PHO23_YEAST
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 03-AUG-2022, entry version 192.
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}.
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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 AlphaFoldDB; P50947; -.
DR SMR; P50947; -.
DR BioGRID; 35726; 845.
DR ComplexPortal; CPX-1852; RPD3L histone deacetylase complex.
DR DIP; DIP-4243N; -.
DR IntAct; P50947; 7.
DR MINT; P50947; -.
DR STRING; 4932.YNL097C; -.
DR iPTMnet; P50947; -.
DR MaxQB; P50947; -.
DR PaxDb; P50947; -.
DR PRIDE; P50947; -.
DR EnsemblFungi; YNL097C_mRNA; YNL097C; YNL097C.
DR GeneID; 855626; -.
DR KEGG; sce:YNL097C; -.
DR SGD; S000005041; PHO23.
DR VEuPathDB; FungiDB:YNL097C; -.
DR eggNOG; KOG1973; Eukaryota.
DR HOGENOM; CLU_031900_2_1_1; -.
DR InParanoid; P50947; -.
DR OMA; EALYCYC; -.
DR BioCyc; YEAST:G3O-33125-MON; -.
DR Reactome; R-SCE-3214847; HATs acetylate histones.
DR Reactome; R-SCE-3899300; SUMOylation of transcription cofactors.
DR Reactome; R-SCE-6804758; Regulation of TP53 Activity through Acetylation.
DR Reactome; R-SCE-6811555; PI5P Regulates TP53 Acetylation.
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:0016573; P:histone acetylation; IEA:GOC.
DR GO; GO:0010507; P:negative regulation of autophagy; 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:0016479; P:negative regulation of transcription by RNA polymerase I; 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: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:0061408; P:positive regulation of transcription from RNA polymerase II promoter in response to heat stress; IMP:SGD.
DR GO; GO:2001159; P:regulation of protein localization by the Cvt pathway; IMP:SGD.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IC:ComplexPortal.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR Gene3D; 3.30.40.10; -; 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; PTHR10333; 1.
DR Pfam; PF12998; ING; 1.
DR SMART; SM01408; ING; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Metal-binding; Nucleus; Reference proteome; Repressor;
KW Transcription; Transcription regulation; 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"
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
