P20433 (RPB4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	RPB4
Ordered Locus Names:	YJL140W
ORF Names:	J0654

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	221 AA.
Sequence status	Complete.
Protein existence	Evidence 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.15
Subcellular location	Nucleus. Cytoplasm. Cytoplasm › P-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 process	DNA damage DNA repair Transcription mRNA processing
Cellular component	Cytoplasm DNA-directed RNA polymerase Nucleus
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA 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 initiation from RNA polymerase II promoter Inferred from direct assay Ref.8. Source: SGD
Cellular_component	DNA-directed RNA polymerase II, core complex Inferred from direct assay PubMed 1331084PubMed 2183013PubMed 2186966. Source: SGD cytoplasmic mRNA processing body Inferred from direct assay Ref.13. Source: SGD
Molecular_function	DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NIP1	P32497	5	EBI-15777,EBI-8965
RPB7	P34087	4	EBI-15777,EBI-15790

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 221

221

DNA-directed RNA polymerase II subunit RPB4

PRO_0000073984

Secondary structure

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221

Helix Strand Turn

Details...

Beta strand

6 – 8

3

Helix

17 – 19

3

Beta strand

25 – 27

3

Helix

31 – 33

3

Beta strand

35 – 38

4

Turn

40 – 42

3

Beta strand

44 – 46

3

Beta strand

47 – 50

4

Helix

52 – 71

20

Helix

73 – 75

3

Helix

119 – 133

15

Helix

139 – 151

13

Helix

157 – 168

12

Turn

169 – 171

3

Helix

174 – 182

9

Helix

188 – 194

7

Helix

196 – 198

3

Turn

199 – 201

3

Helix

204 – 217

14

Sequences

	Sequence		Length	Mass (Da)
	P20433 [UniParc]. Last modified February 1, 1991. Version 1. Checksum: 72A8A26871B87775	FASTA	221	25,414
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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]	"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.
[16]	"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.
[17]	"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.
[18]	"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.
[19]	"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.
[20]	"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.
[21]	"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.

PIR

A32490.

RefSeq

NP_012395.1. NM_001181573.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NT9	X-ray	4.20	D	1-221	[»]
1PQV	X-ray	3.80	D	1-221	[»]
1WCM	X-ray	3.80	D	4-221	[»]
1Y14	X-ray	2.30	A/C	35-221	[»]
1Y1V	X-ray	3.80	D	1-221	[»]
1Y1W	X-ray	4.00	D	1-221	[»]
1Y1Y	X-ray	4.00	D	1-221	[»]
1Y77	X-ray	4.50	D	1-221	[»]
2B63	X-ray	3.80	D	1-221	[»]
2B8K	X-ray	4.15	D	1-221	[»]
2JA5	X-ray	3.80	D	1-221	[»]
2JA6	X-ray	4.00	D	1-221	[»]
2JA7	X-ray	3.80	D/P	1-221	[»]
2JA8	X-ray	3.80	D	1-221	[»]
2R7Z	X-ray	3.80	D	1-221	[»]
2R92	X-ray	3.80	D	1-221	[»]
2R93	X-ray	4.00	D	1-221	[»]
2VUM	X-ray	3.40	D	1-221	[»]
3FKI	X-ray	3.88	D	1-221	[»]
3H3V	X-ray	4.00	E	1-221	[»]
3HOU	X-ray	3.20	D/P	1-221	[»]
3HOV	X-ray	3.50	D	1-221	[»]
3HOW	X-ray	3.60	D	1-221	[»]
3HOX	X-ray	3.65	D	1-221	[»]
3HOY	X-ray	3.40	D	1-221	[»]
3HOZ	X-ray	3.65	D	1-221	[»]
3I4M	X-ray	3.70	D	1-221	[»]
3I4N	X-ray	3.90	D	1-221	[»]
3J1N	electron microscopy	16.00	D	4-221	[»]
3K1F	X-ray	4.30	D	1-221	[»]
3PO2	X-ray	3.30	D	1-221	[»]
3PO3	X-ray	3.30	D	1-221	[»]
3QT1	X-ray	4.30	D	3-221	[»]
4A3B	X-ray	3.50	D	1-221	[»]
4A3C	X-ray	3.50	D	1-221	[»]
4A3D	X-ray	3.40	D	1-221	[»]
4A3E	X-ray	3.40	D	1-221	[»]
4A3F	X-ray	3.50	D	1-221	[»]
4A3G	X-ray	3.50	D	1-221	[»]
4A3I	X-ray	3.80	D	1-221	[»]
4A3J	X-ray	3.70	D	1-221	[»]
4A3K	X-ray	3.50	D	1-221	[»]
4A3L	X-ray	3.50	D	1-221	[»]
4A3M	X-ray	3.90	D	1-221	[»]
4A93	X-ray	3.40	D	1-221	[»]
4BBR	X-ray	3.40	D	1-221	[»]
4BBS	X-ray	3.60	D	1-221	[»]

ProteinModelPortal

P20433.

SMR

P20433. Positions 1-221.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-55N.

IntAct

P20433. 18 interactions.

MINT

MINT-538215.

STRING

4932.YJL140W.

Proteomic databases

PaxDb

P20433.

PeptideAtlas

P20433.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YJL140W; YJL140W; YJL140W.

GeneID

853301.

KEGG

sce:YJL140W.

Organism-specific databases

CYGD

YJL140w.

SGD

S000003676. RPB4.

Phylogenomic databases

eggNOG

COG5250.

GeneTree

ENSGT00390000004912.

HOGENOM

HOG000195281.

KO

K03012.

OMA

GTLECED.

OrthoDB

EOG4ZGSNW.

Gene expression databases

Genevestigator

P20433.

GermOnline

YJL140W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]

Pfam

PF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]

SMART

SM00657. RPOL4c. 1 hit.
[Graphical view]

SUPFAM

SSF47819. HRDC_like. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P20433.

NextBio

973621.

Entry information

Entry name

RPB4_YEAST

Accession

Primary (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:	May 1, 2013
This is version 128 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program