ID RPD3_YEAST Reviewed; 433 AA. AC P32561; D6W0L7; DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-1993, sequence version 1. DT 27-MAR-2024, entry version 217. DE RecName: Full=Histone deacetylase RPD3; DE EC=3.5.1.98 {ECO:0000269|PubMed:12110674}; DE AltName: Full=Transcriptional regulatory protein RPD3; GN Name=RPD3; Synonyms=MOF6, REC3, SDI2, SDS6; OrderedLocusNames=YNL330C; GN ORFNames=N0305; OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast). OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; OC Saccharomycetales; Saccharomycetaceae; Saccharomyces. OX NCBI_TaxID=559292; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION. RX PubMed=1944291; DOI=10.1128/mcb.11.12.6317-6327.1991; RA Vidal M., Gaber R.F.; RT "RPD3 encodes a second factor required to achieve maximum positive and RT negative transcriptional states in Saccharomyces cerevisiae."; RL Mol. Cell. Biol. 11:6317-6327(1991). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=ATCC 96604 / S288c / FY1679; RX PubMed=8533474; DOI=10.1002/yea.320111010; RA van Dyck L., Pascual-Ahuir A., Purnelle B., Goffeau A.; RT "An 8.2 kb DNA segment from chromosome XIV carries the RPD3 and PAS8 genes RT as well as the Saccharomyces cerevisiae homologue of the thiamine-repressed RT nmt1 gene and a chromosome III-duplicated gene for a putative aryl-alcohol RT dehydrogenase."; RL Yeast 11:987-991(1995). RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=9169873; RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F., RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.; RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its RT evolutionary implications."; RL Nature 387:93-98(1997). RN [4] RP GENOME REANNOTATION. RC STRAIN=ATCC 204508 / S288c; RX PubMed=24374639; DOI=10.1534/g3.113.008995; RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.; RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now."; RL G3 (Bethesda) 4:389-398(2014). RN [5] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=17322287; DOI=10.1101/gr.6037607; RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J., RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., RA LaBaer J.; RT "Approaching a complete repository of sequence-verified protein-encoding RT clones for Saccharomyces cerevisiae."; RL Genome Res. 17:536-543(2007). RN [6] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-201. RC STRAIN=S288c / FY1676; RX PubMed=7645347; DOI=10.1002/yea.320110606; RA Maftahi M., Nicaud J.-M., Levesque H., Gaillardin C.; RT "Sequencing analysis of a 15.4 kb fragment of yeast chromosome XIV RT identifies the RPD3, PAS8 and KRE1 loci, five new open reading frames."; RL Yeast 11:567-572(1995). RN [7] RP FUNCTION. RC STRAIN=ATCC 200060 / W303; RX PubMed=8978024; DOI=10.1093/genetics/144.4.1343; RA Vannier D., Balderes D., Shore D.; RT "Evidence that the transcriptional regulators SIN3 and RPD3, and a novel RT gene (SDS3) with similar functions, are involved in transcriptional RT silencing in S. cerevisiae."; RL Genetics 144:1343-1353(1996). RN [8] RP FUNCTION, AND IDENTIFICATION IN A HISTONE DEACETYLASE COMPLEX. RX PubMed=8962081; DOI=10.1073/pnas.93.25.14503; RA Rundlett S.E., Carmen A.A., Kobayashi R., Bavykin S., Turner B.M., RA Grunstein M.; RT "HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes RT that regulate silencing and