ID   RCO1_YEAST              Reviewed;         684 AA.
AC   Q04779; D6VZP9;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 1.
DT   27-MAR-2024, entry version 189.
DE   RecName: Full=Transcriptional regulatory protein RCO1;
GN   Name=RCO1; OrderedLocusNames=YMR075W; ORFNames=YM9916.14;
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 [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169872;
RA   Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA   Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA   Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA   Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL   Nature 387:90-93(1997).
RN   [2]
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   [3]
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   [4]
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   [5]
RP   IDENTIFICATION IN THE RPD3C(S) COMPLEX, IDENTIFICATION BY MASS
RP   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   [6]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-68 AND SER-683, 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   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-683, 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).
RN   [8]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA   Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA   Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA   Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT   "N-terminal acetylome analyses and functional insights of the N-terminal
RT   acetyltransferase NatB.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC   -!- FUNCTION: Catalytic component of the RPD3C(S) histone deacetylase
CC       complex responsible for the deacetylation of lysine residues on the N-
CC       terminal part of the core histones (H2A, H2B, H3 and H4). Histone
CC       deacetylation gives a tag for epigenetic repression and plays an
CC       important role in transcriptional regulation, cell cycle progression,
CC       DNA damage response, osmotic stress response and developmental events.
CC       {ECO:0000269|PubMed:16286008}.
CC   -!- SUBUNIT: Component of the RPD3C(S) complex composed of at least EAF3,
CC       RCO1, RPD3, SIN3, and UME1. {ECO:0000269|PubMed:16286008}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
CC   -!- MISCELLANEOUS: Present with 486 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
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DR   EMBL; Z48952; CAA88800.1; -; Genomic_DNA.
DR   EMBL; BK006946; DAA09973.1; -; Genomic_DNA.
DR   PIR; S52835; S52835.
DR   RefSeq; NP_013791.1; NM_001182574.1.
DR   PDB; 7YI0; EM; 3.20 A; D/F=1-684.
DR   PDB; 7YI2; EM; 3.40 A; D/E=1-684.
DR   PDB; 7YI3; EM; 3.30 A; D/E=1-684.
DR   PDB; 7YI4; EM; 3.96 A; D/F=1-684.
DR   PDB; 7YI5; EM; 3.96 A; D/F=1-684.
DR   PDB; 8KC7; EM; 3.46 A; E/G=1-684.
DR   PDB; 8KD2; EM; 3.02 A; E/G=1-684.
DR   PDB; 8KD3; EM; 2.90 A; E/G=1-684.
DR   PDB; 8KD4; EM; 2.93 A; E/G=1-684.
DR   PDB; 8KD5; EM; 2.90 A; E/G=1-684.
DR   PDB; 8KD6; EM; 3.07 A; E/G=1-684.
DR   PDB; 8KD7; EM; 3.09 A; E/G=1-684.
DR   PDBsum; 7YI0; -.
DR   PDBsum; 7YI2; -.
DR   PDBsum; 7YI3; -.
DR   PDBsum; 7YI4; -.
DR   PDBsum; 7YI5; -.
DR   PDBsum; 8KC7; -.
DR   PDBsum; 8KD2; -.
DR   PDBsum; 8KD3; -.
DR   PDBsum; 8KD4; -.
DR   PDBsum; 8KD5; -.
DR   PDBsum; 8KD6; -.
DR   PDBsum; 8KD7; -.
DR   AlphaFoldDB; Q04779; -.
DR   EMDB; EMD-33845; -.
DR   EMDB; EMD-33849; -.
DR   EMDB; EMD-33850; -.
DR   EMDB; EMD-33851; -.
DR   EMDB; EMD-33852; -.
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; Q04779; -.
DR   BioGRID; 35250; 432.
DR   ComplexPortal; CPX-1851; RPD3S histone deacetylase complex.
DR   DIP; DIP-1959N; -.
DR   IntAct; Q04779; 50.
DR   MINT; Q04779; -.
DR   STRING; 4932.YMR075W; -.
