P40356 (MED3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	PGD1
Synonyms:	HRS1, MED3
Ordered Locus Names:	YGL025C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	397 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Activator
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA polymerase II transcriptional preinitiation complex assembly Inferred from mutant phenotype PubMed 12482986. Source: SGD negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.7. Source: SGD positive regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 12558798. Source: SGD
Cellular_component	core mediator complex Inferred from direct assay PubMed 9891034. Source: SGD mediator complex Inferred from electronic annotation. Source: InterPro
Molecular_function	RNA polymerase II activating transcription factor binding Inferred from direct assay PubMed 11073972. Source: SGD RNA polymerase II transcription cofactor activity Inferred from electronic annotation. Source: InterPro RNA polymerase II transcription factor recruiting transcription factor activity Inferred from mutant phenotype PubMed 15254252. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CYC8	P14922	3	EBI-13268,EBI-18215
TUP1	P16649	3	EBI-13268,EBI-19654

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 397	397	Mediator of RNA polymerase II transcription subunit 3		PRO_0000096382
Regions
	Compositional bias	347 – 362	16	Gln-rich
Experimental info
	Sequence conflict	158	1	A → T in AAT92986. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	P40356 [UniParc]. Last modified October 25, 2005. Version 2. Checksum: 69D60CE55EA30F18	FASTA	397	43,079
	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

References

	« Hide 'large scale' referencesShow '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. , 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 96604 / S288c / FY1679.
[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. , 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. , 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]	"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.
PIR	S46594.
RefSeq	NP_011490.2. NM_001180890.1.
3D structure databases
ProteinModelPortal	P40356.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1186N.
IntAct	P40356. 12 interactions.
MINT	MINT-391184.
STRING	4932.YGL025C.
Proteomic databases
PaxDb	P40356.
PeptideAtlas	P40356.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YGL025C; YGL025C; YGL025C.
GeneID	852860.
KEGG	sce:YGL025C.
Organism-specific databases
CYGD	YGL025c.
SGD	S000002993. PGD1.
Phylogenomic databases
eggNOG	NOG46412.
KO	K15155.
OMA	NENETRD.
OrthoDB	EOG47M57R.
Enzyme and pathway databases
BioCyc	YEAST:G3O-30543-MONOMER.
Gene expression databases
Genevestigator	P40356.
GermOnline	YGL025C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR020998. Mediator_Med3_fun. [Graphical view]
Pfam	PF11593. Med3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	972466.

Entry information

Entry name

MED3_YEAST

Accession

Primary (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:	May 29, 2013
This is version 111 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program