transcription."; RL Proc. Natl. Acad. Sci. U.S.A. 93:14503-14508(1996). RN [9] RP INTERACTION WITH CPR6 AND CPR7. RX PubMed=8873448; RX DOI=10.1002/(sici)1097-0061(199608)12:10<943::aid-yea997>3.0.co;2-3; RA Duina A.A., Marsh J.A., Gaber R.F.; RT "Identification of two CyP-40-like cyclophilins in Saccharomyces RT cerevisiae, one of which is required for normal growth."; RL Yeast 12:943-952(1996). RN [10] RP IDENTIFICATION IN THE RPD3 COMPLEX. RX PubMed=9234741; DOI=10.1128/mcb.17.8.4852; RA Kasten M.M., Dorland S., Stillman D.J.; RT "A large protein complex containing the yeast Sin3p and Rpd3p RT transcriptional regulators."; RL Mol. Cell. Biol. 17:4852-4858(1997). RN [11] RP FUNCTION, AND MUTAGENESIS OF HIS-150; HIS-151 AND HIS-188. RX PubMed=9512514; DOI=10.1101/gad.12.6.797; RA Kadosh D., Struhl K.; RT "Histone deacetylase activity of Rpd3 is important for transcriptional RT repression in vivo."; RL Genes Dev. 12:797-805(1998). RN [12] RP FUNCTION OF THE RPD3 COMPLEX. RX PubMed=9710596; DOI=10.1128/mcb.18.9.5121; RA Kadosh D., Struhl K.; RT "Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex RT generates a highly localized domain of repressed chromatin in vivo."; RL Mol. Cell. Biol. 18:5121-5127(1998). RN [13] RP DEACETYLATION OF HISTONE H4. RX PubMed=9572144; DOI=10.1038/33952; RA Rundlett S.E., Carmen A.A., Suka N., Turner B.M., Grunstein M.; RT "Transcriptional repression by UME6 involves deacetylation of lysine 5 of RT histone H4 by RPD3."; RL Nature 392:831-835(1998). RN [14] RP FUNCTION. RX PubMed=10079324; DOI=10.1007/s002940050434; RA Dora E.G., Rudin N., Martell J.R., Esposito M.S., Ramirez R.M.; RT "RPD3 (REC3) mutations affect mitotic recombination in Saccharomyces RT cerevisiae."; RL Curr. Genet. 35:68-76(1999). RN [15] RP FUNCTION OF THE RPD3 COMPLEX. RX PubMed=10388812; DOI=10.1093/genetics/152.3.921; RA Sun Z.-W., Hampsey M.; RT "A general requirement for the Sin3-Rpd3 histone deacetylase complex in RT regulating silencing in Saccharomyces cerevisiae."; RL Genetics 152:921-932(1999). RN [16] RP FUNCTION. RX PubMed=10359799; DOI=10.1073/pnas.96.12.6835; RA Burgess S.M., Ajimura M., Kleckner N.; RT "GCN5-dependent histone H3 acetylation and RPD3-dependent histone H4 RT deacetylation have distinct, opposing effects on IME2 transcription, during RT meiosis and during vegetative growth, in budding yeast."; RL Proc. Natl. Acad. Sci. U.S.A. 96:6835-6840(1999). RN [17] RP INTERACTION WITH CPR1 AND ESS1. RX PubMed=10899127; DOI=10.1093/emboj/19.14.3739; RA Arevalo-Rodriguez M., Cardenas M.E., Wu X., Hanes S.D., Heitman J.; RT "Cyclophilin A and Ess1 interact with and regulate silencing by the Sin3- RT Rpd3 histone deacetylase."; RL EMBO J. 19:3739-3749(2000). RN [18] RP FUNCTION. RX PubMed=11069890; DOI=10.1101/gad.829100; RA Watson A.D., Edmondson D.G., Bone J.R., Mukai Y., Yu Y., Du W., RA Stillman D.J., Roth S.Y.; RT "Ssn6-Tup1 interacts with class I histone deacetylases required for RT repression."; RL Genes Dev. 14:2737-2744(2000). RN [19] RP FUNCTION. RX PubMed=10931932; DOI=10.1093/nar/28.16.3160; RA Elkhaimi M., Kaadige M.R., Kamath D., Jackson J.C., Biliran H. Jr., RA Lopes J.M.; RT "Combinatorial regulation of phospholipid biosynthetic gene expression by RT the UME6, SIN3 and RPD3 genes."; RL Nucleic Acids Res. 28:3160-3167(2000). RN [20] RP INTERACTION WITH CYC8. RX