DR   GlyGen; Q04779; 3 sites, 1 O-linked glycan (3 sites).
DR   iPTMnet; Q04779; -.
DR   MaxQB; Q04779; -.
DR   PaxDb; 4932-YMR075W; -.
DR   PeptideAtlas; Q04779; -.
DR   EnsemblFungi; YMR075W_mRNA; YMR075W; YMR075W.
DR   GeneID; 855097; -.
DR   KEGG; sce:YMR075W; -.
DR   AGR; SGD:S000004680; -.
DR   SGD; S000004680; RCO1.
DR   VEuPathDB; FungiDB:YMR075W; -.
DR   eggNOG; KOG4299; Eukaryota.
DR   GeneTree; ENSGT00990000209321; -.
DR   HOGENOM; CLU_016350_0_0_1; -.
DR   InParanoid; Q04779; -.
DR   OMA; CCDPPIE; -.
DR   OrthoDB; 5491843at2759; -.
DR   BioCyc; YEAST:G3O-32777-MONOMER; -.
DR   BioGRID-ORCS; 855097; 0 hits in 10 CRISPR screens.
DR   PRO; PR:Q04779; -.
DR   Proteomes; UP000002311; Chromosome XIII.
DR   RNAct; Q04779; Protein.
DR   GO; GO:0000118; C:histone deacetylase complex; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; HDA:SGD.
DR   GO; GO:0032221; C:Rpd3S complex; IDA:SGD.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0060195; P:negative regulation of antisense RNA transcription; IMP:SGD.
DR   GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; NAS:ComplexPortal.
DR   GO; GO:0006334; P:nucleosome assembly; NAS:ComplexPortal.
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; IBA:GO_Central.
DR   GO; GO:0006368; P:transcription elongation by RNA polymerase II; IGI:SGD.
DR   CDD; cd15535; PHD1_Rco1; 1.
DR   CDD; cd15534; PHD2_PHF12_Rco1; 1.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 2.
DR   InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR   InterPro; IPR011011; Znf_FYVE_PHD.
DR   InterPro; IPR001965; Znf_PHD.
DR   InterPro; IPR019787; Znf_PHD-finger.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   PANTHER; PTHR47636; TRANSCRIPTIONAL REGULATORY PROTEIN RCO1; 1.
DR   PANTHER; PTHR47636:SF1; TRANSCRIPTIONAL REGULATORY PROTEIN RCO1; 1.
DR   Pfam; PF00628; PHD; 1.
DR   SMART; SM00249; PHD; 2.
DR   SUPFAM; SSF57903; FYVE/PHD zinc finger; 2.
DR   PROSITE; PS01359; ZF_PHD_1; 1.
DR   PROSITE; PS50016; ZF_PHD_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; Chromatin regulator; Metal-binding; Nucleus;
KW   Phosphoprotein; Reference proteome; Repeat; Repressor; Transcription;
KW   Transcription regulation; Zinc; Zinc-finger.
