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P27999 (RPB9_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 155. 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·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA-directed RNA polymerase II subunit RPB9

Short name=RNA polymerase II subunit B9
Alternative name(s):
B12.6
DNA-directed RNA polymerase II 14.2 kDa polypeptide
DNA-directed RNA polymerase II subunit 9
Gene names
Name:RPB9
Ordered Locus Names:YGL070C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length122 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. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template. Involved in the regulation of transcription elongation. Involved in DNA repair of damage in the transcribed strand. Mediates a transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER). Ref.7

Subunit structure

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.

Subcellular location

Nucleus.

Miscellaneous

Present with 2440 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family.

Contains 1 TFIIS-type zinc finger.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 122122DNA-directed RNA polymerase II subunit RPB9
PRO_0000121474

Regions

Zinc finger7 – 3226C4-type Potential
Zinc finger71 – 11141TFIIS-type

Sites

Metal binding71Zinc 1
Metal binding101Zinc 1
Metal binding291Zinc 1
Metal binding321Zinc 1
Metal binding751Zinc 2
Metal binding781Zinc 2
Metal binding1031Zinc 2
Metal binding1061Zinc 2

Amino acid modifications

Modified residue401Phosphoserine Ref.9

Secondary structure

................................ 122
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P27999 [UniParc].

Last modified August 1, 1992. Version 1.
Checksum: A80D69678A722881

FASTA12214,288
        10         20         30         40         50         60 
MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT NIGETAGVVQ 

        70         80         90        100        110        120 
DIGSDPTLPR SDRECPKCHS RENVFFQSQQ RRKDTSMVLF FVCLSCSHIF TSDQKNKRTQ 


FS 

« Hide

References

« Hide 'large scale' references
[1]"Yeast RNA polymerase II subunit RPB9 is essential for growth at temperature extremes."
Woychik N.A., Lane W.S., Young R.A.
J. Biol. Chem. 266:19053-19055(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 46-62.
[2]"Sequence analysis of 203 kilobases from Saccharomyces cerevisiae chromosome VII."
Rieger M., Brueckner M., Schaefer M., Mueller-Auer S.
Yeast 13:1077-1090(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. expand/collapse author list , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"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.
[6]"RNA polymerase II subunit Rpb9 regulates transcription elongation in vivo."
Hemming S.A., Jansma D.B., Macgregor P.F., Goryachev A., Friesen J.D., Edwards A.M.
J. Biol. Chem. 275:35506-35511(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN TRANSCRIPTION ELONGATION.
[7]"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.
[8]"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].
[9]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-40, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"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.
[11]"Structural basis of transcription: RNA polymerase II at 2.8 A resolution."
Cramer P., Bushnell D.A., Kornberg R.D.
Science 292:1863-1876(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[12]"Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution."
Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D.
Science 292:1876-1882(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[13]"Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution."
Bushnell D.A., Cramer P., Kornberg R.D.
Proc. Natl. Acad. Sci. U.S.A. 99:1218-1222(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX IN COMPLEX WITH ALPHA-AMANITIN.
[14]"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.
[15]"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.
[16]"Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription."
Bushnell D.A., Kornberg R.D.
Proc. Natl. Acad. Sci. U.S.A. 100:6969-6973(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.1 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[17]"Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center."
Westover K.D., Bushnell D.A., Kornberg R.D.
Cell 119:481-489(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF THE RNA POL II CORE 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).
[19]"Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms."
Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D.
Science 303:983-988(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.
[20]"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.
[21]"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.
[22]"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
M73060 Genomic DNA. Translation: AAA34997.1.
Z72592 Genomic DNA. Translation: CAA96774.1.
AY557799 Genomic DNA. Translation: AAS56125.1.
BK006941 Genomic DNA. Translation: DAA08033.1.
PIRRNBY29. A41016.
RefSeqNP_011445.1. NM_001180935.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10I1-122[»]
1I50X-ray2.80I1-122[»]
1I6HX-ray3.30I1-122[»]
1K83X-ray2.80I1-122[»]
1NIKX-ray4.10I1-122[»]
1NT9X-ray4.20I1-122[»]
1PQVX-ray3.80I1-122[»]
1R5UX-ray4.50I1-122[»]
1R9SX-ray4.25I1-122[»]
1R9TX-ray3.50I1-122[»]
1SFOX-ray3.61I1-122[»]
1TWAX-ray3.20I1-122[»]
1TWCX-ray3.00I1-122[»]
1TWFX-ray2.30I1-122[»]
1TWGX-ray3.30I1-122[»]
1TWHX-ray3.40I1-122[»]
1WCMX-ray3.80I1-122[»]
1Y1VX-ray3.80I1-122[»]
1Y1WX-ray4.00I1-122[»]
1Y1YX-ray4.00I1-122[»]
1Y77X-ray4.50I1-122[»]
2B63X-ray3.80I1-122[»]
2B8KX-ray4.15I1-122[»]
2E2HX-ray3.95I1-122[»]
2E2IX-ray3.41I1-122[»]
2E2JX-ray3.50I1-122[»]
2JA5X-ray3.80I1-122[»]
2JA6X-ray4.00I1-122[»]
2JA7X-ray3.80I/U1-122[»]
2JA8X-ray3.80I1-122[»]
2NVQX-ray2.90I1-122[»]
2NVTX-ray3.36I1-122[»]
2NVXX-ray3.60I1-122[»]
2NVYX-ray3.40I1-122[»]
2NVZX-ray4.30I1-122[»]
2R7ZX-ray3.80I1-122[»]
2R92X-ray3.80I1-122[»]
2R93X-ray4.00I1-122[»]
2VUMX-ray3.40I1-122[»]
2YU9X-ray3.40I1-122[»]
3CQZX-ray2.80I1-122[»]
3FKIX-ray3.88I1-122[»]
3GTGX-ray3.78I1-122[»]
3GTJX-ray3.42I1-122[»]
3GTKX-ray3.80I1-122[»]
3GTLX-ray3.38I1-122[»]
3GTMX-ray3.80I1-122[»]
3GTOX-ray4.00I1-122[»]
3GTPX-ray3.90I1-122[»]
3GTQX-ray3.80I1-122[»]
3H3VX-ray4.00J1-122[»]
3HOUX-ray3.20I/U1-122[»]
3HOVX-ray3.50I1-122[»]
3HOWX-ray3.60I1-122[»]
3HOXX-ray3.65I1-122[»]
3HOYX-ray3.40I1-122[»]
3HOZX-ray3.65I1-122[»]
3I4MX-ray3.70I1-122[»]
3I4NX-ray3.90I1-122[»]
3J1Nelectron microscopy16.00I1-122[»]
3K1FX-ray4.30I1-122[»]
3K7AX-ray3.80I1-122[»]
3M3YX-ray3.18I1-122[»]
3M4OX-ray3.57I1-122[»]
3PO2X-ray3.30I1-122[»]
3PO3X-ray3.30I1-122[»]
3QT1X-ray4.30I1-87[»]
3RZDX-ray3.30I1-122[»]
3RZOX-ray3.00I1-122[»]
3S14X-ray2.85I1-122[»]
3S15X-ray3.30I1-122[»]
3S16X-ray3.24I1-122[»]
3S17X-ray3.20I1-122[»]
3S1MX-ray3.13I1-122[»]
3S1NX-ray3.10I1-122[»]
3S1QX-ray3.30I1-122[»]
3S1RX-ray3.20I1-122[»]
3S2DX-ray3.20I1-122[»]
3S2HX-ray3.30I1-122[»]
4A3BX-ray3.50I1-122[»]
4A3CX-ray3.50I1-122[»]
4A3DX-ray3.40I1-122[»]
4A3EX-ray3.40I1-122[»]
4A3FX-ray3.50I1-122[»]
4A3GX-ray3.50I1-122[»]
4A3IX-ray3.80I1-122[»]
4A3JX-ray3.70I1-122[»]
4A3KX-ray3.50I1-122[»]
4A3LX-ray3.50I1-122[»]
4A3MX-ray3.90I1-122[»]
4A93X-ray3.40I1-122[»]
4BBRX-ray3.40I1-122[»]
4BBSX-ray3.60I1-122[»]
4BXXX-ray3.28I1-122[»]
4BXZX-ray4.80I1-122[»]
4BY1X-ray3.60I1-122[»]
4BY7X-ray3.15I1-122[»]
ProteinModelPortalP27999.
SMRP27999. Positions 1-122.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33178. 76 interactions.
DIPDIP-610N.
IntActP27999. 17 interactions.
MINTMINT-474033.
STRING4932.YGL070C.

