P27999 (RPB9_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	122 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. 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. Ref.8
Sequence similarities	Belongs to the archaeal rpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family. Contains 1 TFIIS-type zinc finger.

Ontologies

Keywords
Biological process	DNA damage DNA repair Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD transcription initiation from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD
Cellular component	DNA-directed RNA polymerase II, core complex Inferred from direct assay. Source: SGD
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 122

122

DNA-directed RNA polymerase II subunit RPB9

PRO_0000121474

Regions

Zinc finger

7 – 32

26

C4-type Potential

Zinc finger

71 – 111

41

TFIIS-type

Sites

Metal binding

7

1

Zinc 1

Metal binding

10

1

Zinc 1

Metal binding

29

1

Zinc 1

Metal binding

32

1

Zinc 1

Metal binding

75

1

Zinc 2

Metal binding

78

1

Zinc 2

Metal binding

103

1

Zinc 2

Metal binding

106

1

Zinc 2

Amino acid modifications

Modified residue

33

1

Phosphoserine Ref.9

Modified residue

34

1

Phosphotyrosine Ref.9

Modified residue

40

1

Phosphoserine Ref.9

Secondary structure

1

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122

Helix Strand Turn

Details...

Beta strand

8 – 10

3

Beta strand

15 – 19

5

Turn

20 – 23

4

Beta strand

24 – 28

5

Beta strand

30 – 33

4

Beta strand

35 – 37

3

Beta strand

41 – 49

9

Helix

62 – 64

3

Turn

76 – 78

3

Beta strand

83 – 87

5

Beta strand

99 – 103

5

Turn

104 – 106

3

Beta strand

109 – 111

3

Sequences

	Sequence		Length	Mass (Da)
	P27999 [UniParc]. Last modified August 1, 1992. Version 1. Checksum: A80D69678A722881	FASTA	122	14,288
	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

References

	« Hide 'large scale' referencesShow '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: 1918023] [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: 9290212] [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. , 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: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[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. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [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: 10938084] [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: 12411509] [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: 14562106] [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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-33; TYR-34 AND SER-40, MASS SPECTROMETRY.
[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: 14580350] [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: 11313498] [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: 11313499] [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: 11805306] [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: 12914699] [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: 12746495] [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: 12746498] [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: 15537538] [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: 15610738] [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: 14963322] [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: 15591044] [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: 16341226] [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: 16765890] [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.

PIR

RNBY29. A41016.

