; Hydrolase; Nucleus; Phosphoprotein; Reference proteome; Repressor; Transcription; Transcription regulation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 433 AA 
Protein Sequence
MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK 60
MEIYRAKPAT KQEMCQFHTD EYIDFLSRVT PDNLEMFKRE SVKFNVGDDC PVFDGLYEYC 120
SISGGGSMEG AARLNRGKCD VAVNYAGGLH HAKKSEASGF CYLNDIVLGI IELLRYHPRV 180
LYIDIDVHHG DGVEEAFYTT DRVMTCSFHK YGEFFPGTGE LRDIGVGAGK NYAVNVPLRD 240
GIDDATYRSV FEPVIKKIME WYQPSAVVLQ CGGDSLSGDR LGCFNLSMEG HANCVNYVKS 300
FGIPMMVVGG GGYTMRNVAR TWCFETGLLN NVVLDKDLPY NEYYEYYGPD YKLSVRPSNM 360
FNVNTPEYLD KVMTNIFANL ENTKYAPSVQ LNHTPRDAED LGDVEEDSAE AKDTKGGSQY 420
ARDLHVEHDN EFY 433 
Gene Ontology
 GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
 GO:0033698; C:Rpd3L complex; IDA:SGD.
 GO:0070210; C:Rpd3L-Expanded complex; IDA:SGD.
 GO:0032221; C:Rpd3S complex; IDA:SGD.
 GO:0070211; C:Snt2C complex; IDA:SGD.
 GO:0004407; F:histone deacetylase activity; IDA:SGD.
 GO:0032041; F:NAD-dependent histone deacetylase activity (H3-K14 specific); IEA:EC.
 GO:0097372; F:NAD-dependent histone deacetylase activity (H3-K18 specific); IEA:EC.
 GO:0046969; F:NAD-dependent histone deacetylase activity (H3-K9 specific); IEA:EC.
 GO:0046970; F:NAD-dependent histone deacetylase activity (H4-K16 specific); IEA:EC.
 GO:0003713; F:transcription coactivator activity; IMP:SGD.
 GO:0003714; F:transcription corepressor activity; IMP:SGD.
 GO:0070932; P:histone H3 deacetylation; IMP:SGD.
 GO:0070933; P:histone H4 deacetylation; IMP:SGD.
 GO:0061188; P:negative regulation of chromatin silencing at rDNA; IMP:SGD.
 GO:0061186; P:negative regulation of chromatin silencing at silent mating-type cassette; IMP:SGD.
 GO:0031939; P:negative regulation of chromatin silencing at telomere; IDA:SGD.
 GO:0045128; P:negative regulation of reciprocal meiotic recombination; IMP:SGD.
 GO:0051038; P:negative regulation of transcription during meiosis; IMP:SGD.
 GO:0016479; P:negative regulation of transcription from RNA polymerase I promoter; IMP:SGD.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:SGD.
 GO:0016239; P:positive regulation of macroautophagy; IMP:SGD.
 GO:0061408; P:positive regulation of transcription from RNA polymerase II promoter in response to heat stress; IMP:SGD.
 GO:0034503; P:protein localization to nucleolar rDNA repeats; IMP:SGD.
 GO:0030174; P:regulation of DNA-dependent DNA replication initiation; IMP:SGD.
 GO:0034401; P:regulation of transcription by chromatin organization; IMP:SGD.
 GO:0000083; P:regulation of transcription involved in G1/S phase of mitotic cell cycle; IGI:SGD.
 GO:0000117; P:regulation of transcription involved in G2/M-phase of mitotic cell cycle; IGI:SGD.
 GO:0000115; P:regulation of transcription involved in S phase of mitotic cell cycle; IMP:SGD.
 GO:0001302; P:replicative cell aging; IMP:SGD.
 GO:0006368; P:transcription elongation from RNA polymerase II promoter; IGI:SGD. 
Interpro
 IPR000286; His_deacetylse.
 IPR003084; His_deacetylse_1.
 IPR023801; His_deacetylse_dom. 
Pfam
 PF00850; Hist_deacetyl 
SMART
  
PROSITE
  
PRINTS
 PR01270; HDASUPER.
 PR01271; HISDACETLASE.