Proteomic databases

PaxDbP27999.
PeptideAtlasP27999.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYGL070C; YGL070C; YGL070C.
GeneID852810.
KEGGsce:YGL070C.

Organism-specific databases

CYGDYGL070c.
SGDS000003038. RPB9.

Phylogenomic databases

eggNOGCOG1594.
GeneTreeENSGT00550000075063.
HOGENOMHOG000228134.
KOK03017.
OMAMHEIDEL.
OrthoDBEOG7B05RW.

Enzyme and pathway databases

BioCycYEAST:G3O-30573-MONOMER.

Gene expression databases

GenevestigatorP27999.

Family and domain databases

InterProIPR019761. DNA-dir_RNA_pol-M_15_CS.
IPR001529. DNA-dir_RNA_pol_M/15kDasu.
IPR012164. DNA-dir_RNApol_C11.
IPR001222. Znf_TFIIS.
[Graphical view]
PfamPF02150. RNA_POL_M_15KD. 1 hit.
PF01096. TFIIS_C. 1 hit.
[Graphical view]
PIRSFPIRSF005586. RNApol_RpoM. 1 hit.
SMARTSM00661. RPOL9. 1 hit.
SM00440. ZnF_C2C2. 1 hit.
[Graphical view]
PROSITEPS01030. RNA_POL_M_15KD. 1 hit.
PS00466. ZF_TFIIS_1. 1 hit.
PS51133. ZF_TFIIS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP27999.
NextBio972339.
PROP27999.

Entry information

Entry nameRPB9_YEAST
AccessionPrimary (citable) accession number: P27999
Secondary accession number(s): D6VU72
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: April 16, 2014
This is version 155 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 VII

Yeast (Saccharomyces cerevisiae) chromosome VII: 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