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Protein

DNA-directed RNA polymerase II subunit RPB4

Gene

RPB4

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

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. The RPB4-RPB7 subcomplex is necessary for promoter-directed transcription initiation but is not required for recruitment of Pol II to active preinitiation complexes and seems to be dispensable for transcription elongation and termination. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II. Involved in DNA repair of damage in the transcribed strand. RPB4 is dispensable under optimal growth conditions, but becomes essential during heat or cold shock and under nutrient depletion. Suppresses the RBP9-mediated transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER) but facilitates the RAD26-mediated TCR subpathway. Under stress conditions only, involved in mRNA export to the cytoplasm. Involved in mRNA decay. Promotes or enhances the deadenylation process of specific mRNAs and may recruit PAT1 and the LSM1-7 complex to these mRNAs, thus stimulating their decapping and further decay.7 Publications

GO - Molecular functioni

GO - Biological processi

  • DNA repair Source: UniProtKB-KW
  • mRNA export from nucleus in response to heat stress Source: SGD
  • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: SGD
  • positive regulation of translational initiation Source: SGD
  • recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex Source: SGD
  • transcription, RNA-templated Source: GOC
  • transcription from RNA polymerase II promoter Source: SGD
  • transcription initiation from RNA polymerase II promoter Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, mRNA processing, Transcription

Enzyme and pathway databases

BioCyciYEAST:G3O-31585-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-SCE-72086. mRNA Capping.
R-SCE-72165. mRNA Splicing - Minor Pathway.
R-SCE-73776. RNA Polymerase II Promoter Escape.
R-SCE-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SCE-75953. RNA Polymerase II Transcription Initiation.
R-SCE-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB4
Short name:
RNA polymerase II subunit B4
Alternative name(s):
B32
DNA-directed RNA polymerase II 32 kDa polypeptide
Gene namesi
Name:RPB4
Ordered Locus Names:YJL140W
ORF Names:J0654
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJL140W.
SGDiS000003676. RPB4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic mRNA processing body Source: SGD
  • DNA-directed RNA polymerase II, core complex Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000739841 – 221DNA-directed RNA polymerase II subunit RPB4Add BLAST221

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei91PhosphothreonineCombined sources1
Modified residuei92PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP20433.
PRIDEiP20433.

PTM databases

iPTMnetiP20433.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a dissociable subcomplex associated with the 10-subunit Pol II core complex. In exponentially proliferating cells, only approximative 20 % of the Pol II complexes contain the RPB4-RPB7 subcomplex. In starving cells, that enter stationary phase, RPB4-RPB7 is associated with Pol II in a stoechiometric manner. The RPB4-RPB7 subcomplex probably associates with TFG1. Interacts with LSM2 and PAT1.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
NIP1P324975EBI-15777,EBI-8965
RPB7P340874EBI-15777,EBI-15790

GO - Molecular functioni

  • translation initiation factor binding Source: SGD

Protein-protein interaction databases

BioGridi33617. 129 interactors.
DIPiDIP-55N.
IntActiP20433. 21 interactors.
MINTiMINT-538215.

Structurei

Secondary structure

1221
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 8Combined sources3
Helixi17 – 19Combined sources3
Beta strandi24 – 27Combined sources4
Helixi31 – 33Combined sources3
Beta strandi35 – 38Combined sources4
Turni40 – 42Combined sources3
Beta strandi44 – 46Combined sources3
Beta strandi47 – 50Combined sources4
Helixi52 – 71Combined sources20
Turni73 – 75Combined sources3
Helixi119 – 133Combined sources15
Helixi139 – 151Combined sources13
Helixi157 – 168Combined sources12
Turni169 – 171Combined sources3
Helixi174 – 182Combined sources9
Helixi188 – 194Combined sources7
Helixi196 – 198Combined sources3
Turni199 – 201Combined sources3
Helixi204 – 217Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NT9X-ray4.20D1-221[»]
1PQVX-ray3.80D1-85[»]
D115-221[»]
1WCMX-ray3.80D4-221[»]
1Y14X-ray2.30A/C35-221[»]
1Y1VX-ray3.80D1-221[»]
1Y1WX-ray4.00D1-221[»]
1Y1YX-ray4.00D1-221[»]
1Y77X-ray4.50D1-221[»]
2B63X-ray3.80D1-221[»]
2B8KX-ray4.15D1-221[»]
2JA5X-ray3.80D1-221[»]
2JA6X-ray4.00D1-221[»]
2JA7X-ray3.80D/P1-221[»]
2JA8X-ray3.80D1-221[»]
2R7ZX-ray3.80D1-221[»]
2R92X-ray3.80D1-221[»]
2R93X-ray4.00D1-221[»]
2VUMX-ray3.40D1-221[»]
3FKIX-ray3.88D1-221[»]
3H3VX-ray4.00E1-221[»]
3HOUX-ray3.20D/P1-221[»]
3HOVX-ray3.50D1-221[»]
3HOWX-ray3.60D1-221[»]
3HOXX-ray3.65D1-221[»]
3HOYX-ray3.40D1-221[»]
3HOZX-ray3.65D1-221[»]
3I4MX-ray3.70D1-221[»]
3I4NX-ray3.90D1-221[»]
3J0Kelectron microscopy36.00D1-221[»]
3J1Nelectron microscopy16.00D4-221[»]
3K1FX-ray4.30D1-221[»]
3PO2X-ray3.30D1-221[»]
3PO3X-ray3.30D1-221[»]
3QT1X-ray4.30D3-221[»]
4A3BX-ray3.50D1-221[»]
4A3CX-ray3.50D1-221[»]
4A3DX-ray3.40D1-221[»]
4A3EX-ray3.40D1-221[»]
4A3FX-ray3.50D1-221[»]
4A3GX-ray3.50D1-221[»]
4A3IX-ray3.80D1-221[»]
4A3JX-ray3.70D1-221[»]
4A3KX-ray3.50D1-221[»]
4A3LX-ray3.50D1-221[»]
4A3MX-ray3.90D1-221[»]
4A93X-ray3.40D1-221[»]
4BBRX-ray3.40D1-221[»]
4BBSX-ray3.60D1-221[»]
4BXXX-ray3.28D1-221[»]
4BXZX-ray4.80D1-221[»]
4BY1X-ray3.60D1-221[»]
4BY7X-ray3.15D1-221[»]
4V1Nelectron microscopy7.80D1-221[»]
4V1Oelectron microscopy9.70D1-221[»]
5C3EX-ray3.70D1-221[»]
5C44X-ray3.95D1-221[»]
5C4AX-ray4.20D1-221[»]
5C4XX-ray4.00D1-221[»]
5FMFelectron microscopy6.00D3-221[»]
5FYWelectron microscopy4.35D1-221[»]
5FZ5electron microscopy8.80D1-221[»]
5IP7X-ray3.52D1-221[»]
5IP9X-ray3.90D1-221[»]
5SVAelectron microscopy15.30D1-221[»]
ProteinModelPortaliP20433.
SMRiP20433.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP20433.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000004912.
HOGENOMiHOG000195281.
InParanoidiP20433.
KOiK03012.
OMAiLHPFEIA.
OrthoDBiEOG092C5NLC.

Family and domain databases

InterProiIPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]
PfamiPF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]
SMARTiSM00657. RPOL4c. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 1 hit.

Sequencei

Sequence statusi: Complete.

P20433-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL
60 70 80 90 100
NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENANDE TTAVEDEDDD
110 120 130 140 150
LDEDDVNADD DDFMHSETRE KELESIDVLL EQTTGGNNKD LKNTMQYLTN
160 170 180 190 200
FSRFRDQETV GAVIQLLKST GLHPFEVAQL GSLACDTADE AKTLIPSLNN
210 220
KISDDELERI LKELSNLETL Y
Length:221
Mass (Da):25,414
Last modified:February 1, 1991 - v1
Checksum:i72A8A26871B87775
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27253 Genomic DNA. Translation: AAA34996.1.
X58099 Genomic DNA. Translation: CAA41112.1.
X87371 Genomic DNA. Translation: CAA60815.1.
Z49415 Genomic DNA. Translation: CAA89435.1.
AY557856 Genomic DNA. Translation: AAS56182.1.
BK006943 Genomic DNA. Translation: DAA08660.1.
PIRiA32490.
RefSeqiNP_012395.1. NM_001181573.1.

