P20434 (RPAB1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerases I, II, and III subunit RPABC1
Short name=RNA polymerases I, II, and III subunit ABC1

Alternative name(s):
ABC27
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide

Gene names

Name:	RPB5
Synonyms:	RPA7, RPC9
Ordered Locus Names:	YBR154C
ORF Names:	YBR1204

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	215 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. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process By similarity.
Subunit structure	Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes consisting of at least 14, 12 and 17 subunits, respectively.
Subcellular location	Nucleus.
Sequence similarities	Belongs to the archaeal rpoH/eukaryotic RPB5 RNA polymerase subunit family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Ligand	DNA-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	tRNA transcription from RNA polymerase III promoter Inferred from direct assay. Source: SGD transcription from RNA polymerase I promoter Inferred from mutant phenotype. Source: SGD transcription from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD
Cellular component	DNA-directed RNA polymerase I complex Inferred from direct assay. Source: SGD DNA-directed RNA polymerase II, core complex Inferred from direct assay Ref.1. Source: SGD DNA-directed RNA polymerase III complex Inferred from direct assay. Source: SGD
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RPB2	P08518	3	EBI-15781,EBI-15767

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 215

215

DNA-directed RNA polymerases I, II, and III subunit RPABC1

PRO_0000146086

Experimental info

Sequence conflict

37

1

L → W in AAC60556. Ref.2

Secondary structure

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215

Helix Strand Turn

Details...

Helix

7 – 25

19

Helix

32 – 35

4

Helix

39 – 46

8

Helix

55 – 57

3

Beta strand

60 – 62

3

Helix

66 – 71

6

Beta strand

78 – 82

5

Beta strand

84 – 88

5

Helix

90 – 102

13

Beta strand

106 – 116

11

Helix

118 – 121

4

Turn

122 – 125

4

Beta strand

131 – 136

6

Helix

137 – 140

4

Helix

144 – 146

3

Beta strand

152 – 155

4

Helix

158 – 167

10

Helix

172 – 174

3

Helix

183 – 188

6

Beta strand

195 – 199

5

Beta strand

204 – 206

3

Beta strand

210 – 214

5

Sequences

	Sequence		Length	Mass (Da)
	P20434 [UniParc]. Last modified February 1, 1991. Version 1. Checksum: 2A15F7114D69D829	FASTA	215	25,079
	10 20 30 40 50 60 MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF 70 80 90 100 110 120 QANPTEESIS KFPDMGSLWV EFCDEPSVGV KTMKTFVIHI QEKNFQTGIF VYQNNITPSA 130 140 150 160 170 180 MKLVPSIPPA TIETFNEAAL VVNITHHELV PKHIRLSSDE KRELLKRYRL KESQLPRIQR 190 200 210 ADPVALYLGL KRGEVVKIIR KSETSGRYAS YRICM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Subunits shared by eukaryotic nuclear RNA polymerases." Woychik N.A., Liao S.-M., Kolodziej P.A., Young R.A. Genes Dev. 4:313-323(1990) [PubMed: 2186966] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Sequence of a 4.8 kb fragment of Saccharomyces cerevisiae chromosome II including three essential open reading frames." Baur A., Schaaff-Gerstenschlaeger I., Boles E., Miosga T., Rose M., Zimmermann F.K. Yeast 9:289-293(1993) [PubMed: 8488729] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed: 7813418] [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]	"The yeast RNA polymerase III transcription machinery: a paradigm for eukaryotic gene activation." Chedin S., Ferri M.L., Peyroche G., Andrau J.-C., Jourdain S., Lefebvre O., Werner M., Carles C., Sentenac A. Cold Spring Harb. Symp. Quant. Biol. 63:381-389(1998) [PubMed: 10384303] [Abstract] Cited for: REVIEW ON THE RNA POL III COMPLEX.
[6]	"Differential roles of phosphorylation in the formation of transcriptional active RNA polymerase I." Fath S., Milkereit P., Peyroche G., Riva M., Carles C., Tschochner H. Proc. Natl. Acad. Sci. U.S.A. 98:14334-14339(2001) [PubMed: 11717393] [Abstract] Cited for: IDENTIFICATION IN THE RNA POL I COMPLEX.
[7]	"Rpa12p, a conserved RNA polymerase I subunit with two functional domains." Van Mullem V., Landrieux E., Vandenhaute J., Thuriaux P. Mol. Microbiol. 43:1105-1113(2002) [PubMed: 11918799] [Abstract] Cited for: IDENTIFICATION IN THE RNA POL I COMPLEX.
[8]	"The A14-A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4-Rpb7 pol II subunits." Peyroche G., Levillain E., Siaut M., Callebaut I., Schultz P., Sentenac A., Riva M., Carles C. Proc. Natl. Acad. Sci. U.S.A. 99:14670-14675(2002) [PubMed: 12407181] [Abstract] Cited for: IDENTIFICATION IN THE RNA POL I COMPLEX.
[9]	"Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target." Todone F., Weinzierl R.O.J., Brick P., Onesti S. Proc. Natl. Acad. Sci. U.S.A. 97:6306-6310(2000) [PubMed: 10841537] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[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]	"Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model." Jasiak A.J., Armache K.J., Martens B., Jansen R.P., Cramer P. Mol. Cell 23:71-81(2006) [PubMed: 16818233] [Abstract] Cited for: 3D-STRUCTURE MODELING OF THE POL III CORE 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: 16341226] [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: 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

