ID   DEP1_YEAST              Reviewed;         405 AA.
AC   P31385; D6VPK5; Q86ZS5;
DT   01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT   27-JUL-2011, sequence version 3.
DT   04-NOV-2026, entry version 182.
DE   RecName: Full=Transcriptional regulatory protein DEP1;
GN   Name=DEP1; Synonyms=FUN54; OrderedLocusNames=YAL013W;
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].
RC   STRAIN=ATCC 204511 / S288c / AB972;
RX   PubMed=8458570; DOI=10.1139/g93-005;
RA   Ouellette B.F.F., Clark M.W., Keng T., Storms R.K., Zhong W.-W., Zeng B.,
RA   Fortin N., Delaney S., Barton A.B., Kaback D.B., Bussey H.;
RT   "Sequencing of chromosome I from Saccharomyces cerevisiae: analysis of a 32
RT   kb region between the LTE1 and SPO7 genes.";
RL   Genome 36:32-42(1993).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=8144453; DOI=10.1128/jb.176.7.1872-1880.1994;
RA   Barton A.B., Kaback D.B.;
RT   "Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae:
RT   analysis of the genes in the FUN38-MAK16-SPO7 region.";
RL   J. Bacteriol. 176:1872-1880(1994).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=7731988; DOI=10.1073/pnas.92.9.3809;
RA   Bussey H., Kaback D.B., Zhong W.-W., Vo D.H., Clark M.W., Fortin N.,
RA   Hall J., Ouellette B.F.F., Keng T., Barton A.B., Su Y., Davies C.J.,
RA   Storms R.K.;
RT   "The nucleotide sequence of chromosome I from Saccharomyces cerevisiae.";
RL   Proc. Natl. Acad. Sci. U.S.A. 92:3809-3813(1995).
RN   [4]
RP   SEQUENCE REVISION TO C-TERMINUS.
RA   Sethuraman A., Cherry J.M.;
RL   Submitted (DEC-2003) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   GENOME REANNOTATION, AND SEQUENCE REVISION TO 405.
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   [6]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 302-361.
RC   STRAIN=ATCC 204511 / S288c / AB972;
RX   PubMed=12844361; DOI=10.1186/gb-2003-4-7-r45;
RA   Brachat S., Dietrich F.S., Voegeli S., Zhang Z., Stuart L., Lerch A.,
RA   Gates K., Gaffney T.D., Philippsen P.;
RT   "Reinvestigation of the Saccharomyces cerevisiae genome annotation by
RT   comparison to the genome of a related fungus: Ashbya gossypii.";
RL   Genome Biol. 4:R45.1-R45.13(2003).
RN   [7]
RP   FUNCTION.
RX   PubMed=8056324; DOI=10.1093/genetics/137.1.55;
RA   Lamping E., Lueckl J., Paltauf F., Henry S.A., Kohlwein S.D.;
RT   "Isolation and characterization of a mutant of Saccharomyces cerevisiae
RT   with pleiotropic deficiencies in transcriptional activation and
RT   repression.";
RL   Genetics 137:55-65(1994).
RN   [8]
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   [9]
RP   IDENTIFICATION IN THE RPD3C(L) COMPLEX, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
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   [10]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-120 AND SER-370, 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   [11]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-56 AND SER-120, AND
RP   IDENTIFICATION BY 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: Component of the RPD3C(L) histone deacetylase complex (HDAC)
CC       responsible for the deacetylation of lysine residues on the N-terminal
CC       part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation
CC       gives a tag for epigenetic repression and plays an important role in
CC       transcriptional regulation, cell cycle progression and developmental
CC       events. {ECO:0000269|PubMed:8056324}.
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       {ECO:0000269|PubMed:16286008, ECO:0000269|PubMed:16314178}.
CC   -!- INTERACTION:
CC       P31385; P34233: ASH1; NbExp=2; IntAct=EBI-5755, EBI-3027;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAC04944.2; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; L05146; AAC04944.2; ALT_FRAME; Genomic_DNA.
DR   EMBL; AY260888; AAP21756.1; -; Genomic_DNA.
DR   EMBL; BK006935; DAA06975.2; -; Genomic_DNA.
DR   PIR; S36721; S36721.
DR   RefSeq; NP_009389.3; NM_001178158.2.
DR   PDB; 8GA8; EM; 3.50 A; G=1-405.
DR   PDB; 8HPO; EM; 2.60 A; H=1-405.
DR   PDB; 9V2V; EM; 3.00 A; E=177-295.
DR   PDB; 9V2W; EM; 3.40 A; E=177-295.
DR   AlphaFoldDB; P31385; -.
DR   EMDB; EMD-29892; -.
DR   EMDB; EMD-34935; -.
DR   EMDB; EMD-64741; -.
DR   EMDB; EMD-64742; -.
DR   SMR; P31385; -.
DR   BioGRID; 31753; 897.
DR   ComplexPortal; CPX-1852; RPD3L histone deacetylase complex.
DR   DIP; DIP-5922N; -.