Genome annotation databases

EnsemblFungiiYJL140W; YJL140W; YJL140W.
GeneIDi853301.
KEGGisce:YJL140W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27253 Genomic DNA. Translation: AAA34996.1.
X58099 Genomic DNA. Translation: CAA41112.1.
X87371 Genomic DNA. Translation: CAA60815.1.
Z49415 Genomic DNA. Translation: CAA89435.1.
AY557856 Genomic DNA. Translation: AAS56182.1.
BK006943 Genomic DNA. Translation: DAA08660.1.
PIRiA32490.
RefSeqiNP_012395.1. NM_001181573.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NT9X-ray4.20D1-221[»]
1PQVX-ray3.80D1-85[»]
D115-221[»]
1WCMX-ray3.80D4-221[»]
1Y14X-ray2.30A/C35-221[»]
1Y1VX-ray3.80D1-221[»]
1Y1WX-ray4.00D1-221[»]
1Y1YX-ray4.00D1-221[»]
1Y77X-ray4.50D1-221[»]
2B63X-ray3.80D1-221[»]
2B8KX-ray4.15D1-221[»]
2JA5X-ray3.80D1-221[»]
2JA6X-ray4.00D1-221[»]
2JA7X-ray3.80D/P1-221[»]
2JA8X-ray3.80D1-221[»]
2R7ZX-ray3.80D1-221[»]
2R92X-ray3.80D1-221[»]
2R93X-ray4.00D1-221[»]
2VUMX-ray3.40D1-221[»]
3FKIX-ray3.88D1-221[»]
3H3VX-ray4.00E1-221[»]
3HOUX-ray3.20D/P1-221[»]
3HOVX-ray3.50D1-221[»]
3HOWX-ray3.60D1-221[»]
3HOXX-ray3.65D1-221[»]
3HOYX-ray3.40D1-221[»]
3HOZX-ray3.65D1-221[»]
3I4MX-ray3.70D1-221[»]
3I4NX-ray3.90D1-221[»]
3J0Kelectron microscopy36.00D1-221[»]
3J1Nelectron microscopy16.00D4-221[»]
3K1FX-ray4.30D1-221[»]
3PO2X-ray3.30D1-221[»]
3PO3X-ray3.30D1-221[»]
3QT1X-ray4.30D3-221[»]
4A3BX-ray3.50D1-221[»]
4A3CX-ray3.50D1-221[»]
4A3DX-ray3.40D1-221[»]
4A3EX-ray3.40D1-221[»]
4A3FX-ray3.50D1-221[»]
4A3GX-ray3.50D1-221[»]
4A3IX-ray3.80D1-221[»]
4A3JX-ray3.70D1-221[»]
4A3KX-ray3.50D1-221[»]
4A3LX-ray3.50D1-221[»]
4A3MX-ray3.90D1-221[»]
4A93X-ray3.40D1-221[»]
4BBRX-ray3.40D1-221[»]
4BBSX-ray3.60D1-221[»]
4BXXX-ray3.28D1-221[»]
4BXZX-ray4.80D1-221[»]
4BY1X-ray3.60D1-221[»]
4BY7X-ray3.15D1-221[»]
4V1Nelectron microscopy7.80D1-221[»]
4V1Oelectron microscopy9.70D1-221[»]
5C3EX-ray3.70D1-221[»]
5C44X-ray3.95D1-221[»]
5C4AX-ray4.20D1-221[»]
5C4XX-ray4.00D1-221[»]
5FMFelectron microscopy6.00D3-221[»]
5FYWelectron microscopy4.35D1-221[»]
5FZ5electron microscopy8.80D1-221[»]
5IP7X-ray3.52D1-221[»]
5IP9X-ray3.90D1-221[»]
5SVAelectron microscopy15.30D1-221[»]
ProteinModelPortaliP20433.
SMRiP20433.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33617. 129 interactors.
DIPiDIP-55N.
IntActiP20433. 21 interactors.
MINTiMINT-538215.

PTM databases

iPTMnetiP20433.

Proteomic databases

MaxQBiP20433.
PRIDEiP20433.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJL140W; YJL140W; YJL140W.
GeneIDi853301.
KEGGisce:YJL140W.

Organism-specific databases

EuPathDBiFungiDB:YJL140W.
SGDiS000003676. RPB4.

Phylogenomic databases

GeneTreeiENSGT00390000004912.
HOGENOMiHOG000195281.
InParanoidiP20433.
KOiK03012.
OMAiLHPFEIA.
OrthoDBiEOG092C5NLC.

Enzyme and pathway databases

BioCyciYEAST:G3O-31585-MONOMER.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-SCE-72086. mRNA Capping.
R-SCE-72165. mRNA Splicing - Minor Pathway.
R-SCE-73776. RNA Polymerase II Promoter Escape.
R-SCE-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SCE-75953. RNA Polymerase II Transcription Initiation.
R-SCE-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

EvolutionaryTraceiP20433.
PROiP20433.

Family and domain databases

InterProiIPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]
PfamiPF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]
SMARTiSM00657. RPOL4c. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRPB4_YEAST
AccessioniPrimary (citable) accession number: P20433
Secondary accession number(s): D6VW44
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1991
Last modified: November 30, 2016
This is version 165 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: 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.