ID   TOD6_YEAST              Reviewed;         525 AA.
AC   P34219; D6VPU6;
DT   01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1994, sequence version 1.
DT   27-MAR-2024, entry version 174.
DE   RecName: Full=Transcriptional regulatory protein TOD6;
DE   AltName: Full=PAC-binding factor 1;
DE   AltName: Full=Twin of DOT6;
GN   Name=TOD6; Synonyms=PBF1; OrderedLocusNames=YBL054W;
GN   ORFNames=YBL0509, YBL0513;
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 204508 / S288c;
RX   PubMed=8154187; DOI=10.1002/yea.320091210;
RA   Scherens B., el Bakkoury M., Vierendeels F., Dubois E., Messenguy F.;
RT   "Sequencing and functional analysis of a 32,560 bp segment on the left arm
RT   of yeast chromosome II. Identification of 26 open reading frames, including
RT   the KIP1 and SEC17 genes.";
RL   Yeast 9:1355-1371(1993).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA   Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA   Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA   Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA   Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA   Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA   Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA   Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA   Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA   Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA   Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA   Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA   Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA   Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA   Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA   Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA   Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA   Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA   Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA   Mewes H.-W., Kleine K.;
RT   "Complete DNA sequence of yeast chromosome II.";
RL   EMBO J. 13:5795-5809(1994).
RN   [3]
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   [4]
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   [5]
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   [6]
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   [7]
RP   FUNCTION.
RX   PubMed=16544271; DOI=10.1002/yea.1353;
RA   Wade C.H., Umbarger M.A., McAlear M.A.;
RT   "The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains
RT   over 200 genes.";
RL   Yeast 23:293-306(2006).
RN   [8]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-366, 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   [9]
RP   IDENTIFICATION IN THE RPD3(L) COMPLEX, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
RX   PubMed=19040720; DOI=10.1186/gb-2008-9-11-r167;
RA   Shevchenko A., Roguev A., Schaft D., Buchanan L., Habermann B., Sakalar C.,
RA   Thomas H., Krogan N.J., Shevchenko A., Stewart A.F.;
RT   "Chromatin Central: towards the comparative proteome by accurate mapping of
RT   the yeast proteomic environment.";
RL   Genome Biol. 9:R167.1-R167.22(2008).
RN   [10]
RP   DNA-BINDING.
RX   PubMed=19111667; DOI=10.1016/j.molcel.2008.11.020;
RA   Badis G., Chan E.T., van Bakel H., Pena-Castillo L., Tillo D., Tsui K.,
RA   Carlson C.D., Gossett A.J., Hasinoff M.J., Warren C.L., Gebbia M.,
RA   Talukder S., Yang A., Mnaimneh S., Terterov D., Coburn D., Li Yeo A.,
RA   Yeo Z.X., Clarke N.D., Lieb J.D., Ansari A.Z., Nislow C., Hughes T.R.;
RT   "A library of yeast transcription factor motifs reveals a widespread
RT   function for Rsc3 in targeting nucleosome exclusion at promoters.";
RL   Mol. Cell 32:878-887(2008).
RN   [11]
RP   FUNCTION.
RX   PubMed=19158363; DOI=10.1101/gr.090233.108;
RA   Zhu C., Byers K.J., McCord R.P., Shi Z., Berger M.F., Newburger D.E.,
RA   Saulrieta K., Smith Z., Shah M.V., Radhakrishnan M., Philippakis A.A.,
RA   Hu Y., De Masi F., Pacek M., Rolfs A., Murthy T.V.S., Labaer J.,
RA   Bulyk M.L.;
RT   "High-resolution DNA-binding specificity analysis of yeast transcription
RT   factors.";
RL   Genome Res. 19:556-566(2009).
RN   [12]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-280; SER-333 AND SER-341, 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 RPD3 histone deacetylase complex RPD3C(L)
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. TOD6 binds to sequences containing the core CGATG, which
CC       resembles the PAC (Polymerase A and C) motif.
CC       {ECO:0000269|PubMed:16544271, ECO:0000269|PubMed:19158363}.
CC   -!- SUBUNIT: Component of the RPD3C(L) complex composed of at least ASH1,
CC       CTI6, DEP1, DOT6, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, TOD6;
CC       UME1 and UME6. {ECO:0000269|PubMed:19040720}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC       {ECO:0000255|PROSITE-ProRule:PRU00625, ECO:0000269|PubMed:14562095}.
CC   -!- MISCELLANEOUS: Present with 830 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the DOT6 family. {ECO:0000305}.
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DR   EMBL; Z23261; CAA80793.1; -; Genomic_DNA.
DR   EMBL; Z35815; CAA84874.1; -; Genomic_DNA.