PubMed=12234935; DOI=10.1093/emboj/cdf498; RA Sandmeier J.J., French S., Osheim Y., Cheung W.L., Gallo C.M., Beyer A.L., RA Smith J.S.; RT "RPD3 is required for the inactivation of yeast ribosomal DNA genes in RT stationary phase."; RL EMBO J. 21:4959-4968(2002). RN [21] RP CATALYTIC ACTIVITY, DOMAIN, AND MUTAGENESIS OF TRP-322; GLU-325; GLY-327; RP LEU-328; LEU-329; VAL-332; LEU-334; ASP-335; LEU-338 AND PRO-339. RX PubMed=12110674; DOI=10.1074/jbc.m204640200; RA Adachi N., Kimura A., Horikoshi M.; RT "A conserved motif common to the histone acetyltransferase Esa1 and the RT histone deacetylase Rpd3."; RL J. Biol. Chem. 277:35688-35695(2002). RN [22] RP FUNCTION. RX PubMed=12192044; DOI=10.1128/mcb.22.18.6458-6470.2002; RA Deckert J., Struhl K.; RT "Targeted recruitment of Rpd3 histone deacetylase represses transcription RT by inhibiting recruitment of Swi/Snf, SAGA, and TATA binding protein."; RL Mol. Cell. Biol. 22:6458-6470(2002). RN [23] RP FUNCTION, AND DNA-BINDING. RX PubMed=12089521; DOI=10.1038/ng907; RA Kurdistani S.K., Robyr D., Tavazoie S., Grunstein M.; RT "Genome-wide binding map of the histone deacetylase Rpd3 in yeast."; RL Nat. Genet. 31:248-254(2002). RN [24] RP IDENTIFICATION IN THE RPD3 COMPLEX, AND IDENTIFICATION BY MASS RP SPECTROMETRY. RX PubMed=12672825; DOI=10.1074/jbc.c300036200; RA Nourani A., Howe L., Pray-Grant M.G., Workman J.L., Grant P.A., Cote J.; RT "Opposite role of yeast ING family members in p53-dependent transcriptional RT activation."; RL J. Biol. Chem. 278:19171-19175(2003). RN [25] RP FUNCTION OF THE RPD3 COMPLEX. RX PubMed=12808094; DOI=10.1128/mcb.23.13.4522-4531.2003; RA Scott K.L., Plon S.E.; RT "Loss of Sin3/Rpd3 histone deacetylase restores the DNA damage response in RT checkpoint-deficient strains of Saccharomyces cerevisiae."; RL Mol. Cell. Biol. 23:4522-4531(2003). RN [26] RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS]. RX PubMed=14562095; DOI=10.1038/nature02026; RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., RA Weissman J.S., O'Shea E.K.; RT "Global analysis of protein localization in budding yeast."; RL Nature 425:686-691(2003). RN [27] RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS]. RX PubMed=14562106; DOI=10.1038/nature02046; RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., RA O'Shea E.K., Weissman J.S.; RT "Global analysis of protein expression in yeast."; RL Nature 425:737-741(2003). RN [28] RP INTERACTION WITH HAC1, AND FUNCTION OF THE RPD3 COMPLEX. RX PubMed=15141165; DOI=10.1038/sj.emboj.7600233; RA Schroeder M., Clark R., Liu C.Y., Kaufman R.J.; RT "The unfolded protein response represses differentiation through the RPD3- RT SIN3 histone deacetylase."; RL EMBO J. 23:2281-2292(2004). RN [29] RP FUNCTION. RX PubMed=15143171; DOI=10.1128/mcb.24.11.4769-4780.2004; RA Aparicio J.G., Viggiani C.J., Gibson D.G., Aparicio O.M.; RT "The Rpd3-Sin3 histone deacetylase regulates replication timing and enables RT intra-S origin control in Saccharomyces cerevisiae."; RL Mol. Cell. Biol. 24:4769-4780(2004). RN [30] RP FUNCTION. RX PubMed=15456858; DOI=10.1128/mcb.24.20.8823-8833.2004; RA Sabet N., Volo S., Yu C., Madigan J.P., Morse R.H.; RT "Genome-wide analysis of the relationship between transcriptional RT regulation by Rpd3p and the histone H3 and H4 amino termini in budding RT yeast."; RL Mol. Cell. Biol. 