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P50947 (PHO23_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Transcriptional regulatory protein PHO23
Gene names
Name:PHO23
Ordered Locus Names:YNL097C
ORF Names:N2205
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length330 AA.
Sequence statusComplete.
Protein existenceEvidence 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 processTranscription
Transcription regulation
   Cellular componentNucleus
   DomainZinc-finger
   LigandMetal-binding
Zinc
   Molecular functionChromatin regulator
Repressor
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processchromatin 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

Inferred from mutant phenotype PubMed 17210643. 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-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentRpd3L complex

Inferred from direct assay PubMed 16286007Ref.13Ref.12. Source: SGD

histone deacetylase complex

Inferred from direct assay Ref.9. Source: SGD

   Molecular_functionmethylated 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 330330Transcriptional regulatory protein PHO23
PRO_0000203440

Regions

Zinc finger280 – 32950PHD-type

Sites

Binding site2821Histone H3K4me3 By similarity
Binding site2931Histone H3K4me3 By similarity
Binding site2971Histone H3K4me3 By similarity
Binding site3051Histone H3K4me3 By similarity

Natural variations

Natural variant81F → L in strain: SK1. Ref.1
Natural variant351I → V in strain: SK1. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P50947 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 3BF7B519E77ED6EF

FASTA33037,024
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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 204508 / S288c.
[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. expand/collapse author list , 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, IDENTIFICATION BY 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, IDENTIFICATION BY 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, IDENTIFICATION BY 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. expand/collapse author list , 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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+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.
PIRS58255.
RefSeqNP_014302.3. NM_001182935.3.

3D structure databases

ProteinModelPortalP50947.
SMRP50947. Positions 278-326.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid35726. 508 interactions.
DIPDIP-4243N.
IntActP50947. 7 interactions.
MINTMINT-496149.
STRING4932.YNL097C.

Proteomic databases

PaxDbP50947.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYNL097C; YNL097C; YNL097C.
GeneID855626.
KEGGsce:YNL097C.

Organism-specific databases

CYGDYNL097c.
SGDS000005041. PHO23.

Phylogenomic databases

eggNOGCOG5034.
GeneTreeENSGT00550000074538.
HOGENOMHOG000248215.
OMAIKYFTLL.
OrthoDBEOG7G1VHM.

Enzyme and pathway databases

BioCycYEAST:G3O-33125-MONOMER.

Gene expression databases

GenevestigatorP50947.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR028651. ING_fam.
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]
PANTHERPTHR10333. PTHR10333. 1 hit.
PfamPF12998. ING. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio979828.
PROP50947.

Entry information

Entry namePHO23_YEAST
AccessionPrimary (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: April 16, 2014
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XIV

Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families