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P40356 (MED3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 117. 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:PGD1
Synonyms:HRS1, MED3
Ordered Locus Names:YGL025C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length397 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.7 Ref.14 Ref.15 Ref.16

Subunit structure

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. Ref.7 Ref.18

Subcellular location

Nucleus Ref.2 Ref.9 Ref.17.

Miscellaneous

Present with 556 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the mediator complex subunit 3 family.

Sequence caution

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.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CYC8P149223EBI-13268,EBI-18215
TUP1P166493EBI-13268,EBI-19654

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 397397Mediator of RNA polymerase II transcription subunit 3
PRO_0000096382

Regions

Compositional bias347 – 36216Gln-rich

Amino acid modifications

Modified residue11N-acetylmethionine Ref.20

Experimental info

Sequence conflict1581A → T in AAT92986. Ref.5

Sequences

Sequence LengthMass (Da)Tools
P40356 [UniParc].

Last modified October 25, 2005. Version 2.
Checksum: 69D60CE55EA30F18

FASTA39743,079
        10         20         30         40         50         60 
MDSIIPAGVK LDDLQVILAK NENETRDKVC KQINEARDEI LPLRLQFNEF IQIMANIDQE 

        70         80         90        100        110        120 
GSKQADRMAK YLHIRDKILQ LNDRFQTLSS HLEALQPLFS TVPEYLKTAD NRDRSFQLLE 

       130        140        150        160        170        180 
PLSTYNKNGN AVCSTATVVS TNHSAAASTP TTTATPHANP ITHAHSLSNP NSTATMQHNP 

       190        200        210        220        230        240 
LAGKRGPKSG STMGTPTVHN STAAAPIAAP KKPRKPRQTK KAKAQAQAQA QAQAQVYAQQ 

       250        260        270        280        290        300 
STVQTPITAS MAAALPNPTP SMINSVSPTN VMGTPLTNMM SPMGNAYSMG AQNQGGQVSM 

       310        320        330        340        350        360 
SQFNGSGNGS NPNTNTNSNN TPLQSQLNLN NLTPANILNM SMNNDFQQQQ QQQQQQQQPQ 

       370        380        390 
PQYNMNMGMN NMNNGGKELD SLDLNNLELG GLNMDFL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]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]"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]"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].
[10]"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].
[11]"A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II."
Bourbon H.-M., Aguilera A., Ansari A.Z., Asturias F.J., Berk A.J., Bjoerklund S., Blackwell T.K., Borggrefe T., Carey M., Carlson M., Conaway J.W., Conaway R.C., Emmons S.W., Fondell J.D., Freedman L.P., Fukasawa T., Gustafsson C.M., Han M. expand/collapse author list , He X., Herman P.K., Hinnebusch A.G., Holmberg S., Holstege F.C.P., Jaehning J.A., Kim Y.-J., Kuras L., Leutz A., Lis J.T., Meisterernest M., Naeaer A.M., Nasmyth K., Parvin J.D., Ptashne M., Reinberg D., Ronne H., Sadowski I., Sakurai H., Sipiczki M., Sternberg P.W., Stillman D.J., Strich R., Struhl K., Svejstrup J.Q., Tuck S., Winston F., Roeder R.G., Kornberg R.D.
Mol. Cell 14:553-557(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NOMENCLATURE.
[12]"A high resolution protein interaction map of the yeast Mediator complex."
Guglielmi B., van Berkum N.L., Klapholz B., Bijma T., Boube M., Boschiero C., Bourbon H.-M., Holstege F.C.P., Werner M.
Nucleic Acids Res. 32:5379-5391(2004) [PubMed] [Europe PMC] [Abstract]
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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS46594.
RefSeqNP_011490.2. NM_001180890.1.

3D structure databases

ProteinModelPortalP40356.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33222. 185 interactions.
DIPDIP-1186N.
IntActP40356. 12 interactions.
MINTMINT-391184.
STRING4932.YGL025C.

Proteomic databases

PaxDbP40356.
PeptideAtlasP40356.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYGL025C; YGL025C; YGL025C.
GeneID852860.
KEGGsce:YGL025C.

Organism-specific databases

CYGDYGL025c.
SGDS000002993. PGD1.

Phylogenomic databases

eggNOGNOG46412.
KOK15155.
OMANENETRD.
OrthoDBEOG7CZKJF.

Enzyme and pathway databases

BioCycYEAST:G3O-30543-MONOMER.

Gene expression databases

GenevestigatorP40356.

Family and domain databases

InterProIPR020998. Mediator_Med3_fun.
[Graphical view]
PfamPF11593. Med3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio972466.

Entry information

Entry nameMED3_YEAST
AccessionPrimary (citable) accession number: P40356
Secondary accession number(s): D6VUB3, Q6B1W3
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: October 25, 2005
Last modified: April 16, 2014
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VII

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

Yeast

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

SIMILARITY comments

Index of protein domains and families