24:8823-8833(2004). RN [31] RP INTERACTION WITH HOG1, AND FUNCTION OF THE RPD3 COMPLEX. RX PubMed=14737171; DOI=10.1038/nature02258; RA De Nadal E., Zapater M., Alepuz P.M., Sumoy L., Mas G., Posas F.; RT "The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive RT genes."; RL Nature 427:370-374(2004). RN [32] RP FUNCTION OF THE RPD3 COMPLEX. RX PubMed=14711989; DOI=10.1073/pnas.0304797101; RA Jazayeri A., McAinsh A.D., Jackson S.P.; RT "Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break RT repair."; RL Proc. Natl. Acad. Sci. U.S.A. 101:1644-1649(2004). RN [33] RP IDENTIFICATION IN THE RPD3C(L) COMPLEX, AND IDENTIFICATION BY MASS RP SPECTROMETRY. RX PubMed=16314178; DOI=10.1016/j.bbaexp.2005.09.005; RA Carrozza M.J., Florens L., Swanson S.K., Shia W.-J., Anderson S., Yates J., RA Washburn M.P., Workman J.L.; RT "Stable incorporation of sequence specific repressors Ash1 and Ume6 into RT the Rpd3L complex."; RL Biochim. Biophys. Acta 1731:77-87(2005). RN [34] RP IDENTIFICATION IN THE RPD3C(L) AND RPD3C(S) COMPLEXES, IDENTIFICATION BY RP MASS SPECTROMETRY, AND FUNCTION OF THE RPD3C(S) COMPLEX. RX PubMed=16286008; DOI=10.1016/j.cell.2005.10.025; RA Keogh M.-C., Kurdistani S.K., Morris S.A., Ahn S.H., Podolny V., RA Collins S.R., Schuldiner M., Chin K., Punna T., Thompson N.J., Boone C., RA Emili A., Weissman J.S., Hughes T.R., Strahl B.D., Grunstein M., RA Greenblatt J.F., Buratowski S., Krogan N.J.; RT "Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a RT repressive Rpd3 complex."; RL Cell 123:593-605(2005). RN [35] RP DISRUPTION PHENOTYPE. RX PubMed=16079223; DOI=10.1534/genetics.105.046938; RA Jambunathan N., Martinez A.W., Robert E.C., Agochukwu N.B., Ibos M.E., RA Dugas S.L., Donze D.; RT "Multiple bromodomain genes are involved in restricting the spread of RT heterochromatic silencing at the Saccharomyces cerevisiae HMR-tRNA RT boundary."; RL Genetics 171:913-922(2005). RN [36] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-394, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC STRAIN=ADR376; RX PubMed=17330950; DOI=10.1021/pr060559j; RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., RA Elias J.E., Gygi S.P.; RT "Large-scale phosphorylation analysis of alpha-factor-arrested RT Saccharomyces cerevisiae."; RL J. Proteome Res. 6:1190-1197(2007). RN [37] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-394 AND SER-408, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200; RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.; RT "A multidimensional chromatography technology for in-depth phosphoproteome RT analysis."; RL Mol. Cell. Proteomics 7:1389-1396(2008). RN [38] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-408, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=19779198; DOI=10.1126/science.1172867; RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.; RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights RT into evolution."; RL Science 325:1682-1686(2009). CC -!