P50947 (PHO23_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcriptional regulatory protein PHO23

Gene names

Name:	PHO23
Ordered Locus Names:	YNL097C
ORF Names:	N2205

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	330 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the RPD3C(L) histone deacetylase complex (HDAC) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Ref.7 Ref.8 Ref.9
Subunit structure	Interacts with H3K4me3 and to a lesser extent with H3K4me2. Component of the RPD3C(L) complex composed of at least ASH1, CTI6, DEP1, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, UME1 and UME6. Ref.8 Ref.9 Ref.12 Ref.13 Ref.14
Subcellular location	Nucleus Ref.10.
Domain	The PHD-type zinc finger mediates the binding to H3K4me3. Ref.14
Miscellaneous	Present with 3250 molecules/cell in log phase SD medium.
Sequence similarities	Contains 1 PHD-type zinc finger.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Chromatin regulator Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chromatin modification Inferred from mutant phenotype Ref.7. Source: SGD negative regulation of chromatin silencing at rDNA Inferred from mutant phenotype Ref.13. Source: SGD negative regulation of chromatin silencing at silent mating-type cassette Inferred from mutant phenotype Ref.13. Source: SGD negative regulation of chromatin silencing at telomere Inferred from mutant phenotype Ref.13Ref.12PubMed 19372273. Source: SGD negative regulation of transcription from RNA polymerase I promoter Inferred from mutant phenotype PubMed 19270272. Source: SGD positive regulation of transcription from RNA polymerase II promoter in response to heat stress Inferred from mutant phenotype PubMed 20398213. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	Rpd3L complex Inferred from direct assay PubMed 16286007Ref.13Ref.12PubMed 19040720. Source: SGD Rpd3L-Expanded complex Inferred from direct assay PubMed 19040720. Source: SGD
Molecular_function	methylated histone residue binding Inferred from direct assay Ref.14. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 330	330	Transcriptional regulatory protein PHO23		PRO_0000203440
Regions
	Zinc finger	280 – 329	50	PHD-type
Sites
	Binding site	282	1	Histone H3K4me3 By similarity
	Binding site	293	1	Histone H3K4me3 By similarity
	Binding site	297	1	Histone H3K4me3 By similarity
	Binding site	305	1	Histone H3K4me3 By similarity
Amino acid modifications
	Modified residue	234	1	Phosphoserine Ref.15
Natural variations
	Natural variant	8	1	F → L in strain: SK1. Ref.1
	Natural variant	35	1	I → V in strain: SK1. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P50947 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: 3BF7B519E77ED6EF	FASTA	330	37,024
	10 20 30 40 50 60 MSSPANLFPG LNDITDVLEE FPLATSRYLT LLHEIDAKCV HSMPNLNERI DKFLKKDFNK 70 80 90 100 110 120 DHQTQVRLLN NINKIYEELM PSLEEKMHVS SIMLDNLDRL TSRLELAYEV AIKNTEIPRG 130 140 150 160 170 180 LRLGVDNHPA MHLHHELMEK IESKSNSKSS QALKSESRRE AMAANRRQGE HYSASTHQQD 190 200 210 220 230 240 DSKNDANYGG SRHESQDHTG NNTNSRKRAN AANTNNADPE TKKRKRRVAT TAVSPSTIST 250 260 270 280 290 300 ATAVNNGRIG TSTASRGVSS VGNSNNSRIS RPKTNDYGEP LYCYCNQVAY GEMVGCDGAD 310 320 330 CELEWFHLPC IGLETLPKGK WYCDDCKKKL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Quantitative trait loci mapped to single-nucleotide resolution in yeast." Deutschbauer A.M., Davis R.W. Nat. Genet. 37:1333-1340(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS LEU-8 AND VAL-35. Strain: SK1.
[2]	"The sequence of a 21.3 kb DNA fragment from the left arm of yeast chromosome XIV reveals LEU4, MET4, POL1, RAS2, and six new open reading frames." Saiz J.E., Buitrago M.J., Soler A., del Rey F., Revuelta J.L. Yeast 12:403-409(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"Sequence analysis of a 14.2 kb fragment of Saccharomyces cerevisiae chromosome XIV that includes the ypt53, tRNALeu and gsr m2 genes and four new open reading frames." Garcia-Cantalejo J.M., Boskovic J., Jimenez A. Yeast 12:599-608(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-20.
