RPD3_YEAST
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 03-AUG-2022, entry version 208.
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}.
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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 AlphaFoldDB; P32561; -.
DR SMR; P32561; -.
DR BioGRID; 35511; 1038.
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; P32561; -.
DR PRIDE; P32561; -.
DR EnsemblFungi; YNL330C_mRNA; YNL330C; YNL330C.
DR GeneID; 855386; -.
DR KEGG; sce:YNL330C; -.
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; WAIHTAT; -.
DR BioCyc; YEAST:G3O-33314-MON; -.
DR BRENDA; 3.5.1.98; 984.
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; IC:ComplexPortal.
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/Clr6-CII 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:0044804; P:autophagy of nucleus; IMP:SGD.
DR GO; GO:0016575; P:histone deacetylation; IEA:InterPro.
DR GO; GO:0045128; P:negative regulation of reciprocal meiotic recombination; IMP:SGD.
DR GO; GO:0061188; P:negative regulation of ribosomal DNA heterochromatin assembly; IMP:SGD.
DR GO; GO:0061186; P:negative regulation of silent mating-type cassette heterochromatin assembly; 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:0051038; P:negative regulation of transcription involved in meiotic cell cycle; IMP:SGD.
DR GO; GO:0006334; P:nucleosome assembly; IC: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:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0000083; P:regulation of transcription involved in G1/S transition of mitotic cell cycle; IGI:SGD.
DR GO; GO:0000117; P:regulation of transcription involved in G2/M transition of mitotic cell cycle; IGI:SGD.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IC:ComplexPortal.
DR GO; GO:0006979; P:response to oxidative stress; IC:ComplexPortal.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IGI:SGD.
DR GO; GO:0061587; P:transfer RNA gene-mediated silencing; IMP:SGD.
DR Gene3D; 3.40.800.20; -; 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 Pfam; PF00850; Hist_deacetyl; 1.
DR PIRSF; PIRSF037913; His_deacetylse_1; 1.
DR PRINTS; PR01270; HDASUPER.
DR PRINTS; PR01271; HISDACETLASE.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Cytoplasm; Hydrolase; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; Transcription; 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: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 325
FT /note="E->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 327
FT /note="G->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 328
FT /note="L->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 329
FT /note="L->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 332
FT /note="V->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 334
FT /note="L->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 335
FT /note="D->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 338
FT /note="L->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
FT MUTAGEN 339
FT /note="P->A: Reduces strongly HDAC activity."
FT /evidence="ECO:0000269|PubMed:12110674"
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