X53287 Genomic DNA. Translation: CAA37381.1.
X71329 Genomic DNA. Translation: CAA50472.1.
S59774 Genomic DNA. Translation: AAC60556.1.
Z36023 Genomic DNA. Translation: CAA85113.1.
BK006936 Genomic DNA. Translation: DAA07269.1.

PIR

A34588.

RefSeq

NP_009712.1. NM_001178502.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DZF	X-ray	1.90	A	1-215	[»]
1I3Q	X-ray	3.10	E	1-215	[»]
1I50	X-ray	2.80	E	1-215	[»]
1I6H	X-ray	3.30	E	1-215	[»]
1K83	X-ray	2.80	E	1-215	[»]
1NIK	X-ray	4.10	E	1-215	[»]
1NT9	X-ray	4.20	E	1-215	[»]
1PQV	X-ray	3.80	E	1-215	[»]
1R5U	X-ray	4.50	E	1-215	[»]
1R9S	X-ray	4.25	E	1-215	[»]
1R9T	X-ray	3.50	E	1-215	[»]
1SFO	X-ray	3.61	E	1-215	[»]
1TWA	X-ray	3.20	E	1-215	[»]
1TWC	X-ray	3.00	E	1-215	[»]
1TWF	X-ray	2.30	E	1-215	[»]
1TWG	X-ray	3.30	E	1-215	[»]
1TWH	X-ray	3.40	E	1-215	[»]
1WCM	X-ray	3.80	E	1-215	[»]
1Y1V	X-ray	3.80	E	1-215	[»]
1Y1W	X-ray	4.00	E	1-215	[»]
1Y1Y	X-ray	4.00	E	1-215	[»]
1Y77	X-ray	4.50	E	1-215	[»]
2B63	X-ray	3.80	E	1-215	[»]
2B8K	X-ray	4.15	E	1-215	[»]
2E2H	X-ray	3.95	E	1-215	[»]
2E2I	X-ray	3.41	E	1-215	[»]
2E2J	X-ray	3.50	E	1-215	[»]
2JA5	X-ray	3.80	E	1-215	[»]
2JA6	X-ray	4.00	E	1-215	[»]
2JA7	X-ray	3.80	E/Q	1-215	[»]
2JA8	X-ray	3.80	E	1-215	[»]
2NVQ	X-ray	2.90	E	1-215	[»]
2NVT	X-ray	3.36	E	1-215	[»]
2NVX	X-ray	3.60	E	1-215	[»]
2NVY	X-ray	3.40	E	1-215	[»]
2NVZ	X-ray	4.30	E	1-215	[»]
2R7Z	X-ray	3.80	E	1-215	[»]
2R92	X-ray	3.80	E	1-215	[»]
2R93	X-ray	4.00	E	1-215	[»]
2VUM	X-ray	3.40	E	1-215	[»]
2YU9	X-ray	3.40	E	1-215	[»]
3CQZ	X-ray	2.80	E	1-215	[»]
3FKI	X-ray	3.88	E	1-215	[»]
3GTG	X-ray	3.78	E	1-215	[»]
3GTJ	X-ray	3.42	E	1-215	[»]
3GTK	X-ray	3.80	E	1-215	[»]
3GTL	X-ray	3.38	E	1-215	[»]
3GTM	X-ray	3.80	E	1-215	[»]
3GTO	X-ray	4.00	E	1-215	[»]
3GTP	X-ray	3.90	E	1-215	[»]
3GTQ	X-ray	3.80	E	1-215	[»]
3H3V	X-ray	4.00	F	1-215	[»]
3HOU	X-ray	3.20	E/Q	1-215	[»]
3HOV	X-ray	3.50	E	1-215	[»]
3HOW	X-ray	3.60	E	1-215	[»]
3HOX	X-ray	3.65	E	1-215	[»]
3HOY	X-ray	3.40	E	1-215	[»]
3HOZ	X-ray	3.65	E	1-215	[»]
3I4M	X-ray	3.70	E	1-215	[»]
3I4N	X-ray	3.90	E	1-215	[»]
3K1F	X-ray	4.30	E	1-215	[»]
3K7A	X-ray	3.80	E	1-215	[»]
3M3Y	X-ray	3.18	E	1-215	[»]
3M4O	X-ray	3.57	E	1-215	[»]
3PO2	X-ray	3.30	E	1-215	[»]
3PO3	X-ray	3.30	E	1-215	[»]
3QT1	X-ray	4.30	E	1-215	[»]
3RZD	X-ray	3.30	E	1-215	[»]
3RZO	X-ray	3.00	E	1-215	[»]
3S14	X-ray	2.85	E	1-215	[»]
3S15	X-ray	3.30	E	1-215	[»]
3S16	X-ray	3.24	E	1-215	[»]
3S17	X-ray	3.20	E	1-215	[»]
3S1M	X-ray	3.13	E	1-215	[»]
3S1N	X-ray	3.10	E	1-215	[»]
3S1Q	X-ray	3.30	E	1-215	[»]
3S1R	X-ray	3.20	E	1-215	[»]
3S2D	X-ray	3.20	E	1-215	[»]
3S2H	X-ray	3.30	E	1-215	[»]
4A3C	X-ray	3.50	E	1-215	[»]