[7]	"Three yeast proteins related to the human candidate tumor suppressor p33(ING1) are associated with histone acetyltransferase activities." Loewith R., Meijer M., Lees-Miller S.P., Riabowol K., Young D. Mol. Cell. Biol. 20:3807-3816(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae." Loewith R., Smith J.S., Meijer M., Williams T.J., Bachman N., Boeke J.D., Young D. J. Biol. Chem. 276:24068-24074(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE RPD3 COMPLEX.
[9]	"Opposite role of yeast ING family members in p53-dependent transcriptional activation." Nourani A., Howe L., Pray-Grant M.G., Workman J.L., Grant P.A., Cote J. J. Biol. Chem. 278:19171-19175(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE RPD3 COMPLEX, MASS SPECTROMETRY.
[10]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[11]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]	"Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex." Carrozza M.J., Florens L., Swanson S.K., Shia W.-J., Anderson S., Yates J., Washburn M.P., Workman J.L. Biochim. Biophys. Acta 1731:77-87(2005) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE RPD3C(L) COMPLEX, MASS SPECTROMETRY.
[13]	"Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex." Keogh M.-C., Kurdistani S.K., Morris S.A., Ahn S.H., Podolny V., Collins S.R., Schuldiner M., Chin K., Punna T., Thompson N.J., Boone C., Emili A., Weissman J.S., Hughes T.R., Strahl B.D., Grunstein M., Greenblatt J.F., Buratowski S., Krogan N.J. Cell 123:593-605(2005) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE RPD3C(L) COMPLEX, MASS SPECTROMETRY.
[14]	"ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression." Shi X., Hong T., Walter K.L., Ewalt M., Michishita E., Hung T., Carney D., Pena P., Lan F., Kaadige M.R., Lacoste N., Cayrou C., Davrazou F., Saha A., Cairns B.R., Ayer D.E., Kutateladze T.G., Shi Y. , Cote J., Chua K.F., Gozani O. Nature 442:96-99(2006) [PubMed] [Europe PMC] [Abstract] Cited for: DOMAIN PHD-TYPE ZINC FINGER, INTERACTION WITH HISTONES H3K4ME3 AND H3K4ME2.
[15]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-234, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	DQ115393 Genomic DNA. Translation: AAZ22511.1. Z50161 Genomic DNA. Translation: CAA90529.1. AY693076 Genomic DNA. Translation: AAT93095.1. Z71373 Genomic DNA. Translation: CAA95973.1. BK006947 Genomic DNA. Translation: DAA10449.1.
PIR	S58255.
RefSeq	NP_014302.3. NM_001182935.3.
3D structure databases
ProteinModelPortal	P50947.
SMR	P50947. Positions 278-326.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-4243N.
IntAct	P50947. 7 interactions.
MINT	MINT-496149.
STRING	4932.YNL097C.
Proteomic databases
PaxDb	P50947.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YNL097C; YNL097C; YNL097C.
GeneID	855626.
KEGG	sce:YNL090W. sce:YNL097C.
Organism-specific databases
CYGD	YNL097c.
SGD	S000005041. PHO23.
Phylogenomic databases
eggNOG	COG5034.
GeneTree	ENSGT00550000074538.
HOGENOM	HOG000248215.
KO	K07975.
OMA	LPCIGLE.
OrthoDB	EOG47DDRZ.
Gene expression databases
Genevestigator	P50947.
GermOnline	YNL097C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.30.40.10. 1 hit.
InterPro	IPR024610. ING_N. IPR019786. Zinc_finger_PHD-type_CS. IPR011011. Znf_FYVE_PHD. IPR001965. Znf_PHD. IPR019787. Znf_PHD-finger. IPR013083. Znf_RING/FYVE/PHD. [Graphical view]
Pfam	PF12998. ING. 1 hit. PF00628. PHD. 1 hit. [Graphical view]
SMART	SM00249. PHD. 1 hit. [Graphical view]
SUPFAM	SSF57903. FYVE_PHD_ZnF. 1 hit.
PROSITE	PS01359. ZF_PHD_1. 1 hit. PS50016. ZF_PHD_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	979828.

Entry information

Entry name

PHO23_YEAST

Accession

Primary (citable) accession number: P50947
Secondary accession number(s): D6W183, Q45TZ9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	May 1, 2013
This is version 119 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program