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P40356

- MED3_YEAST

UniProt

P40356 - MED3_YEAST

Protein

Mediator of RNA polymerase II transcription subunit 3

Gene

PGD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 121 (01 Oct 2014)
      Sequence version 2 (25 Oct 2005)
      Previous versions | rss
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    Functioni

    Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. PGD1/MED3 is also involved in direct repeat recombination.5 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. RNA polymerase II activating transcription factor binding Source: SGD
    3. RNA polymerase II repressing transcription factor binding Source: SGD
    4. RNA polymerase II transcription cofactor activity Source: InterPro
    5. RNA polymerase II transcription factor recruiting transcription factor activity Source: SGD

    GO - Biological processi

    1. negative regulation of transcription from RNA polymerase II promoter Source: SGD
    2. positive regulation of transcription from RNA polymerase II promoter Source: SGD
    3. RNA polymerase II transcriptional preinitiation complex assembly Source: SGD

    Keywords - Molecular functioni

    Activator

    Keywords - Biological processi

    Transcription, Transcription regulation

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30543-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Mediator of RNA polymerase II transcription subunit 3
    Alternative name(s):
    Hyper-recombination suppressor protein 1
    Mediator complex subunit 3
    Poly-glutamine domain protein 1
    Gene namesi
    Name:PGD1
    Synonyms:HRS1, MED3
    Ordered Locus Names:YGL025C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGL025c.
    SGDiS000002993. PGD1.

    Subcellular locationi

    Nucleus 3 Publications

    GO - Cellular componenti

    1. core mediator complex Source: SGD
    2. mediator complex Source: InterPro

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 397397Mediator of RNA polymerase II transcription subunit 3PRO_0000096382Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP40356.
    PaxDbiP40356.
    PeptideAtlasiP40356.

    Expressioni

    Gene expression databases

    GenevestigatoriP40356.

    Interactioni

    Subunit structurei

    Component of the Mediator complex, which is composed of at least 21 subunits that form three structurally distinct submodules. The Mediator head module contains MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22, the middle module contains MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31, and the tail module contains MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. PGD1/MED3 interacts directly with the CYC8-TUP1 corepressor proteins.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CYC8P149223EBI-13268,EBI-18215
    TUP1P166493EBI-13268,EBI-19654

    Protein-protein interaction databases

    BioGridi33222. 186 interactions.
    DIPiDIP-1186N.
    IntActiP40356. 12 interactions.
    MINTiMINT-391184.
    STRINGi4932.YGL025C.

    Structurei

    3D structure databases

    ProteinModelPortaliP40356.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi347 – 36216Gln-richAdd
    BLAST

    Sequence similaritiesi

    Belongs to the mediator complex subunit 3 family.Curated

    Phylogenomic databases

    eggNOGiNOG46412.
    KOiK15155.
    OMAiHANPITH.
    OrthoDBiEOG7CZKJF.

    Family and domain databases

    InterProiIPR020998. Mediator_Med3_fun.
    [Graphical view]
    PfamiPF11593. Med3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P40356-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDSIIPAGVK LDDLQVILAK NENETRDKVC KQINEARDEI LPLRLQFNEF    50
    IQIMANIDQE GSKQADRMAK YLHIRDKILQ LNDRFQTLSS HLEALQPLFS 100
    TVPEYLKTAD NRDRSFQLLE PLSTYNKNGN AVCSTATVVS TNHSAAASTP 150
    TTTATPHANP ITHAHSLSNP NSTATMQHNP LAGKRGPKSG STMGTPTVHN 200
    STAAAPIAAP KKPRKPRQTK KAKAQAQAQA QAQAQVYAQQ STVQTPITAS 250
    MAAALPNPTP SMINSVSPTN VMGTPLTNMM SPMGNAYSMG AQNQGGQVSM 300
    SQFNGSGNGS NPNTNTNSNN TPLQSQLNLN NLTPANILNM SMNNDFQQQQ 350
    QQQQQQQQPQ PQYNMNMGMN NMNNGGKELD SLDLNNLELG GLNMDFL 397
    Length:397
    Mass (Da):43,079
    Last modified:October 25, 2005 - v2
    Checksum:i69D60CE55EA30F18
    GO

    Sequence cautioni

    The sequence AAT92986.1 differs from that shown. Reason: Erroneous initiation.
    The sequence CAA57213.1 differs from that shown. Reason: Erroneous initiation.
    The sequence CAA81213.1 differs from that shown. Reason: Erroneous initiation.
    The sequence CAA96725.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti158 – 1581A → T in AAT92986. (PubMed:17322287)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X81457 Genomic DNA. Translation: CAA57213.1. Different initiation.
    Z26254 Genomic DNA. Translation: CAA81213.1. Different initiation.
    Z72547 Genomic DNA. Translation: CAA96725.1. Different initiation.
    AY692967 Genomic DNA. Translation: AAT92986.1. Different initiation.
    BK006941 Genomic DNA. Translation: DAA08074.1.
    PIRiS46594.
    RefSeqiNP_011490.2. NM_001180890.1.

