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P40356

- MED3_YEAST

UniProt

P40356 - MED3_YEAST

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Protein

Mediator of RNA polymerase II transcription subunit 3

Gene
PGD1, HRS1, MED3, YGL025C
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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
Complete GO annotation...

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.

Family & Domainsi

Compositional bias

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

Sequence similaritiesi

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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti158 – 1581A → T in AAT92986. 1 Publication

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 120 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.

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

Similar proteinsi