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P34087 (RPB7_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 134. 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 RPB7

Short name=RNA polymerase II subunit B7
Alternative name(s):
B16
Gene names
Name:RPB7
Ordered Locus Names:YDR404C
ORF Names:D9509.22
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length171 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. RPB7 is part of a subcomplex with RPB4 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 recruits FCP1 to Pol II. Ref.5 Ref.6 Ref.10

Subunit structure

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the 10-subunit Pol II core complex. The RPB4-RPB7 subcomplex probably associates with TFG1. Interacts with NRD1 and PAT1. Ref.8 Ref.9 Ref.10

Subcellular location

Nucleus. Cytoplasm. CytoplasmP-body. Note: Seems to shuttle between nucleus and cytoplasm in a complex with RPB4. Ref.7 Ref.10

Miscellaneous

Present with 6420 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the eukaryotic RPB7/RPC8 RNA polymerase subunit family.

Ontologies

Keywords
   Biological processTranscription
   Cellular componentCytoplasm
DNA-directed RNA polymerase
Nucleus
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processnuclear-transcribed mRNA catabolic process, exonucleolytic

Inferred from genetic interaction Ref.10. Source: SGD

positive regulation of nuclear-transcribed mRNA poly(A) tail shortening

Inferred from mutant phenotype Ref.10. Source: SGD

positive regulation of translational initiation

Inferred from mutant phenotype PubMed 21074047. Source: SGD

transcription from RNA polymerase II promoter

Inferred from genetic interaction PubMed 10082533. Source: SGD

transcription initiation from RNA polymerase II promoter

Inferred from direct assay Ref.5. 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.7. Source: SGD

cytoplasmic mRNA processing body

Inferred from direct assay Ref.10. Source: SGD

nucleus

Inferred from direct assay Ref.7. Source: SGD

   Molecular_functionDNA-directed RNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

single-stranded DNA binding

Inferred from direct assay Ref.5. Source: SGD

single-stranded RNA binding

Inferred from direct assay Ref.5. Source: SGD

translation initiation factor binding

Inferred from physical interaction PubMed 21074047. Source: SGD

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

RPB4P204334EBI-15790,EBI-15777

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 171171DNA-directed RNA polymerase II subunit RPB7
PRO_0000073993

Experimental info

Mutagenesis108 – 1136Missing: Lowers nucleic-acid binding of RPB4-RPB7 by 10-fold; no effect on association with Pol II core complex; abolishes transcriptional activity of Pol II. Ref.5
Mutagenesis151 – 1588Missing: No effect on nucleic-acid binding of RPB4-RPB7 and on association with Pol II core complex; abolishes transcriptional activity of Pol II. Ref.5

Secondary structure

....................................... 171
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P34087 [UniParc].

Last modified February 1, 1994. Version 1.
Checksum: 44C85603A93CDE67

FASTA17119,058
        10         20         30         40         50         60 
MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR 

        70         80         90        100        110        120 
ILPTDGSAEF NVKYRAVVFK PFKGEVVDGT VVSCSQHGFE VQVGPMKVFV TKHLMPQDLT 

       130        140        150        160        170 
FNAGSNPPSY QSSEDVITIK SRIRVKIEGC ISQVSSIHAI GSIKEDYLGA I 

« Hide

References

« Hide 'large scale' references
[1]"RPB7, one of two dissociable subunits of yeast RNA polymerase II, is essential for cell viability."
McKune K., Richards K.L., Edwards A.M., Young R.A., Woychik N.A.
Yeast 9:295-299(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. expand/collapse author list , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"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].
[5]"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, RNA-BINDING, MUTAGENESIS OF 108-VAL--HIS-113 AND 151-ILE--HIS-158.
[6]"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.
[7]"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.
[8]"Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts."
Mitsuzawa H., Kanda E., Ishihama A.
Nucleic Acids Res. 31:4696-4701(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH NRD1.
[9]"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.
[10]"The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms."
Lotan R., Goler-Baron V., Duek L., Haimovich G., Choder M.
J. Cell Biol. 178:1133-1143(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PAT1.
[11]"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.
[12]"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.
[13]"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.
[14]"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.
[15]"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.
[16]"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
S59775 Genomic DNA. Translation: AAC60558.1.
U32274 Genomic DNA. Translation: AAB64844.1.
BK006938 Genomic DNA. Translation: DAA12246.1.
PIRS30140.
RefSeqNP_010692.3. NM_001180712.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1NT9X-ray4.20G1-171[»]
1PQVX-ray3.80G1-171[»]
1WCMX-ray3.80G1-171[»]
1Y14X-ray2.30B/D1-171[»]
1Y1VX-ray3.80G1-171[»]
1Y1WX-ray4.00G1-171[»]
1Y1YX-ray4.00G1-171[»]
1Y77X-ray4.50G1-171[»]
2B63X-ray3.80G1-171[»]
2B8KX-ray4.15G1-171[»]
2JA5X-ray3.80G1-171[»]
2JA6X-ray4.00G1-171[»]
2JA7X-ray3.80G/S1-171[»]
2JA8X-ray3.80G1-171[»]
2R7ZX-ray3.80G1-171[»]
2R92X-ray3.80G1-171[»]
2R93X-ray4.00G1-171[»]
2VUMX-ray3.40G1-171[»]
3FKIX-ray3.88G1-171[»]
3H3VX-ray4.00H1-171[»]
3HOUX-ray3.20G/S1-171[»]
3HOVX-ray3.50G1-171[»]
3HOWX-ray3.60G1-171[»]
3HOXX-ray3.65G1-171[»]
3HOYX-ray3.40G1-171[»]
3HOZX-ray3.65G1-171[»]
3I4MX-ray3.70G1-171[»]
3I4NX-ray3.90G1-171[»]
3J1Nelectron microscopy16.00G1-171[»]
3K1FX-ray4.30G1-171[»]
3PO2X-ray3.30G1-171[»]
3PO3X-ray3.30G1-171[»]
3QT1X-ray4.30G1-171[»]
4A3BX-ray3.50G1-171[»]
4A3CX-ray3.50G1-171[»]
4A3DX-ray3.40G1-171[»]
4A3EX-ray3.40G1-171[»]
4A3FX-ray3.50G1-171[»]
4A3GX-ray3.50G1-171[»]
4A3IX-ray3.80G1-171[»]
4A3JX-ray3.70G1-171[»]
4A3KX-ray3.50G1-171[»]
4A3LX-ray3.50G1-171[»]
4A3MX-ray3.90G1-171[»]
4A93X-ray3.40G1-171[»]
4BBRX-ray3.40G1-171[»]
4BBSX-ray3.60G1-171[»]
4BXXX-ray3.28G1-171[»]
4BXZX-ray4.80G1-171[»]
4BY1X-ray3.60G1-171[»]
4BY7X-ray3.15G1-171[»]
ProteinModelPortalP34087.
SMRP34087. Positions 1-171.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32464. 77 interactions.
DIPDIP-725N.
IntActP34087. 23 interactions.
MINTMINT-539630.
STRING4932.YDR404C.

Proteomic databases

PaxDbP34087.
PeptideAtlasP34087.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDR404C; YDR404C; YDR404C.
GeneID852013.
KEGGsce:YDR404C.

Organism-specific databases

CYGDYDR404c.
SGDS000002812. RPB7.

Phylogenomic databases

eggNOGCOG1095.
GeneTreeENSGT00390000008975.
HOGENOMHOG000158201.
KOK03015.
OMAPPQFTNN.
OrthoDBEOG7X0VTZ.

Enzyme and pathway databases

BioCycYEAST:G3O-29948-MONOMER.

Gene expression databases

GenevestigatorP34087.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
3.30.1490.120. 1 hit.
InterProIPR012340. NA-bd_OB-fold.
IPR003029. Rbsml_prot_S1_RNA-bd_dom.
IPR022967. RNA-binding_domain_S1.
IPR005576. RNA_pol_Rpb7_N.
[Graphical view]
PfamPF00575. S1. 1 hit.
PF03876. SHS2_Rpb7-N. 1 hit.
[Graphical view]
SMARTSM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
SSF88798. SSF88798. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP34087.
NextBio970216.
PROP34087.

Entry information

Entry nameRPB7_YEAST
AccessionPrimary (citable) accession number: P34087
Secondary accession number(s): D6VT36
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: April 16, 2014
This is version 134 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 IV

Yeast (Saccharomyces cerevisiae) chromosome IV: 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