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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: 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

  • RNA polymerase II activating transcription factor binding Source: SGD
  • RNA polymerase II core promoter sequence-specific DNA binding Source: SGD
  • RNA polymerase II repressing transcription factor binding Source: SGD
  • RNA polymerase II transcription cofactor activity Source: InterPro
  • transcription factor activity, RNA polymerase II transcription factor recruiting Source: SGD

GO - Biological processi

  • negative regulation of transcription from RNA polymerase II promoter Source: SGD
  • positive regulation of transcription from RNA polymerase II promoter Source: SGD
  • 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
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGL025C.
SGDiS000002993. PGD1.

Subcellular locationi

GO - Cellular componenti

  • core mediator complex Source: SGD
  • mediator complex Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000963821 – 397Mediator of RNA polymerase II transcription subunit 3Add BLAST397

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP40356.
PRIDEiP40356.

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

GO - Molecular functioni

  • RNA polymerase II activating transcription factor binding Source: SGD
  • RNA polymerase II repressing transcription factor binding Source: SGD

Protein-protein interaction databases

BioGridi33222. 184 interactors.
DIPiDIP-1186N.
IntActiP40356. 15 interactors.
MINTiMINT-391184.

Structurei

3D structure databases

ProteinModelPortaliP40356.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi347 – 362Gln-richAdd BLAST16

Sequence similaritiesi

Belongs to the mediator complex subunit 3 family.Curated

Phylogenomic databases

InParanoidiP40356.
KOiK15155.
OMAiHANPITH.
OrthoDBiEOG092C3V5G.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

P40356-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDSIIPAGVK LDDLQVILAK NENETRDKVC KQINEARDEI LPLRLQFNEF
60 70 80 90 100
IQIMANIDQE GSKQADRMAK YLHIRDKILQ LNDRFQTLSS HLEALQPLFS
110 120 130 140 150
TVPEYLKTAD NRDRSFQLLE PLSTYNKNGN AVCSTATVVS TNHSAAASTP
160 170 180 190 200
TTTATPHANP ITHAHSLSNP NSTATMQHNP LAGKRGPKSG STMGTPTVHN
210 220 230 240 250
STAAAPIAAP KKPRKPRQTK KAKAQAQAQA QAQAQVYAQQ STVQTPITAS
260 270 280 290 300
MAAALPNPTP SMINSVSPTN VMGTPLTNMM SPMGNAYSMG AQNQGGQVSM
310 320 330 340 350
SQFNGSGNGS NPNTNTNSNN TPLQSQLNLN NLTPANILNM SMNNDFQQQQ
360 370 380 390
QQQQQQQQPQ PQYNMNMGMN NMNNGGKELD SLDLNNLELG GLNMDFL
Length:397
Mass (Da):43,079
Last modified:October 25, 2005 - v2
Checksum:i69D60CE55EA30F18
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti158A → T in AAT92986 (PubMed:17322287).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP40356.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33222. 184 interactors.
DIPiDIP-1186N.
IntActiP40356. 15 interactors.
MINTiMINT-391184.

Proteomic databases

MaxQBiP40356.
PRIDEiP40356.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YGL025C.
SGDiS000002993. PGD1.

Phylogenomic databases

InParanoidiP40356.
KOiK15155.
OMAiHANPITH.
OrthoDBiEOG092C3V5G.

Enzyme and pathway databases

BioCyciYEAST:G3O-30543-MONOMER.

Miscellaneous databases

PROiP40356.

Family and domain databases

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

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: November 2, 2016
This is version 138 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

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 one 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.