DR   FunCoup; P31385; 200.
DR   IntAct; P31385; 10.
DR   STRING; 4932.YAL013W; -.
DR   iPTMnet; P31385; -.
DR   PaxDb; 4932-YAL013W; -.
DR   PeptideAtlas; P31385; -.
DR   EnsemblFungi; YAL013W_mRNA; YAL013W; YAL013W.
DR   GeneID; 851220; -.
DR   KEGG; sce:YAL013W; -.
DR   AGR; SGD:S000000011; -.
DR   SGD; S000000011; DEP1.
DR   VEuPathDB; FungiDB:YAL013W; -.
DR   eggNOG; ENOG502S36P; Eukaryota.
DR   HOGENOM; CLU_028822_0_0_1; -.
DR   InParanoid; P31385; -.
DR   OMA; ACESIEY; -.
DR   OrthoDB; 20886at2759; -.
DR   BioCyc; YEAST:G3O-28825-MONOMER; -.
DR   Reactome; R-SCE-3214815; HDACs deacetylate histones.
DR   BioGRID-ORCS; 851220; 6 hits in 10 CRISPR screens.
DR   PRO; PR:P31385; -.
DR   Proteomes; UP000002311; Chromosome I.
DR   RNAct; P31385; protein.
DR   GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0033698; C:Rpd3L complex; IDA:SGD.
DR   GO; GO:0070210; C:Rpd3L-Expanded complex; HDA:SGD.
DR   GO; GO:0070822; C:Sin3-type complex; IBA:GO_Central.
DR   GO; GO:0042826; F:histone deacetylase binding; IBA:GO_Central.
DR   GO; GO:0034605; P:cellular response to heat; IMP:SGD.
DR   GO; GO:1900089; P:negative regulation of inositol biosynthetic process; IMP:SGD.
DR   GO; GO:2001246; P:negative regulation of phosphatidylcholine biosynthetic process; IMP:SGD.
DR   GO; GO:1900469; P:negative regulation of phosphatidylserine biosynthetic process; IMP:SGD.
DR   GO; GO:0061188; P:negative regulation of rDNA heterochromatin formation; IMP:SGD.
DR   GO; GO:0061186; P:negative regulation of silent mating-type cassette heterochromatin formation; IMP:SGD.
DR   GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR   GO; GO:0006334; P:nucleosome assembly; NAS:ComplexPortal.
DR   GO; GO:1900090; P:positive regulation of inositol biosynthetic process; IMP:SGD.
DR   GO; GO:2001247; P:positive regulation of phosphatidylcholine biosynthetic process; IMP:SGD.
DR   GO; GO:1900470; P:positive regulation of phosphatidylserine biosynthetic process; IMP:SGD.
DR   GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; 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; IMP:SGD.
DR   InterPro; IPR013907; Sds3.
DR   PANTHER; PTHR21964; BREAST CANCER METASTASIS-SUPPRESSOR 1; 1.
DR   Pfam; PF08598; Sds3; 1.
DR   SMART; SM01401; Sds3; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Chromatin regulator; Cytoplasm; Nucleus; Phosphoprotein;
KW   Reference proteome; Repressor; Transcription; Transcription regulation.
FT   CHAIN           1..405
FT                   /note="Transcriptional regulatory protein DEP1"
FT                   /id="PRO_0000079864"
FT   REGION          1..26
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          49..171
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..12
FT                   /note="Low complexity"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        86..108
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        116..139
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        140..157
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         56
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         120
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         370
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   HELIX           172..215
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   TURN            216..218
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   TURN            221..225
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   TURN            228..230
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   HELIX           231..294
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   TURN            315..321
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   HELIX           337..341
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   STRAND          348..350
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   HELIX           356..379
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   HELIX           386..389
FT                   /evidence="ECO:0007829|PDB:8HPO"
FT   HELIX           394..402
FT                   /evidence="ECO:0007829|PDB:8HPO"
SQ   SEQUENCE   405 AA;  46978 MW;  3A67F052C3920A22 CRC64;
     MSQQTPQESE QTTAKEQDLD QESVLSNIDF NTDLNHNLNL SEYCISSDAG TEKMDSDEEK
     SLANLPELKY APKLSSLVKQ ETLTESLKRP HEDEKEAIDE AKKMKVPGEN EDESKEEEKS
     QELEEAIDSK EKSTDARDEQ GDEGDNEEEN NEEDNENENE HTAPPALVMP SPIEMEEQRM
     TALKEITDIE YKFAQLRQKL YDNQLVRLQT ELQMCLEGSH PELQVYYSKI AAIRDYKLHR
     AYQRQKYELS CINTETIATR TFIHQDFHKK VTDLRARLLN RTTQTWYDIN KERRDMDIVI
     PDVNYHVPIK LDNKTLSCIT GYASAAQLCY PGEPVAEDLA CESIEYRYRA NPVDKLEVIV
     DRMRLNNEIS DLEGLRKYFH SFPGAPELNP LRDSEINDDF HQWAQ
//