DEP1_YEAST
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 03-AUG-2022, entry version 165.
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 -!- 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 AlphaFoldDB; P31385; -.
DR SMR; P31385; -.
DR BioGRID; 31753; 887.
DR ComplexPortal; CPX-1852; RPD3L histone deacetylase complex.
DR DIP; DIP-5922N; -.
DR IntAct; P31385; 7.
DR MINT; P31385; -.
DR STRING; 4932.YAL013W; -.
DR iPTMnet; P31385; -.
DR MaxQB; P31385; -.
DR PaxDb; P31385; -.
DR PRIDE; P31385; -.
DR EnsemblFungi; YAL013W_mRNA; YAL013W; YAL013W.
DR GeneID; 851220; -.
DR KEGG; sce:YAL013W; -.
DR SGD; S000000011; DEP1.
DR VEuPathDB; FungiDB:YAL013W; -.
DR eggNOG; ENOG502S36P; Eukaryota.
DR HOGENOM; CLU_028822_0_0_1; -.
DR InParanoid; P31385; -.
DR OMA; ATRCFIH; -.
DR BioCyc; YEAST:G3O-28825-MON; -.
DR Reactome; R-SCE-3214815; HDACs deacetylate histones.
DR PRO; PR:P31385; -.
DR Proteomes; UP000002311; Chromosome I.
DR RNAct; P31385; protein.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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:0070822; C:Sin3-type complex; IBA:GO_Central.
DR GO; GO:0042826; F:histone deacetylase binding; IBA:GO_Central.
DR GO; GO:0016575; P:histone deacetylation; 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:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0006334; P:nucleosome assembly; IC:ComplexPortal.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0061408; P:positive regulation of transcription from RNA polymerase II promoter in response to heat stress; 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; PTHR21964; 2.
DR Pfam; PF08598; Sds3; 1.
DR SMART; SM01401; Sds3; 1.
PE 1: Evidence at protein level;
KW 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 84..139
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 140..156
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"
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
