ID PHO23_YEAST Reviewed; 330 AA. AC P50947; D6W183; Q45TZ9; DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-1996, sequence version 1. DT 27-MAR-2024, entry version 200. DE RecName: Full=Transcriptional regulatory protein PHO23; GN Name=PHO23; OrderedLocusNames=YNL097C; ORFNames=N2205; 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 VARIANTS LEU-8 AND VAL-35. RC STRAIN=SK1; RX PubMed=16273108; DOI=10.1038/ng1674; RA Deutschbauer A.M., Davis R.W.; RT "Quantitative trait loci mapped to single-nucleotide resolution in yeast."; RL Nat. Genet. 37:1333-1340(2005). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=ATCC 96604 / S288c / FY1679; RX PubMed=8701612; RX DOI=10.1002/(sici)1097-0061(19960330)12:4<403::aid-yea923>3.0.co;2-h; RA Saiz J.E., Buitrago M.J., Soler A., del Rey F., Revuelta J.L.; RT "The sequence of a 21.3 kb DNA fragment from the left arm of yeast RT chromosome XIV reveals LEU4, MET4, POL1, RAS2, and six new open reading RT frames."; RL Yeast 12:403-409(1996). 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 1-20. RX PubMed=8771715; RX DOI=10.1002/(sici)1097-0061(199605)12:6<599::aid-yea938>3.0.co;2-9; RA Garcia-Cantalejo J.M., Boskovic J., Jimenez A.; RT "Sequence analysis of a 14.2 kb fragment of Saccharomyces cerevisiae RT chromosome XIV that includes the ypt53, tRNALeu and gsr m2 genes and four RT new open reading frames."; RL Yeast 12:599-608(1996). RN [7] RP FUNCTION. RX PubMed=10805724; DOI=10.1128/mcb.20.11.3807-3816.2000; RA Loewith R., Meijer M., Lees-Miller S.P., Riabowol K., Young D.; RT "Three yeast proteins related to the human candidate tumor suppressor RT p33(ING1) are associated with histone acetyltransferase activities."; RL Mol. Cell. Biol. 20:3807-3816(2000). RN [8] RP FUNCTION, AND IDENTIFICATION IN THE RPD3 COMPLEX. RX PubMed=11306585; DOI=10.1074/jbc.m102176200; RA Loewith R., Smith J.S., Meijer M., Williams T.J., Bachman N., Boeke J.D., RA Young D.; RT "Pho23 is associated with the Rpd3 histone deacetylase and is required for RT its normal function in regulation of gene expression and silencing in RT Saccharomyces cerevisiae."; RL J. Biol. Chem. 276:24068-24074(2001). RN [9] RP FUNCTION, 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 [10] 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 [11] 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 [12] 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 [13] 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 [14] RP DOMAIN PHD-TYPE ZINC-FINGER, AND INTERACTION WITH HISTONES H3K4ME3 AND RP H3K4ME2. RX PubMed=16728974; DOI=10.1038/nature04835; RA Shi X., Hong T., Walter K.L., Ewalt M., Michishita E., Hung T., Carney D., RA Pena P., Lan F., Kaadige M.R., Lacoste N., Cayrou C., Davrazou F., Saha A., RA Cairns B.R., Ayer D.E., Kutateladze T.G., Shi Y., Cote J., Chua K.F., RA Gozani O.; RT "ING2 PHD domain links histone H3 lysine 4 methylation to active gene RT repression."; RL Nature 442:96-99(2006). RN [15] 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). 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:10805724, ECO:0000269|PubMed:11306585, CC ECO:0000269|PubMed:12672825}. CC -!- SUBUNIT: Interacts with H3K4me3 and to a lesser extent with H3K4me2. CC Component of the RPD3C(L) complex composed of at least ASH1, CTI6, CC DEP1, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, UME1 and UME6. CC {ECO:0000269|PubMed:11306585, ECO:0000269|PubMed:12672825, CC ECO:0000269|PubMed:16286008, ECO:0000269|PubMed:16314178, CC ECO:0000269|PubMed:16728974}. CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}. CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3. CC {ECO:0000269|PubMed:16728974}. CC -!- MISCELLANEOUS: Present with 3250 molecules/cell in log phase SD medium. CC {ECO:0000269|PubMed:14562106}. CC -!- SIMILARITY: Belongs to the ING family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; DQ115393; AAZ22511.1; -; Genomic_DNA. DR EMBL; Z50161; CAA90529.1; -; Genomic_DNA. DR EMBL; AY693076; AAT93095.1; -; Genomic_DNA. DR EMBL; Z71373; CAA95973.1; -; Genomic_DNA. DR EMBL; BK006947; DAA10449.1; -; Genomic_DNA. DR PIR; S58255; S58255. DR RefSeq; NP_014302.3; NM_001182935.3. DR PDB; 8GA8; EM; 3.50 A; L=1-330. DR PDB; 8HPO; EM; 2.60 A; C=1-330. DR PDBsum; 8GA8; -. DR PDBsum; 8HPO; -. DR AlphaFoldDB; P50947; -. DR EMDB; EMD-29892; -. DR EMDB; EMD-34935; -. DR SMR; P50947; -. DR BioGRID; 35726; 853. DR ComplexPortal; CPX-1852; RPD3L histone deacetylase complex. DR DIP; DIP-4243N; -. DR IntAct; P50947; 7. DR MINT; P50947; -. DR STRING; 4932.YNL097C; -. DR GlyGen; P50947; 