FT   CHAIN           1..684
FT                   /note="Transcriptional regulatory protein RCO1"
FT                   /id="PRO_0000203282"
FT   ZN_FING         260..309
FT                   /note="PHD-type 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   ZN_FING         414..472
FT                   /note="PHD-type 2; atypical"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          1..48
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        10..29
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         1
FT                   /note="N-acetylmethionine"
FT                   /evidence="ECO:0007744|PubMed:22814378"
FT   MOD_RES         68
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   MOD_RES         683
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
FT   TURN            36..38
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          43..45
FT                   /evidence="ECO:0007829|PDB:8KD7"
FT   STRAND          47..49
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   HELIX           52..54
FT                   /evidence="ECO:0007829|PDB:8KD6"
FT   TURN            55..57
FT                   /evidence="ECO:0007829|PDB:8KD6"
FT   STRAND          115..117
FT                   /evidence="ECO:0007829|PDB:7YI3"
FT   HELIX           121..127
FT                   /evidence="ECO:0007829|PDB:7YI0"
FT   HELIX           169..174
FT                   /evidence="ECO:0007829|PDB:7YI0"
FT   STRAND          177..179
FT                   /evidence="ECO:0007829|PDB:7YI0"
FT   TURN            183..186
FT                   /evidence="ECO:0007829|PDB:7YI0"
FT   STRAND          261..263
FT                   /evidence="ECO:0007829|PDB:8KC7"
FT   TURN            264..266
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          270..274
FT                   /evidence="ECO:0007829|PDB:8KD7"
FT   STRAND          276..279
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          286..289
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          293..295
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   TURN            304..306
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   HELIX           307..310
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   TURN            312..314
FT                   /evidence="ECO:0007829|PDB:8KD6"
FT   STRAND          315..317
FT                   /evidence="ECO:0007829|PDB:8KD6"
FT   STRAND          319..321
FT                   /evidence="ECO:0007829|PDB:8KD6"
FT   HELIX           322..329
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          330..332
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   HELIX           334..336
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   HELIX           337..341
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          342..346
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   TURN            355..357
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   HELIX           358..360
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          361..363
FT                   /evidence="ECO:0007829|PDB:8KC7"
FT   STRAND          364..366
FT                   /evidence="ECO:0007829|PDB:7YI3"
FT   STRAND          368..370
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          373..376
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          392..394
FT                   /evidence="ECO:0007829|PDB:8KC7"
FT   HELIX           401..406
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          409..412
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          418..421
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          428..430
FT                   /evidence="ECO:0007829|PDB:8KD7"
FT   HELIX           431..433
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          437..439
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          441..443
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          446..448
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   TURN            449..453
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          460..462
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          467..469
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          472..476
FT                   /evidence="ECO:0007829|PDB:7YI0"
FT   STRAND          490..493
FT                   /evidence="ECO:0007829|PDB:7YI0"
FT   TURN            501..504
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          511..513
FT                   /evidence="ECO:0007829|PDB:8KD6"
FT   STRAND          521..523
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   STRAND          541..543
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   HELIX           544..560
FT                   /evidence="ECO:0007829|PDB:8KD2"
FT   HELIX           562..568
FT                   /evidence="ECO:0007829|PDB:8KD6"
SQ   SEQUENCE   684 AA;  78836 MW;  CFC282DC9A782E5C CRC64;
     MDTSKKDTTR SPSHSNSSSP SSSSLSSSSS KEKKRPKRLS SQNVNYDLKR RKIITSEGIE
     RSFKNEHSNL AVEDNIPEEE PKELLEKDSK GNIIKLNEPS TISEDSKVSV TGLPLNKGPS
     EKIKRESLWN YRKNLGGQSN NSEMTLVPSK RFTQVPKNFQ DLNRNDLKTF LTENMTEESN
     IRSTIGWNGD IINRTRDREP ESDRDNKKLS NIRTKIILST NATYDSKSKL FGQNSIKSTS
     NASEKIFRDK NNSTIDFENE DFCSACNQSG SFLCCDTCPK SFHFLCLDPP IDPNNLPKGD
     WHCNECKFKI FINNSMATLK KIESNFIKQN NNVKIFAKLL FNIDSHNPKQ FQLPNYIKET
     FPAVKTGSRG QYSDENDKIP LTDRQLFNTS YGQSITKLDS YNPDTHIDSN SGKFLICYKC
     NQTRLGSWSH PENSRLIMTC DYCQTPWHLD CVPRASFKNL GSKWKCPLHS PTKVYKKIHH
     CQEDNSVNYK VWKKQRLINK KNQLYYEPLQ KIGYQNNGNI QIIPTTSHTD YDFNQDFKIT
     QIDENSIKYD FFDKIYKSKM VQKRKLFQFQ ESLIDKLVSN GSQNGNSEDN MVKDIASLIY
     FQVSNNDKSS NNKSASKSNN LRKLWDLKEL TNVVVPNELD SIQFNDFSSD EIKHLLYLKK
     IIESKPKEEL LKFLNIENPE NQSE
//