RefSeq

NP_011445.1. NM_001180935.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1I3Q	X-ray	3.10	I	1-122	[»]
1I50	X-ray	2.80	I	1-122	[»]
1I6H	X-ray	3.30	I	1-122	[»]
1K83	X-ray	2.80	I	1-122	[»]
1NIK	X-ray	4.10	I	1-122	[»]
1NT9	X-ray	4.20	I	1-122	[»]
1PQV	X-ray	3.80	I	1-122	[»]
1R5U	X-ray	4.50	I	1-122	[»]
1R9S	X-ray	4.25	I	1-122	[»]
1R9T	X-ray	3.50	I	1-122	[»]
1SFO	X-ray	3.61	I	1-122	[»]
1TWA	X-ray	3.20	I	1-122	[»]
1TWC	X-ray	3.00	I	1-122	[»]
1TWF	X-ray	2.30	I	1-122	[»]
1TWG	X-ray	3.30	I	1-122	[»]
1TWH	X-ray	3.40	I	1-122	[»]
1WCM	X-ray	3.80	I	1-122	[»]
1Y1V	X-ray	3.80	I	1-122	[»]
1Y1W	X-ray	4.00	I	1-122	[»]
1Y1Y	X-ray	4.00	I	1-122	[»]
1Y77	X-ray	4.50	I	1-122	[»]
2B63	X-ray	3.80	I	1-122	[»]
2B8K	X-ray	4.15	I	1-122	[»]
2E2H	X-ray	3.95	I	1-122	[»]
2E2I	X-ray	3.41	I	1-122	[»]
2E2J	X-ray	3.50	I	1-122	[»]
2JA5	X-ray	3.80	I	1-122	[»]
2JA6	X-ray	4.00	I	1-122	[»]
2JA7	X-ray	3.80	I/U	1-122	[»]
2JA8	X-ray	3.80	I	1-122	[»]
2NVQ	X-ray	2.90	I	1-122	[»]
2NVT	X-ray	3.36	I	1-122	[»]
2NVX	X-ray	3.60	I	1-122	[»]
2NVY	X-ray	3.40	I	1-122	[»]
2NVZ	X-ray	4.30	I	1-122	[»]
2R7Z	X-ray	3.80	I	1-122	[»]
2R92	X-ray	3.80	I	1-122	[»]
2R93	X-ray	4.00	I	1-122	[»]
2VUM	X-ray	3.40	I	1-122	[»]
2YU9	X-ray	3.40	I	1-122	[»]
3CQZ	X-ray	2.80	I	1-122	[»]
3FKI	X-ray	3.88	I	1-122	[»]
3GTG	X-ray	3.78	I	1-122	[»]
3GTJ	X-ray	3.42	I	1-122	[»]
3GTK	X-ray	3.80	I	1-122	[»]
3GTL	X-ray	3.38	I	1-122	[»]
3GTM	X-ray	3.80	I	1-122	[»]
3GTO	X-ray	4.00	I	1-122	[»]
3GTP	X-ray	3.90	I	1-122	[»]
3GTQ	X-ray	3.80	I	1-122	[»]
3H3V	X-ray	4.00	J	1-122	[»]
3HOU	X-ray	3.20	I/U	1-122	[»]
3HOV	X-ray	3.50	I	1-122	[»]
3HOW	X-ray	3.60	I	1-122	[»]
3HOX	X-ray	3.65	I	1-122	[»]
3HOY	X-ray	3.40	I	1-122	[»]
3HOZ	X-ray	3.65	I	1-122	[»]
3I4M	X-ray	3.70	I	1-122	[»]
3I4N	X-ray	3.90	I	1-122	[»]
3K1F	X-ray	4.30	I	1-122	[»]
3K7A	X-ray	3.80	I	1-122	[»]
3M3Y	X-ray	3.18	I	1-122	[»]
3M4O	X-ray	3.57	I	1-122	[»]
3PO2	X-ray	3.30	I	1-122	[»]
3PO3	X-ray	3.30	I	1-122	[»]
3QT1	X-ray	4.30	I	1-87	[»]
3RZD	X-ray	3.30	I	1-122	[»]
3RZO	X-ray	3.00	I	1-122	[»]
3S14	X-ray	2.85	I	1-122	[»]
3S15	X-ray	3.30	I	1-122	[»]
3S16	X-ray	3.24	I	1-122	[»]
3S17	X-ray	3.20	I	1-122	[»]
3S1M	X-ray	3.13	I	1-122	[»]
3S1N	X-ray	3.10	I	1-122	[»]
3S1Q	X-ray	3.30	I	1-122	[»]
3S1R	X-ray	3.20	I	1-122	[»]
3S2D	X-ray	3.20	I	1-122	[»]
3S2H	X-ray	3.30	I	1-122	[»]
4A3C	X-ray	3.50	I	1-122	[»]

ProteinModelPortal

P27999.

SMR

P27999. Positions 1-122.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-610N.

IntAct

P27999. 18 interactions.

MINT

MINT-474033.

STRING

P27999.

Proteomic databases

PeptideAtlas

P27999.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YGL070C; YGL070C; YGL070C.

GeneID

852810.

KEGG

sce:YGL070C.

NMPDR

fig|4932.3.peg.2550.

Organism-specific databases

CYGD

YGL070c.

SGD

S000003038. RPB9.

Phylogenomic databases

eggNOG

fuNOG08432.

GeneTree

EFGT00050000004174.

HOGENOM

HBG717463.

OMA

REAVFFQ.

OrthoDB

EOG4GJ2ZS.

Gene expression databases

ArrayExpress

P27999.

Genevestigator

P27999.

GermOnline

YGL070C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR019761. DNA-dir_RNA_pol-M_15_CS.
IPR001529. DNA-dir_RNA_pol_M/15kDasu.
IPR012164. DNA-dir_RNApol_C11.
IPR001222. Znf_TFIIS.
[Graphical view]

KO

K03017.

Pfam

PF02150. RNA_POL_M_15KD. 1 hit.
PF01096. TFIIS_C. 1 hit.
[Graphical view]

PIRSF

PIRSF005586. RNApol_RpoM. 1 hit.

SMART

SM00661. RPOL9. 1 hit.
SM00440. ZnF_C2C2. 1 hit.
[Graphical view]

PROSITE

PS01030. RNA_POL_M_15KD. 1 hit.
PS00466. ZF_TFIIS_1. 1 hit.
PS51133. ZF_TFIIS_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

972339.

Entry information

Entry name

RPB9_YEAST

Accession

Primary (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:	January 25, 2012
This is version 136 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program