2 sites, 1 O-linked glycan (2 sites). DR iPTMnet; P50947; -. DR MaxQB; P50947; -. DR PaxDb; 4932-YNL097C; -. DR PeptideAtlas; P50947; -. DR EnsemblFungi; YNL097C_mRNA; YNL097C; YNL097C. DR GeneID; 855626; -. DR KEGG; sce:YNL097C; -. DR AGR; SGD:S000005041; -. DR SGD; S000005041; PHO23. DR VEuPathDB; FungiDB:YNL097C; -. DR eggNOG; KOG1973; Eukaryota. DR HOGENOM; CLU_031900_2_1_1; -. DR InParanoid; P50947; -. DR OMA; HPAMHLH; -. DR OrthoDB; 3140066at2759; -. DR BioCyc; YEAST:G3O-33125-MONOMER; -. DR Reactome; R-SCE-3899300; SUMOylation of transcription cofactors. DR Reactome; R-SCE-6811555; PI5P Regulates TP53 Acetylation. DR BioGRID-ORCS; 855626; 3 hits in 10 CRISPR screens. DR PRO; PR:P50947; -. DR Proteomes; UP000002311; Chromosome XIV. DR RNAct; P50947; Protein. DR GO; GO:0000118; C:histone deacetylase complex; IDA:SGD. DR GO; GO:0005634; C:nucleus; HDA:SGD. DR GO; GO:0033698; C:Rpd3L complex; IDA:SGD. DR GO; GO:0070210; C:Rpd3L-Expanded complex; HDA:SGD. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB. DR GO; GO:0006325; P:chromatin organization; 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:0016479; P:negative regulation of transcription by RNA polymerase I; IMP:SGD. DR GO; GO:0006334; P:nucleosome assembly; NAS:ComplexPortal. DR GO; GO:2000219; P:positive regulation of invasive growth in response to glucose limitation; IMP:SGD. DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP: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; NAS:ComplexPortal. DR CDD; cd17016; ING_Pho23p_like; 1. DR CDD; cd15505; PHD_ING; 1. DR Gene3D; 6.10.140.1740; -; 1. DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1. DR InterPro; IPR028651; ING_fam. DR InterPro; IPR024610; ING_N_histone-binding. 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; PTHR10333; INHIBITOR OF GROWTH PROTEIN; 1. DR PANTHER; PTHR10333:SF42; INHIBITOR OF GROWTH PROTEIN 3; 1. DR Pfam; PF12998; ING; 1. DR SMART; SM01408; ING; 1. DR SMART; SM00249; PHD; 1. DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 1. DR PROSITE; PS01359; ZF_PHD_1; 1. DR PROSITE; PS50016; ZF_PHD_2; 1. PE 1: Evidence at protein level; KW 3D-structure; Chromatin regulator; Metal-binding; Nucleus; KW Reference proteome; Repressor; Transcription; Transcription regulation; KW Zinc; Zinc-finger. FT CHAIN 1..330 FT /note="Transcriptional regulatory protein PHO23" FT /id="PRO_0000203440" FT ZN_FING 280..329 FT /note="PHD-type" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146" FT REGION 139..272 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 193..217 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 230..272 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 283 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT BINDING 285 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT BINDING 296 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT BINDING 301 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT BINDING 307 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT BINDING 310 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT BINDING 323 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT BINDING 326 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT SITE 282 FT /note="Histone H3K4me3 binding" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT SITE 293 FT /note="Histone H3K4me3 binding" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT SITE 297 FT /note="Histone H3K4me3 binding" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT SITE 305 FT /note="Histone H3K4me3 binding" FT /evidence="ECO:0000250|UniProtKB:Q9UK53" FT VARIANT 8 FT /note="F -> L (in strain: SK1)" FT /evidence="ECO:0000269|PubMed:16273108" FT VARIANT 35 FT /note="I -> V (in strain: SK1)" FT /evidence="ECO:0000269|PubMed:16273108" FT HELIX 9..36 FT /evidence="ECO:0007829|PDB:8HPO" FT TURN 37..42 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 43..54 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 65..79 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 82..113 FT /evidence="ECO:0007829|PDB:8HPO" FT TURN 119..121 FT /evidence="ECO:0007829|PDB:8HPO" FT HELIX 132..146 FT /evidence="ECO:0007829|PDB:8HPO" SQ SEQUENCE 330 AA; 37024 MW; 3BF7B519E77ED6EF CRC64; MSSPANLFPG LNDITDVLEE FPLATSRYLT LLHEIDAKCV HSMPNLNERI DKFLKKDFNK DHQTQVRLLN NINKIYEELM PSLEEKMHVS SIMLDNLDRL TSRLELAYEV AIKNTEIPRG LRLGVDNHPA MHLHHELMEK IESKSNSKSS QALKSESRRE AMAANRRQGE HYSASTHQQD DSKNDANYGG SRHESQDHTG NNTNSRKRAN AANTNNADPE TKKRKRRVAT TAVSPSTIST ATAVNNGRIG TSTASRGVSS VGNSNNSRIS RPKTNDYGEP LYCYCNQVAY GEMVGCDGAD CELEWFHLPC IGLETLPKGK WYCDDCKKKL //