ProteinModelPortal

P20434.

SMR

P20434. Positions 1-215.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-71N.

IntAct

P20434. 39 interactions.

MINT

MINT-530046.

STRING

P20434.

Proteomic databases

PeptideAtlas

P20434.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YBR154C; YBR154C; YBR154C.

GeneID

852451.

KEGG

sce:YBR154C.

NMPDR

fig|4932.3.peg.418.

Organism-specific databases

CYGD

YBR154c.

SGD

S000000358. RPB5.

Phylogenomic databases

eggNOG

fuNOG04603.

GeneTree

EFGT00050000006237.

HOGENOM

HBG314635.

OMA

MDDEAET.

OrthoDB

EOG40CMS4.

Enzyme and pathway databases

Reactome

REACT_87991. Transcription.

Gene expression databases

ArrayExpress

P20434.

Genevestigator

P20434.

GermOnline

YBR154C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR014381. DNA-dir_RNA_pol_RPB5_su.
IPR005571. RNA_pol_Rpb5_N.
IPR000783. RNA_pol_subH/Rpb5_C.
IPR020608. RNA_pol_subH/Rpb5_CS.
[Graphical view]

Gene3D

G3DSA:3.40.1340.10. RNA_pol_Rpb5_N. 1 hit.
G3DSA:3.90.940.20. RNApol_RPB5. 1 hit.

KO

K03013.

Pfam

PF01191. RNA_pol_Rpb5_C. 1 hit.
PF03871. RNA_pol_Rpb5_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000747. RPB5. 1 hit.

ProDom

PD005155. RNA_pol_subH/Rpb5_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SUPFAM

SSF53036. RNA_pol_Rpb5_N. 1 hit.
SSF55287. RNApol_RPB5_like. 1 hit.

PROSITE

PS01110. RNA_POL_H_23KD. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

971369.

Entry information

Entry name

RPAB1_YEAST

Accession

Primary (citable) accession number: P20434
Secondary accession number(s): D6VQE9, Q02121

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	February 1, 1991
Last modified:	January 25, 2012
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