P32561 · RPD3_YEAST
- ProteinHistone deacetylase RPD3
- GeneRPD3
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids433 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
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.
Miscellaneous
Present with 3850 molecules/cell in log phase SD medium.
Catalytic activity
- H2O + N6-acetyl-L-lysyl-[histone] = acetate + L-lysyl-[histone]This reaction proceeds in the forward direction.
Features
Showing features for active site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Active site | 151 | |||||
Sequence: H |
GO annotations
Keywords
- Molecular function
- Biological process
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameHistone deacetylase RPD3
- EC number
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageEukaryota > Fungi > Dikarya > Ascomycota > Saccharomycotina > Saccharomycetes > Saccharomycetales > Saccharomycetaceae > Saccharomyces
Accessions
- Primary accessionP32561
- Secondary accessions
Proteomes
Organism-specific databases
Phenotypes & Variants
Disruption phenotype
Heterochromatin spreading downstream of the silent mating-type locus HMR.
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 150 | Impairs histone deacetylase activity and transcription repression. | ||||
Sequence: H → A | ||||||
Mutagenesis | 151 | Impairs histone deacetylase activity and transcription repression. | ||||
Sequence: H → A | ||||||
Mutagenesis | 188 | Impairs histone deacetylase activity and transcription repression. | ||||
Sequence: H → A | ||||||
Mutagenesis | 322 | Strongly reduces HDAC activity. | ||||
Sequence: W → A | ||||||
Mutagenesis | 325 | Strongly reduces HDAC activity. | ||||
Sequence: E → A | ||||||
Mutagenesis | 327 | Strongly reduces HDAC activity. | ||||
Sequence: G → A | ||||||
Mutagenesis | 328 | Strongly reduces HDAC activity. | ||||
Sequence: L → A | ||||||
Mutagenesis | 329 | Strongly reduces HDAC activity. | ||||
Sequence: L → A | ||||||
Mutagenesis | 332 | Strongly reduces HDAC activity. | ||||
Sequence: V → A | ||||||
Mutagenesis | 334 | Strongly reduces HDAC activity. | ||||
Sequence: L → A | ||||||
Mutagenesis | 335 | Strongly reduces HDAC activity. | ||||
Sequence: D → A | ||||||
Mutagenesis | 338 | Strongly reduces HDAC activity. | ||||
Sequence: L → A | ||||||
Mutagenesis | 339 | Strongly reduces HDAC activity. | ||||
Sequence: P → A |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 5 variants from UniProt as well as other sources including ClinVar and dbSNP.
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000114724 | 1-433 | Histone deacetylase RPD3 | |||
Sequence: MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY | ||||||
Modified residue | 394 | Phosphothreonine | ||||
Sequence: T | ||||||
Modified residue | 408 | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
Proteomic databases
PTM databases
Interaction
Subunit
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.
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P32561 | CPR6 P53691 | 2 | EBI-15864, EBI-5429 | |
BINARY | P32561 | CPR7 P47103 | 2 | EBI-15864, EBI-5436 | |
BINARY | P32561 | CYC8 P14922 | 6 | EBI-15864, EBI-18215 | |
BINARY | P32561 | ECM5 Q03214 | 5 | EBI-15864, EBI-27382 | |
BINARY | P32561 | HOT1 Q03213 | 3 | EBI-15864, EBI-27376 | |
BINARY | P32561 | RXT2 P38255 | 7 | EBI-15864, EBI-21537 | |
BINARY | P32561 | SIN3 P22579 | 11 | EBI-15864, EBI-17160 | |
BINARY | P32561 | TUP1 P16649 | 2 | EBI-15864, EBI-19654 |
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Features
Showing features for region, motif, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 19-331 | Histone deacetylase | ||||
Sequence: RRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNN | ||||||
Motif | 320-340 | ESA1-RPD3 motif | ||||
Sequence: RTWCFETGLLNNVVLDKDLPY | ||||||
Region | 388-433 | Disordered | ||||
Sequence: SVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY | ||||||
Compositional bias | 408-433 | Basic and acidic residues | ||||
Sequence: SAEAKDTKGGSQYARDLHVEHDNEFY |
Domain
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.
Sequence similarities
Belongs to the histone deacetylase family. HD type 1 subfamily.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length433
- Mass (Da)48,904
- Last updated1993-10-01 v1
- Checksum34FFD72A7E7425DB
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 408-433 | Basic and acidic residues | ||||
Sequence: SAEAKDTKGGSQYARDLHVEHDNEFY |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
S66438 EMBL· GenBank· DDBJ | AAB20328.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
X83226 EMBL· GenBank· DDBJ | CAA58228.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
Z46259 EMBL· GenBank· DDBJ | CAA86368.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
Z71605 EMBL· GenBank· DDBJ | CAA96262.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
Z71606 EMBL· GenBank· DDBJ | CAA96263.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AY692813 EMBL· GenBank· DDBJ | AAT92832.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BK006947 EMBL· GenBank· DDBJ | DAA10233.1 EMBL· GenBank· DDBJ | Genomic DNA |