    Genome annotation databases

    EnsemblFungiiYGL025C; YGL025C; YGL025C.
    GeneIDi852860.
    KEGGisce:YGL025C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X81457 Genomic DNA. Translation: CAA57213.1 . Different initiation.
    Z26254 Genomic DNA. Translation: CAA81213.1 . Different initiation.
    Z72547 Genomic DNA. Translation: CAA96725.1 . Different initiation.
    AY692967 Genomic DNA. Translation: AAT92986.1 . Different initiation.
    BK006941 Genomic DNA. Translation: DAA08074.1 .
    PIRi S46594.
    RefSeqi NP_011490.2. NM_001180890.1.

    3D structure databases

    ProteinModelPortali P40356.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33222. 186 interactions.
    DIPi DIP-1186N.
    IntActi P40356. 12 interactions.
    MINTi MINT-391184.
    STRINGi 4932.YGL025C.

    Proteomic databases

    MaxQBi P40356.
    PaxDbi P40356.
    PeptideAtlasi P40356.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGL025C ; YGL025C ; YGL025C .
    GeneIDi 852860.
    KEGGi sce:YGL025C.

    Organism-specific databases

    CYGDi YGL025c.
    SGDi S000002993. PGD1.

    Phylogenomic databases

    eggNOGi NOG46412.
    KOi K15155.
    OMAi HANPITH.
    OrthoDBi EOG7CZKJF.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30543-MONOMER.

    Miscellaneous databases

    NextBioi 972466.

    Gene expression databases

    Genevestigatori P40356.

    Family and domain databases

    InterProi IPR020998. Mediator_Med3_fun.
    [Graphical view ]
    Pfami PF11593. Med3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A new nuclear suppressor system for a mitochondrial RNA polymerase mutant identifies an unusual zinc-finger protein and a polyglutamine domain protein in Saccharomyces cerevisiae."
      Broehl S., Lisowsky T., Riemen G., Michaelis G.
      Yeast 10:719-731(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: SC167.
    2. "The yeast HRS1 gene encodes a polyglutamine-rich nuclear protein required for spontaneous and hpr1-induced deletions between direct repeats."
      Santos-Rosa H., Clever B., Heyer W.-D., Aguilera A.
      Genetics 142:705-716(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION.
    3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(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. "The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain."
      Myers L.C., Gustafsson C.M., Bushnell D.A., Lui M., Erdjument-Bromage H., Tempst P., Kornberg R.D.
      Genes Dev. 12:45-54(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, COMPONENT OF MEDIATOR COMPLEX.
    7. "Hrs1/Med3 is a Cyc8-Tup1 corepressor target in the RNA polymerase II holoenzyme."
      Papamichos-Chronakis M., Conlan R.S., Gounalaki N., Copf T., Tzamarias D.
      J. Biol. Chem. 275:8397-8403(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH CYC8 AND TUP1.
    8. "Sequencing and comparison of yeast species to identify genes and regulatory elements."
      Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.
      Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
    9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. Cited for: NOMENCLATURE.
    12. Cited for: TOPOLOGY OF THE MEDIATOR COMPLEX.
    13. "Preponderance of free mediator in the yeast Saccharomyces cerevisiae."
      Takagi Y., Chadick J.Z., Davis J.A., Asturias F.J.
      J. Biol. Chem. 280:31200-31207(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION OF THE MEDIATOR COMPLEX.
    14. "Mediator and TFIIH govern carboxyl-terminal domain-dependent transcription in yeast extracts."
      Nair D., Kim Y., Myers L.C.
      J. Biol. Chem. 280:33739-33748(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE MEDIATOR COMPLEX.
    15. "Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets."
      van de Peppel J., Kettelarij N., van Bakel H., Kockelkorn T.T.J.P., van Leenen D., Holstege F.C.P.
      Mol. Cell 19:511-522(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    16. "Mediator as a general transcription factor."
      Takagi Y., Kornberg R.D.
      J. Biol. Chem. 281:80-89(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE MEDIATOR COMPLEX.
    17. "Genome-wide location of the coactivator mediator: binding without activation and transient Cdk8 interaction on DNA."
      Andrau J.-C., van de Pasch L., Lijnzaad P., Bijma T., Koerkamp M.G., van de Peppel J., Werner M., Holstege F.C.P.
      Mol. Cell 22:179-192(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    18. "Med19(Rox3) regulates intermodule interactions in the Saccharomyces cerevisiae mediator complex."
      Baidoobonso S.M., Guidi B.W., Myers L.C.
      J. Biol. Chem. 282:5551-5559(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION OF THE MEDIATOR COMPLEX, INTERACTION OF THE MEDIATOR COMPLEX WITH RNA POLYMERASE II.
    19. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    20. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    21. "Structure of the yeast RNA polymerase II holoenzyme: mediator conformation and polymerase interaction."
      Davis J.A., Takagi Y., Kornberg R.D., Asturias F.J.
      Mol. Cell 10:409-415(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: ELECTRON MICROSCOPY OF MEDIATOR COMPLEX IN COMPLEX WITH RNA POLYMERASE II.

    Entry informationi

    Entry nameiMED3_YEAST
    AccessioniPrimary (citable) accession number: P40356
    Secondary accession number(s): D6VUB3, Q6B1W3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: October 25, 2005
    Last modified: October 1, 2014
    This is version 121 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 556 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 VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    External Data

    Dasty 3