- FUNCTION: Catalytic component of the RPD3 histone deacetylase (HDAC) CC complexes RPD3C(L) and RPD3C(S) responsible for the deacetylation of CC lysine residues on the N-terminal part of the core histones (H2A, H2B, CC H3 and H4). Histone deacetylation plays an important role in CC transcriptional regulation, cell cycle progression, DNA damage CC response, osmotic stress response and developmental events. Is involved CC in rDNA and telomere silencing and in double strand breaks repair. CC Required for both full transcription repression and activation of many CC genes including cell type-specific genes (STE6, TY2 and HO), cell CC differentiation-specific genes (SPO13), genes that respond to external CC signals (PHO5) and TRK2. The RPD3 complexes regulate also chromosomal CC replication timing. {ECO:0000269|PubMed:10079324, CC ECO:0000269|PubMed:10359799, ECO:0000269|PubMed:10388812, CC ECO:0000269|PubMed:10931932, ECO:0000269|PubMed:11069890, CC ECO:0000269|PubMed:12089521, ECO:0000269|PubMed:12192044, CC ECO:0000269|PubMed:12808094, ECO:0000269|PubMed:14711989, CC ECO:0000269|PubMed:14737171, ECO:0000269|PubMed:15141165, CC ECO:0000269|PubMed:15143171, ECO:0000269|PubMed:15456858, CC ECO:0000269|PubMed:16286008, ECO:0000269|PubMed:1944291, CC ECO:0000269|PubMed:8962081, ECO:0000269|PubMed:8978024, CC ECO:0000269|PubMed:9512514, ECO:0000269|PubMed:9710596}. CC -!- CATALYTIC ACTIVITY: CC Reaction=H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl- CC [histone]; Xref=Rhea:RHEA:58196, Rhea:RHEA-COMP:9845, Rhea:RHEA- CC COMP:11338, ChEBI:CHEBI:15377, ChEBI:CHEBI:29969, ChEBI:CHEBI:30089, CC ChEBI:CHEBI:61930; EC=3.5.1.98; CC Evidence={ECO:0000269|PubMed:12110674}; CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:58197; CC Evidence={ECO:0000269|PubMed:12110674}; CC -!- SUBUNIT: Component of the RPD3C(L) complex composed of at least ASH1, CC CTI6, DEP1, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, UME1 and UME6. CC Component of the RPD3C(S) complex composed of at least EAF3, RCO1, CC RPD3, SIN3, and UME1. Interacts with cyclophilins CPR1, CPR6 and CPR7, CC with the kinase HOG1, and with ESS1, CYC8 and HAC1. CC {ECO:0000269|PubMed:10899127, ECO:0000269|PubMed:12234935, CC ECO:0000269|PubMed:12672825, ECO:0000269|PubMed:14737171, CC ECO:0000269|PubMed:15141165, ECO:0000269|PubMed:16286008, CC ECO:0000269|PubMed:16314178, ECO:0000269|PubMed:8873448, CC ECO:0000269|PubMed:8962081, ECO:0000269|PubMed:9234741}. CC -!- INTERACTION: CC P32561; P53691: CPR6; NbExp=2; IntAct=EBI-15864, EBI-5429; CC P32561; P47103: CPR7; NbExp=2; IntAct=EBI-15864, EBI-5436; CC P32561; P14922: CYC8; NbExp=6; IntAct=EBI-15864, EBI-18215; CC P32561; Q03214: ECM5; NbExp=5; IntAct=EBI-15864, EBI-27382; CC P32561; Q03213: HOT1; NbExp=3; IntAct=EBI-15864, EBI-27376; CC P32561; P38255: RXT2; NbExp=6; IntAct=EBI-15864, EBI-21537; CC P32561; P22579: SIN3; NbExp=10; IntAct=EBI-15864, EBI-17160; CC P32561; P16649: TUP1; NbExp=2; IntAct=EBI-15864, EBI-19654; CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus CC {ECO:0000269|PubMed:14562095}. CC -!- DOMAIN: The ESA1-RPD3 (ER) motif is common to ESA1 and RPD3 and is CC required for ESA1 histone acetyl-transferase (HAT) activity and RPD3 CC histone deacetylase (HDAC) activity. {ECO:0000269|PubMed:12110674}. CC -!- DISRUPTION PHENOTYPE: Heterochromatin spreading downstream of the CC silent mating-type locus HMR. {ECO:0000269|PubMed:16079223}. CC -!- MISCELLANEOUS: Present with 3850 molecules/cell in log phase SD medium. CC {ECO:0000269|PubMed:14562106}. CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 1 CC subfamily. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; S66438; AAB20328.1; -; Genomic_DNA. DR EMBL; X83226; CAA58228.1; -; Genomic_DNA. DR EMBL; Z46259; CAA86368.1; -; Genomic_DNA. DR EMBL; Z71605; CAA96262.1; -; Genomic_DNA. DR EMBL; Z71606; CAA96263.1; -; Genomic_DNA. DR EMBL; AY692813; AAT92832.1; -; Genomic_DNA. DR EMBL; BK006947; DAA10233.1; -; Genomic_DNA. DR PIR; S22284; S22284. DR RefSeq; NP_014069.1; NM_001183168.1. DR PDB; 7YI0; EM; 3.20 A; B=1-433. DR PDB; 7YI2; EM; 3.40 A; B=1-433. DR PDB; 7YI3; EM; 3.30 A; B=1-433. DR PDB; 7YI4; EM; 3.96 A; B=1-433. DR PDB; 7YI5; EM; 3.96 A; B=1-433. DR PDB; 8GA8; EM; 3.50 A; B/E=1-433. DR PDB; 8HPO; EM; 2.60 A; F/G=1-433. DR PDB; 8HXX; EM; 3.00 A; L=1-433. DR PDB; 8HXY; EM; 3.10 A; L=1-433. DR PDB; 8HY0; EM; 3.10 A; L=1-433. DR PDB; 8JHO; EM; 7.60 A; L=1-433. DR PDB; 8KC7; EM; 3.46 A; A=1-433. DR PDB; 8KD2; EM; 3.02 A; A=1-433. DR PDB; 8KD3; EM; 2.90 A; A=1-433. DR PDB; 8KD4; EM; 2.93 A; A=1-433. DR PDB; 8KD5; EM; 2.90 A; A=1-433. DR PDB; 8KD6; EM; 3.07 A; A=1-433. DR PDB; 8KD7; EM; 3.09 A; A=1-433. DR PDBsum; 7YI0; -. DR PDBsum; 7YI2; -. DR PDBsum; 7YI3; -. DR PDBsum; 7YI4; -. DR PDBsum; 7YI5; -. DR PDBsum; 8GA8; -. DR PDBsum; 8HPO; -. DR PDBsum; 8HXX; -. DR PDBsum; 8HXY; -. DR PDBsum; 8HY0; -. DR PDBsum; 8JHO; -. DR PDBsum; 8KC7; -. DR PDBsum; 8KD2; -. DR PDBsum; 8KD3; -. DR PDBsum; 8KD4; -. DR PDBsum; 8KD5; -. DR PDBsum; 8KD6; -. DR PDBsum; 8KD7; -. DR AlphaFoldDB; P32561; -. DR EMDB; EMD-29892; -. DR EMDB; EMD-33845; -. DR EMDB; EMD-33849; -. DR EMDB; EMD-33850; -. DR EMDB; EMD-33851; -. DR EMDB; EMD-33852; -. DR EMDB; EMD-34935; -. DR EMDB; EMD-35081; -. DR EMDB; EMD-35082; -. DR EMDB; EMD-35084; -. DR EMDB; EMD-36283; -. DR EMDB; EMD-37096; -. DR EMDB; EMD-37122; -. DR EMDB; EMD-37123; -. DR EMDB; EMD-37124; -. DR EMDB; EMD-37125; -. DR EMDB; EMD-37126; -. DR EMDB; EMD-37127; -. DR SMR; P32561; -. DR BioGRID; 35511; 1051. DR ComplexPortal; CPX-1372; SNT2C histone deacetylase complex. DR ComplexPortal; CPX-1851; RPD3S histone deacetylase complex. DR ComplexPortal; CPX-1852; RPD3L histone deacetylase complex. DR DIP; DIP-681N; -. DR IntAct; P32561; 78. DR MINT; P32561; -. DR STRING; 4932.YNL330C; -. DR iPTMnet; P32561; -. DR MaxQB; P32561; -. DR PaxDb; 4932-YNL330C; -. DR PeptideAtlas; P32561; -. DR EnsemblFungi; YNL330C_mRNA; YNL330C; YNL330C. DR GeneID; 855386; -. DR KEGG; sce:YNL330C; -. DR AGR; SGD:S000005274; -. DR SGD; S000005274; RPD3. DR VEuPathDB; FungiDB:YNL330C; -. DR eggNOG; KOG1342; Eukaryota. DR GeneTree; ENSGT00940000165542; -. DR HOGENOM; CLU_007727_7_4_1; -. DR InParanoid; P32561; -. DR OMA; GKIMEWY; -. DR OrthoDB; 1327607at2759; -. DR BioCyc; YEAST:G3O-33314-MONOMER; -. DR BRENDA; 3.5.1.98; 984. DR Reactome; R-SCE-3214815; HDACs deacetylate histones. DR Reactome; R-SCE-4551638; SUMOylation of chromatin organization proteins. DR BioGRID-ORCS; 855386; 0 hits in 10 CRISPR screens. DR PRO; PR:P32561; -. DR Proteomes; UP000002311; Chromosome XIV. DR RNAct; P32561; Protein. DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell. DR GO; GO:0000118; C:histone deacetylase complex; IDA:SGD. DR GO; GO:0034399; C:nuclear periphery; IDA:SGD. DR GO; GO:0005634; C:nucleus; IBA:GO_Central. DR GO; GO:0033698; C:Rpd3L complex; IDA:SGD. DR GO; GO:0070210; C:Rpd3L-Expanded complex; HDA:SGD. DR GO; GO:0032221; C:Rpd3S complex; IDA:SGD. DR GO; GO:0070822; C:Sin3-type complex; IDA:SGD. DR GO; GO:0070211; C:Snt2C complex; IPI:ComplexPortal. DR GO; GO:0004407; F:histone