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Protein

Transcriptional regulatory protein PHO23

Gene

PHO23

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei282 – 2821Histone H3K4me3By similarity
Binding sitei293 – 2931Histone H3K4me3By similarity
Binding sitei297 – 2971Histone H3K4me3By similarity
Binding sitei305 – 3051Histone H3K4me3By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri280 – 32950PHD-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • chromatin modification Source: SGD
  • negative regulation of chromatin silencing at rDNA Source: SGD
  • negative regulation of chromatin silencing at silent mating-type cassette Source: SGD
  • negative regulation of chromatin silencing at telomere Source: SGD
  • negative regulation of transcription from RNA polymerase I promoter Source: SGD
  • positive regulation of invasive growth in response to glucose limitation Source: SGD
  • positive regulation of transcription from RNA polymerase II promoter Source: SGD
  • positive regulation of transcription from RNA polymerase II promoter in response to heat stress Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-33125-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcriptional regulatory protein PHO23
Gene namesi
Name:PHO23
Ordered Locus Names:YNL097C
ORF Names:N2205
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XIV

Organism-specific databases

CYGDiYNL097c.
EuPathDBiFungiDB:YNL097C.
SGDiS000005041. PHO23.

Subcellular locationi

GO - Cellular componenti

  • histone deacetylase complex Source: SGD
  • Rpd3L complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 330330Transcriptional regulatory protein PHO23PRO_0000203440Add
BLAST

Proteomic databases

MaxQBiP50947.
PaxDbiP50947.

Interactioni

Subunit structurei

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 UME6.5 Publications

Protein-protein interaction databases

BioGridi35726. 508 interactions.
DIPiDIP-4243N.
IntActiP50947. 7 interactions.
MINTiMINT-496149.
STRINGi4932.YNL097C.

Structurei

3D structure databases

ProteinModelPortaliP50947.
SMRiP50947. Positions 278-326.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

The PHD-type zinc finger mediates the binding to H3K4me3.1 Publication

Sequence similaritiesi

Belongs to the ING family.Curated
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri280 – 32950PHD-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG5034.
GeneTreeiENSGT00790000123821.
HOGENOMiHOG000248215.
InParanoidiP50947.
OMAiIKYFTLL.
OrthoDBiEOG7G1VHM.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR028651. 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]
PANTHERiPTHR10333. PTHR10333. 1 hit.
PfamiPF12998. ING. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P50947-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSPANLFPG LNDITDVLEE FPLATSRYLT LLHEIDAKCV HSMPNLNERI
60 70 80 90 100
DKFLKKDFNK DHQTQVRLLN NINKIYEELM PSLEEKMHVS SIMLDNLDRL
110 120 130 140 150
TSRLELAYEV AIKNTEIPRG LRLGVDNHPA MHLHHELMEK IESKSNSKSS
160 170 180 190 200
QALKSESRRE AMAANRRQGE HYSASTHQQD DSKNDANYGG SRHESQDHTG
210 220 230 240 250
NNTNSRKRAN AANTNNADPE TKKRKRRVAT TAVSPSTIST ATAVNNGRIG
260 270 280 290 300
TSTASRGVSS VGNSNNSRIS RPKTNDYGEP LYCYCNQVAY GEMVGCDGAD
310 320 330
CELEWFHLPC IGLETLPKGK WYCDDCKKKL
Length:330
Mass (Da):37,024
Last modified:October 1, 1996 - v1
Checksum:i3BF7B519E77ED6EF
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti8 – 81F → L in strain: SK1. 1 Publication
Natural varianti35 – 351I → V in strain: SK1. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS58255.
RefSeqiNP_014302.3. NM_001182935.3.

Genome annotation databases

EnsemblFungiiYNL097C; YNL097C; YNL097C.
GeneIDi855626.
KEGGisce:YNL097C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiS58255.
RefSeqiNP_014302.3. NM_001182935.3.

3D structure databases

ProteinModelPortaliP50947.
SMRiP50947. Positions 278-326.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35726. 508 interactions.
DIPiDIP-4243N.
IntActiP50947. 7 interactions.
MINTiMINT-496149.
STRINGi4932.YNL097C.

Proteomic databases

MaxQBiP50947.
PaxDbiP50947.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL097C; YNL097C; YNL097C.
GeneIDi855626.
KEGGisce:YNL097C.

Organism-specific databases

CYGDiYNL097c.
EuPathDBiFungiDB:YNL097C.
SGDiS000005041. PHO23.

Phylogenomic databases

eggNOGiCOG5034.
GeneTreeiENSGT00790000123821.
HOGENOMiHOG000248215.
InParanoidiP50947.
OMAiIKYFTLL.
OrthoDBiEOG7G1VHM.

Enzyme and pathway databases

BioCyciYEAST:G3O-33125-MONOMER.

Miscellaneous databases

NextBioi979828.
PROiP50947.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR028651. 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]
PANTHERiPTHR10333. PTHR10333. 1 hit.
PfamiPF12998. ING. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  11. 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. Cited for: IDENTIFICATION IN THE RPD3C(L) COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  14. 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].

Entry informationi

Entry nameiPHO23_YEAST
AccessioniPrimary (citable) accession number: P50947
Secondary accession number(s): D6W183, Q45TZ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: June 24, 2015
This is version 138 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 3250 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.