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P20433 (RPB4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 136. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | 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:
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 names
Name:RPB4
Ordered Locus Names:YJL140W
ORF Names:J0654
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length221 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13

Subunit structure

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. Ref.13 Ref.17

Subcellular location

Nucleus. Cytoplasm. CytoplasmP-body. Note: Seems to shuttle between nucleus and cytoplasm in a complex with RPB7. Ref.13 Ref.14

Sequence similarities

Belongs to the eukaryotic RPB4 RNA polymerase subunit family.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
mRNA processing
Transcription
   Cellular componentCytoplasm
DNA-directed RNA polymerase
Nucleus
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA export from nucleus in response to heat stress

Inferred from mutant phenotype Ref.11. Source: SGD

nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

Inferred from mutant phenotype Ref.13. Source: SGD

positive regulation of translational initiation

Inferred from mutant phenotype PubMed 21074047. Source: SGD

recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex

Inferred from mutant phenotype PubMed 18195044. Source: SGD

transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 11577101. Source: SGD

transcription initiation from RNA polymerase II promoter

Inferred from direct assay Ref.8. Source: SGD

transcription, RNA-templated

Inferred from direct assay PubMed 18004386. Source: GOC

   Cellular_componentDNA-directed RNA polymerase II, core complex

Inferred from direct assay PubMed 1331084PubMed 2183013PubMed 2186966. Source: SGD

cytoplasm

Inferred from direct assay Ref.11. Source: SGD

cytoplasmic mRNA processing body

Inferred from direct assay Ref.13. Source: SGD

nucleus

Inferred from direct assay Ref.11. Source: SGD

   Molecular_functionDNA-directed RNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

nucleotide binding

Inferred from electronic annotation. Source: InterPro

translation initiation factor binding

Inferred from physical interaction PubMed 21074047. Source: SGD

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

NIP1P324975EBI-15777,EBI-8965
RPB7P340874EBI-15777,EBI-15790

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 221221DNA-directed RNA polymerase II subunit RPB4
PRO_0000073984

Amino acid modifications

Modified residue11N-acetylmethionine Ref.16
Modified residue911Phosphothreonine Ref.15
Modified residue921Phosphothreonine Ref.15

Secondary structure

.................................... 221
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P20433 [UniParc].

Last modified February 1, 1991. Version 1.
Checksum: 72A8A26871B87775

FASTA22125,414
        10         20         30         40         50         60 
MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK 

        70         80         90        100        110        120 
EALVERRRAF KRSQKKHKKK HLKHENANDE TTAVEDEDDD LDEDDVNADD DDFMHSETRE 

       130        140        150        160        170        180 
KELESIDVLL EQTTGGNNKD LKNTMQYLTN FSRFRDQETV GAVIQLLKST GLHPFEVAQL 

       190        200        210        220 
GSLACDTADE AKTLIPSLNN KISDDELERI LKELSNLETL Y 

« Hide

References

« Hide 'large scale' references
[1]"RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth."
Woychik N.A., Young R.A.
Mol. Cell. Biol. 9:2854-2859(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The Saccharomyces cerevisiae RPB4 gene is tightly linked to the TIF2 gene."
Foreman P.K., Davis R.W., Sachs A.B.
Nucleic Acids Res. 19:2781-2781(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Sequence analysis of a 40.7 kb segment from the left arm of yeast chromosome X reveals 14 known genes and 13 new open reading frames including homologues of genes clustered on the right arm of chromosome XI."
Katsoulou C., Tzermia M., Tavernarakis N., Alexandraki D.
Yeast 12:787-797(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[4]"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K. expand/collapse author list , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[6]"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.
[7]"Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro."
Edwards A.M., Kane C.M., Young R.A., Kornberg R.D.
J. Biol. Chem. 266:71-75(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE RPB4-RPB7 COMPLEX.
[8]"Dissociable Rpb4-Rpb7 subassembly of RNA polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation."
Orlicky S.M., Tran P.T., Sayre M.H., Edwards A.M.
J. Biol. Chem. 276:10097-10102(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE RPB4-RPB7 COMPLEX.
[9]"Rpb4, a non-essential subunit of core RNA polymerase II of Saccharomyces cerevisiae is important for activated transcription of a subset of genes."
Pillai B., Sampath V., Sharma N., Sadhale P.
J. Biol. Chem. 276:30641-30647(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[10]"Rpb4 and Rpb9 mediate subpathways of transcription-coupled DNA repair in Saccharomyces cerevisiae."
Li S., Smerdon M.J.
EMBO J. 21:5921-5929(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN DNA REPAIR.
[11]"Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress."
Farago M., Nahari T., Hammel C., Cole C.N., Choder M.
Mol. Biol. Cell 14:2744-2755(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN MRNA EXPORT.
[12]"Structure and mechanism of RNA polymerase II CTD phosphatases."
Kamenski T., Heilmeier S., Meinhart A., Cramer P.
Mol. Cell 15:399-407(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE RPB4-RPB7 COMPLEX.
[13]"The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs."
Lotan R., Bar-On V.G., Harel-Sharvit L., Duek L., Melamed D., Choder M.
Genes Dev. 19:3004-3016(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN MRNA DECAY, SUBCELLULAR LOCATION, INTERACTION WITH PAT1 AND LSM2.
[14]"Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways."
Selitrennik M., Duek L., Lotan R., Choder M.
Eukaryot. Cell 5:2092-2103(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[15]"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-91 AND THR-92, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"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].
[17]"RNA polymerase II/TFIIF structure and conserved organization of the initiation complex."
Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A., Kornberg R.D., Asturias F.J.
Mol. Cell 12:1003-1013(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX, INTERACTION WITH TFG1.
[18]"Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage."
Kettenberger H., Armache K.J., Cramer P.
Cell 114:347-357(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH DST1.
[19]"Architecture of initiation-competent 12-subunit RNA polymerase II."
Armache K.J., Kettenberger H., Cramer P.
Proc. Natl. Acad. Sci. U.S.A. 100:6964-6968(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS) OF THE RNA POL II COMPLEX.
[20]"Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS."
Kettenberger H., Armache K.J., Cramer P.
Mol. Cell 16:955-965(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II COMPLEX.
[21]"Structures of complete RNA polymerase II and its subcomplex, Rpb4/7."
Armache K.J., Mitterweger S., Meinhart A., Cramer P.
J. Biol. Chem. 280:7131-7134(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX.
[22]"Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs."
Kettenberger H., Eisenfuhr A., Brueckner F., Theis M., Famulok M., Cramer P.
Nat. Struct. Mol. Biol. 13:44-48(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX WITH INHIBITING NON-CODING RNA.
[23]"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model."
Meyer P.A., Ye P., Zhang M., Suh M.H., Fu J.
Structure 14:973-982(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.15 ANGSTROMS) OF THE RNA POL II COMPLEX.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA32490.
RefSeqNP_012395.1. NM_001181573.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1NT9X-ray4.20D1-221[»]
1PQVX-ray3.80D1-221[»]
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[»]
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[»]
ProteinModelPortalP20433.
SMRP20433. Positions 1-221.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33617. 117 interactions.
DIPDIP-55N.
IntActP20433. 20 interactions.
MINTMINT-538215.
STRING4932.YJL140W.

Proteomic databases

PaxDbP20433.
PeptideAtlasP20433.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYJL140W; YJL140W; YJL140W.
GeneID853301.
KEGGsce:YJL140W.

Organism-specific databases

CYGDYJL140w.
SGDS000003676. RPB4.

Phylogenomic databases

eggNOGCOG5250.
GeneTreeENSGT00390000004912.
HOGENOMHOG000195281.
KOK03012.
OMAGTLECED.
OrthoDBEOG7NW6NW.

Enzyme and pathway databases

BioCycYEAST:G3O-31585-MONOMER.

Gene expression databases

GenevestigatorP20433.

Family and domain databases

InterProIPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]
PfamPF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]
SMARTSM00657. RPOL4c. 1 hit.
[Graphical view]
SUPFAMSSF47819. SSF47819. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP20433.
NextBio973621.
PROP20433.

Entry information

Entry nameRPB4_YEAST
AccessionPrimary (citable) accession number: P20433
Secondary accession number(s): D6VW44
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1991
Last modified: April 16, 2014
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome X

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

Yeast

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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references