deacetylase activity; IDA:SGD. DR GO; GO:0003713; F:transcription coactivator activity; IMP:SGD. DR GO; GO:0003714; F:transcription corepressor activity; IMP:SGD. DR GO; GO:0061188; P:negative regulation of rDNA heterochromatin formation; IMP:SGD. DR GO; GO:0045128; P:negative regulation of reciprocal meiotic recombination; IMP:SGD. DR GO; GO:0061186; P:negative regulation of silent mating-type cassette heterochromatin formation; IMP:SGD. DR GO; GO:0016479; P:negative regulation of transcription by RNA polymerase I; IMP:SGD. DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD. DR GO; GO:0044804; P:nucleophagy; IMP:SGD. DR GO; GO:0006334; P:nucleosome assembly; NAS:ComplexPortal. DR GO; GO:0016239; P:positive regulation of macroautophagy; IMP:SGD. DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD. DR GO; GO:0034503; P:protein localization to nucleolar rDNA repeats; IMP:SGD. DR GO; GO:0070550; P:rDNA chromatin condensation; IMP:SGD. DR GO; GO:0030174; P:regulation of DNA-templated DNA replication initiation; IMP:SGD. DR GO; GO:0006355; P:regulation of DNA-templated transcription; NAS:ComplexPortal. DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IGI:SGD. DR GO; GO:0006979; P:response to oxidative stress; NAS:ComplexPortal. DR GO; GO:0006368; P:transcription elongation by RNA polymerase II; IGI:SGD. DR CDD; cd10004; RPD3-like; 1. DR Gene3D; 3.40.800.20; Histone deacetylase domain; 1. DR InterPro; IPR000286; His_deacetylse. DR InterPro; IPR003084; His_deacetylse_1. DR InterPro; IPR023801; His_deacetylse_dom. DR InterPro; IPR037138; His_deacetylse_dom_sf. DR InterPro; IPR023696; Ureohydrolase_dom_sf. DR PANTHER; PTHR10625:SF13; HISTONE DEACETYLASE HDAC1; 1. DR PANTHER; PTHR10625; HISTONE DEACETYLASE HDAC1-RELATED; 1. DR Pfam; PF00850; Hist_deacetyl; 1. DR PIRSF; PIRSF037913; His_deacetylse_1; 1. DR PRINTS; PR01270; HDASUPER. DR PRINTS; PR01271; HISDACETLASE. DR SUPFAM; SSF52768; Arginase/deacetylase; 1. PE 1: Evidence at protein level; KW 3D-structure; Chromatin regulator; Cytoplasm; Hydrolase; Nucleus; KW Phosphoprotein; Reference proteome; Repressor; Transcription; KW Transcription regulation. FT CHAIN 1..433 FT /note="Histone deacetylase RPD3" FT /id="PRO_0000114724" FT REGION 19..331 FT /note="Histone deacetylase" FT REGION 388..433 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOTIF 320..340 FT /note="ESA1-RPD3 motif" FT COMPBIAS 408..433 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 151 FT /evidence="ECO:0000305" FT MOD_RES 394 FT /note="Phosphothreonine" FT /evidence="ECO:0007744|PubMed:17330950, FT ECO:0007744|PubMed:18407956" FT MOD_RES 408 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:18407956, FT ECO:0007744|PubMed:19779198" FT MUTAGEN 150 FT /note="H->A: Impairs histone deacetylase activity and FT transcription repression." FT /evidence="ECO:0000269|PubMed:9512514" FT MUTAGEN 151 FT /note="H->A: Impairs histone deacetylase activity and FT transcription repression." FT /evidence="ECO:0000269|PubMed:9512514" FT MUTAGEN 188 FT /note="H->A: Impairs histone deacetylase activity and FT transcription repression." FT /evidence="ECO:0000269|PubMed:9512514" FT MUTAGEN 322 FT /note="W->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 325 FT /note="E->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 327 FT /note="G->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 328 FT /note="L->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 329 FT /note="L->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 332 FT /note="V->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 334 FT /note="L->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 335 FT /note="D->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 338 FT /note="L->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT MUTAGEN 339 FT /note="P->A: Strongly reduces HDAC activity." FT /evidence="ECO:0000269|PubMed:12110674" FT STRAND 21..24 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 29..31 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 43..54 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 57..60 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 61..64 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 71..74 FT /evidence="ECO:0007829|PDB:8HPO" FT TURN 75..77 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 80..88 FT /evidence="ECO:0007829|PDB:8HPO" FT TURN 91..93 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 94..97 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 98..103 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 107..110 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 116..135 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 140..144 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 154..156 FT /evidence="ECO:0007829|PDB:7YI0" FT TURN 158..160 FT /evidence="ECO:0007829|PDB:8KD2" FT STRAND 161..163 FT /evidence="ECO:0007829|PDB:8HXX" FT HELIX 165..174 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 180..184 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 186..188 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 191..196 FT /evidence="ECO:0007829|PDB:8HPO" FT TURN 197..199 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 201..210 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 212..214 FT /evidence="ECO:0007829|PDB:7YI3" FT HELIX 227..229 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 233..238 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 244..261 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 267..270 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 273..275 FT /evidence="ECO:0007829|PDB:8HXX" FT STRAND 276..278 FT /evidence="ECO:0007829|PDB:8KD2" FT HELIX 288..299 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 305..308 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 315..329 FT /evidence="ECO:0007829|PDB:8HPO" FT STRAND 345..347 FT /evidence="ECO:0007829|PDB:8HPO" FT TURN 348..350 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 366..379 FT /evidence="ECO:0007829|PDB:8HPO" FT TURN 380..382 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 405..407 FT /evidence="ECO:0007829|PDB:8KD6" SQ SEQUENCE 433 AA; 48904 MW; 34FFD72A7E7425DB CRC64; MVYEATPFDP ITVKPSDKRR VAYFYDADVG NYAYGAGHPM KPHRIRMAHS LIMNYGLYKK MEIYRAKPAT KQEMCQFHTD EYIDFLSRVT PDNLEMFKRE SVKFNVGDDC PVFDGLYEYC SISGGGSMEG AARLNRGKCD VAVNYAGGLH HAKKSEASGF CYLNDIVLGI IELLRYHPRV LYIDIDVHHG DGVEEAFYTT DRVMTCSFHK YGEFFPGTGE LRDIGVGAGK NYAVNVPLRD GIDDATYRSV FEPVIKKIME WYQPSAVVLQ CGGDSLSGDR LGCFNLSMEG HANCVNYVKS FGIPMMVVGG GGYTMRNVAR TWCFETGLLN NVVLDKDLPY NEYYEYYGPD YKLSVRPSNM FNVNTPEYLD KVMTNIFANL ENTKYAPSVQ LNHTPRDAED LGDVEEDSAE AKDTKGGSQY ARDLHVEHDN EFY //