DR   EMBL; AY692625; AAT92644.1; -; Genomic_DNA.
DR   EMBL; BK006936; DAA07066.1; -; Genomic_DNA.
DR   PIR; S39834; S39834.
DR   RefSeq; NP_009499.1; NM_001178294.1.
DR   AlphaFoldDB; P34219; -.
DR   SMR; P34219; -.
DR   BioGRID; 32645; 86.
DR   DIP; DIP-2636N; -.
DR   IntAct; P34219; 3.
DR   MINT; P34219; -.
DR   STRING; 4932.YBL054W; -.
DR   iPTMnet; P34219; -.
DR   MaxQB; P34219; -.
DR   PaxDb; 4932-YBL054W; -.
DR   PeptideAtlas; P34219; -.
DR   TopDownProteomics; P34219; -.
DR   EnsemblFungi; YBL054W_mRNA; YBL054W; YBL054W.
DR   GeneID; 852226; -.
DR   KEGG; sce:YBL054W; -.
DR   AGR; SGD:S000000150; -.
DR   SGD; S000000150; TOD6.
DR   VEuPathDB; FungiDB:YBL054W; -.
DR   eggNOG; ENOG502RXV1; Eukaryota.
DR   GeneTree; ENSGT00940000176456; -.
DR   HOGENOM; CLU_018984_1_0_1; -.
DR   InParanoid; P34219; -.
DR   OMA; GWKEIAH; -.
DR   OrthoDB; 1978338at2759; -.
DR   BioCyc; YEAST:G3O-28952-MONOMER; -.
DR   BioGRID-ORCS; 852226; 0 hits in 13 CRISPR screens.
DR   PRO; PR:P34219; -.
DR   Proteomes; UP000002311; Chromosome II.
DR   RNAct; P34219; Protein.
DR   GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR   GO; GO:0005634; C:nucleus; HDA:SGD.
DR   GO; GO:0070210; C:Rpd3L-Expanded complex; HDA:SGD.
DR   GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR   GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0043565; F:sequence-specific DNA binding; IDA:SGD.
DR   GO; GO:0006355; P:regulation of DNA-templated transcription; IBA:GO_Central.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:SGD.
DR   CDD; cd00167; SANT; 1.
DR   Gene3D; 1.10.10.60; Homeodomain-like; 1.
DR   InterPro; IPR009057; Homeobox-like_sf.
DR   InterPro; IPR017930; Myb_dom.
DR   InterPro; IPR001005; SANT/Myb.
DR   Pfam; PF13921; Myb_DNA-bind_6; 1.
DR   SMART; SM00717; SANT; 2.
DR   SUPFAM; SSF46689; Homeodomain-like; 1.
DR   PROSITE; PS51294; HTH_MYB; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; DNA-binding; Nucleus; Phosphoprotein; Reference proteome.
FT   CHAIN           1..525
FT                   /note="Transcriptional regulatory protein TOD6"
FT                   /id="PRO_0000197146"
FT   DOMAIN          67..124
FT                   /note="HTH myb-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00625"
FT   DNA_BIND        97..120
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00625"
FT   REGION          22..82
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          283..308
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          451..510
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        22..60
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        471..486
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        495..509
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         280
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         333
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         341
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         366
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950"
SQ   SEQUENCE   525 AA;  59226 MW;  8663DFE2641AA72E CRC64;
     MTLPKLSSVS VSSGHVSANS HGFSILSKHP HPNNLVHSHS LSHTNAKSHL PISSTSTKEN
     STNKEEAESL KKNNPSSWDP SDDIKLRHLK EIKNLGWKEI AHHFPNRTPN ACQFRWRRLK
     SGNLKSNKTA VIDINKLFGV YATGDATPSA GTPSAEEAVK EEAVEDEDIT AGSSAIEDSP
     PDFKPLVKPK YMDRKLITQR STSTFSDHEP QHTKPRKLFV KPRSFSHSIT TNTPNVKTAQ
     QTNLSLYNTT SAKTNKAVNS NDYENIGLVP KIIIRSRRNS FIPSTQIPHS TTKTRKNSHS
     VISSRRSSFN MMHSRRSSFN SHAPTEPISR RASLVVSPYM SPRRLSTSQS VHYHPQHQYY
     LNPIASPNCK TDHANDKITH TRTFLDMQKF ANKHPWSRED DEVLLNNTKD KQNHLSPLEI
     SIVLPNNRSE LEIQQRMDYL KRKGRVSGFH TNEGCKDEEE EDDIDPLHKE NGINTPSQQS
     QNYGMLEAKH DNPKSSELSS MTSANDIRNE QDELPGINSI FKNIF
//