DNA-directed RNA polymerases I, II, and III subunit RPABC4 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P40422 (RPAB4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 130. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerases I, II, and III subunit RPABC4
Short name=RNA polymerases I, II, and III subunit ABC4

Alternative name(s):
ABC10-alpha

Gene names

Name:	RPC10
Synonyms:	RPB12
Ordered Locus Names:	YHR143W-A
ORF Names:	YHR143BW

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	70 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 a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center.
Subunit structure	Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes consisting of 14, 12 and 17 subunits, respectively. Interacts, via its C-terminus, with TFIIIC subunit TFC4. Ref.6
Subcellular location	Nucleus › nucleolus Ref.7.
Post-translational modification	The N-terminus is blocked.
Miscellaneous	Present with 907 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the archaeal RpoP/eukaryotic RPC10 RNA polymerase subunit family.

Ontologies

Keywords
Biological process	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	transcription from RNA polymerase I promoter Inferred from mutant phenotype PubMed 10531351. Source: SGD transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 10531351. Source: SGD transcription from RNA polymerase III promoter Inferred from mutant phenotype PubMed 10531351. Source: SGD
Cellular_component	DNA-directed RNA polymerase I complex Inferred from direct assay PubMed 1748681 PubMed 9837969. Source: SGD DNA-directed RNA polymerase II, core complex Inferred from direct assay PubMed 1331084 PubMed 1748681. Source: SGD DNA-directed RNA polymerase III complex Inferred from direct assay PubMed 10611227 PubMed 1748681. Source: SGD cytoplasm Inferred from direct assay PubMed 22842922. Source: SGD
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 70

DNA-directed RNA polymerases I, II, and III subunit RPABC4

PRO_0000159753

Regions

Zinc finger

31 – 51

C4-type

Sites

Metal binding

Zinc

Metal binding

Zinc

Metal binding

Zinc

Metal binding

Zinc

Amino acid modifications

Modified residue

Phosphoserine Ref.9

Secondary structure

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P40422 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 066A3D982EC7361E
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FASTA

7,716

        10         20         30         40         50         60 
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR 

        70 
TKRLVQFEAR

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"RPC10 encodes a new mini subunit shared by yeast nuclear RNA polymerases." Treich I., Carles C., Riva M., Sentenac A. Gene Expr. 2:31-37(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 4-23 AND 64-70. Strain: ATCC 204508 / S288c.
[2]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. Vaudin M. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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. LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. 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] [Europe PMC] [Abstract] Cited for: REVIEW ON THE RNA POL III COMPLEX.
[6]	"Interaction between yeast RNA polymerase III and transcription factor TFIIIC via ABC10alpha and tau131 subunits." Dumay H., Rubbi L., Sentenac A., Marck C. J. Biol. Chem. 274:33462-33468(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TFC4.
[7]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[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-20, MASS SPECTROMETRY.
[10]	"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.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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.
[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]	"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] [Europe PMC] [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] [Europe PMC] [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] [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

U23378 Genomic DNA. Translation: AAA64417.1.
U10397 Genomic DNA. Translation: AAB68994.1.
AY558549 Genomic DNA. Translation: AAS56875.1.
BK006934 Genomic DNA. Translation: DAA06837.1.

PIR

S58932.

RefSeq

NP_012013.1. NM_001179273.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1I3Q	X-ray	3.10	L	1-70	[»]
1I50	X-ray	2.80	L	1-70	[»]
1I6H	X-ray	3.30	L	1-70	[»]
1K83	X-ray	2.80	L	1-70	[»]
1NIK	X-ray	4.10	L	1-70	[»]
1NT9	X-ray	4.20	L	1-70	[»]
1PQV	X-ray	3.80	L	1-70	[»]
1R5U	X-ray	4.50	L	1-70	[»]
1R9S	X-ray	4.25	L	1-70	[»]
1R9T	X-ray	3.50	L	1-70	[»]
1SFO	X-ray	3.61	L	1-70	[»]
1TWA	X-ray	3.20	L	1-70	[»]
1TWC	X-ray	3.00	L	1-70	[»]
1TWF	X-ray	2.30	L	1-70	[»]
1TWG	X-ray	3.30	L	1-70	[»]
1TWH	X-ray	3.40	L	1-70	[»]
1WCM	X-ray	3.80	L	1-70	[»]
1Y1V	X-ray	3.80	L	1-70	[»]
1Y1W	X-ray	4.00	L	1-70	[»]
1Y1Y	X-ray	4.00	L	1-70	[»]
1Y77	X-ray	4.50	L	1-70	[»]
2B63	X-ray	3.80	L	1-70	[»]
2B8K	X-ray	4.15	L	1-70	[»]
2E2H	X-ray	3.95	L	1-70	[»]
2E2I	X-ray	3.41	L	1-70	[»]
2E2J	X-ray	3.50	L	1-70	[»]
2JA5	X-ray	3.80	L	1-70	[»]
2JA6	X-ray	4.00	L	1-70	[»]
2JA7	X-ray	3.80	L/X	1-70	[»]
2JA8	X-ray	3.80	L	1-70	[»]
2NVQ	X-ray	2.90	L	1-70	[»]
2NVT	X-ray	3.36	L	1-70	[»]
2NVX	X-ray	3.60	L	1-70	[»]
2NVY	X-ray	3.40	L	1-70	[»]
2NVZ	X-ray	4.30	L	1-70	[»]
2R7Z	X-ray	3.80	L	1-70	[»]
2R92	X-ray	3.80	L	1-70	[»]
2R93	X-ray	4.00	L	1-70	[»]
2VUM	X-ray	3.40	L	1-70	[»]
2YU9	X-ray	3.40	L	1-70	[»]
3CQZ	X-ray	2.80	L	1-70	[»]
3FKI	X-ray	3.88	L	1-70	[»]
3GTG	X-ray	3.78	L	1-70	[»]
3GTJ	X-ray	3.42	L	1-70	[»]
3GTK	X-ray	3.80	L	1-70	[»]
3GTL	X-ray	3.38	L	1-70	[»]
3GTM	X-ray	3.80	L	1-70	[»]
3GTO	X-ray	4.00	L	1-70	[»]
3GTP	X-ray	3.90	L	1-70	[»]
3GTQ	X-ray	3.80	L	1-70	[»]
3H3V	X-ray	4.00	M	1-70	[»]
3HOU	X-ray	3.20	L/X	1-70	[»]
3HOV	X-ray	3.50	L	1-70	[»]
3HOW	X-ray	3.60	L	1-70	[»]
3HOX	X-ray	3.65	L	1-70	[»]
3HOY	X-ray	3.40	L	1-70	[»]
3HOZ	X-ray	3.65	L	1-70	[»]
3I4M	X-ray	3.70	L	1-70	[»]
3I4N	X-ray	3.90	L	1-70	[»]
3J1N	electron microscopy	16.00	L	1-70	[»]
3K1F	X-ray	4.30	L	1-70	[»]
3K7A	X-ray	3.80	L	1-70	[»]
3M3Y	X-ray	3.18	L	1-70	[»]
3M4O	X-ray	3.57	L	1-70	[»]
3PO2	X-ray	3.30	L	1-70	[»]
3PO3	X-ray	3.30	L	1-70	[»]
3QT1	X-ray	4.30	L	1-70	[»]
3RZD	X-ray	3.30	L	1-70	[»]
3RZO	X-ray	3.00	L	1-70	[»]
3S14	X-ray	2.85	L	1-70	[»]
3S15	X-ray	3.30	L	1-70	[»]
3S16	X-ray	3.24	L	1-70	[»]
3S17	X-ray	3.20	L	1-70	[»]
3S1M	X-ray	3.13	L	1-70	[»]
3S1N	X-ray	3.10	L	1-70	[»]
3S1Q	X-ray	3.30	L	1-70	[»]
3S1R	X-ray	3.20	L	1-70	[»]
3S2D	X-ray	3.20	L	1-70	[»]
3S2H	X-ray	3.30	L	1-70	[»]
4A3B	X-ray	3.50	L	1-70	[»]
4A3C	X-ray	3.50	L	1-70	[»]
4A3D	X-ray	3.40	L	1-70	[»]
4A3E	X-ray	3.40	L	1-70	[»]
4A3F	X-ray	3.50	L	1-70	[»]
4A3G	X-ray	3.50	L	1-70	[»]
4A3I	X-ray	3.80	L	1-70	[»]
4A3J	X-ray	3.70	L	1-70	[»]
4A3K	X-ray	3.50	L	1-70	[»]
4A3L	X-ray	3.50	L	1-70	[»]
4A3M	X-ray	3.90	L	1-70	[»]
4A93	X-ray	3.40	L	1-70	[»]
4BBR	X-ray	3.40	L	1-70	[»]
4BBS	X-ray	3.60	L	1-70	[»]

ProteinModelPortal

P40422.

SMR

P40422. Positions 25-70.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-936N.

IntAct

P40422. 4 interactions.

MINT

MINT-559375.

STRING

4932.YHR143W-A.

Proteomic databases

PaxDb

P40422.

PeptideAtlas

P40422.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YHR143W-A; YHR143W-A; YHR143W-A.

GeneID

856547.

KEGG

sce:YHR143W-A.

Organism-specific databases

CYGD

YHR143w-a.

SGD

S000001185. RPC10.

Phylogenomic databases

eggNOG

COG1996.

HOGENOM

HOG000191755.

K03009.

OMA

VIYKART.

OrthoDB

EOG46MFVD.

Enzyme and pathway databases

BioCyc

YEAST:G3O-31179-MONOMER.

Reactome

REACT_83470. Gene Expression.
REACT_87991. Transcription.

Gene expression databases

Genevestigator

P40422.

GermOnline

YHR143W-A. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR006591. RNAP_P/RPC10.
[Graphical view]

Pfam

PF03604. DNA_RNApol_7kD. 1 hit.
[Graphical view]

SMART

SM00659. RPOLCX. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P40422.

NextBio

982349.

Entry information

Entry name

RPAB4_YEAST

Accession

Primary (citable) accession number: P40422
Secondary accession number(s): D3DL93

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 29, 2013
This is version 130 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome VIII

Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents