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P16370 (RPB3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 147. 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 RPB3

Short name=RNA polymerase II subunit 3
Short name=RNA polymerase II subunit B3
Alternative name(s):
B44.5
DNA-directed RNA polymerase II 45 kDa polypeptide
Gene names
Name:RPB3
Ordered Locus Names:YIL021W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length318 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination. Ref.5

Subunit structure

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

Subcellular location

Nucleus.

Miscellaneous

Present with 10000 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the archaeal RpoD/eukaryotic RPB3 RNA polymerase subunit family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

RPB11P389024EBI-15773,EBI-15806
RPB2P085185EBI-15773,EBI-15767

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 318317DNA-directed RNA polymerase II subunit RPB3
PRO_0000132748

Sites

Metal binding861Zinc
Metal binding881Zinc
Metal binding921Zinc
Metal binding951Zinc

Amino acid modifications

Modified residue21N-acetylserine Ref.6

Natural variations

Natural variant301A → D in mutant RPB3-1.

Experimental info

Mutagenesis91K → E: Transcript termination readthrough. Ref.5
Sequence conflict1751A → G in AAA34889. Ref.1

Secondary structure

.............................................................. 318
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P16370 [UniParc].

Last modified February 1, 1995. Version 2.
Checksum: 8E1D1E6BB7B51D89

FASTA31835,298
        10         20         30         40         50         60 
MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD 

        70         80         90        100        110        120 
EFIAHRLGLI PLQSMDIEQL EYSRDCFCED HCDKCSVVLT LQAFGESEST TNVYSKDLVI 

       130        140        150        160        170        180 
VSNLMGRNIG HPIIQDKEGN GVLICKLRKG QELKLTCVAK KGIAKEHAKW GPAAAIEFEY 

       190        200        210        220        230        240 
DPWNKLKHTD YWYEQDSAKE WPQSKNCEYE DPPNEGDPFD YKAQADTFYM NVESVGSIPV 

       250        260        270        280        290        300 
DQVVVRGIDT LQKKVASILL ALTQMDQDKV NFASGDNNTA SNMLGSNEDV MMTGAEQDPY 

       310 
SNASQMGNTG SGGYDNAW 

« Hide

References

« Hide 'large scale' references
[1]"RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus."
Kolodziej P., Young R.A.
Mol. Cell. Biol. 9:5387-5394(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 206-223.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX."
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D., Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C. expand/collapse author list , Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.
Nature 387:84-87(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]"cis- and trans-Acting determinants of transcription termination by yeast RNA polymerase II."
Steinmetz E.J., Ng S.B., Cloute J.P., Brow D.A.
Mol. Cell. Biol. 26:2688-2696(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF LYS-9.
[6]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[7]"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.
[8]"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.
[9]"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.
[10]"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.
[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, 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.
[14]"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.
[15]"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).
[16]"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.
[17]"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.
[18]"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.
[19]"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
Z46881 Genomic DNA. Translation: CAA86971.1.
M27496 Genomic DNA. Translation: AAA34889.1.
BK006942 Genomic DNA. Translation: DAA08524.1.
PIRS49961.
RefSeqNP_012243.3. NM_001179371.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10C1-318[»]
1I50X-ray2.80C1-318[»]
1I6HX-ray3.30C1-318[»]
1K83X-ray2.80C1-318[»]
1NIKX-ray4.10C1-318[»]
1NT9X-ray4.20C1-318[»]
1PQVX-ray3.80C1-318[»]
1R5UX-ray4.50C1-318[»]
1R9SX-ray4.25C1-318[»]
1R9TX-ray3.50C1-318[»]
1SFOX-ray3.61C1-318[»]
1TWAX-ray3.20C1-318[»]
1TWCX-ray3.00C1-318[»]
1TWFX-ray2.30C1-318[»]
1TWGX-ray3.30C1-318[»]
1TWHX-ray3.40C1-318[»]
1WCMX-ray3.80C1-318[»]
1Y1VX-ray3.80C1-318[»]
1Y1WX-ray4.00C1-318[»]
1Y1YX-ray4.00C1-318[»]
1Y77X-ray4.50C1-318[»]
2B63X-ray3.80C1-318[»]
2B8KX-ray4.15C1-318[»]
2E2HX-ray3.95C1-318[»]
2E2IX-ray3.41C1-318[»]
2E2JX-ray3.50C1-318[»]
2JA5X-ray3.80C1-318[»]
2JA6X-ray4.00C1-318[»]
2JA7X-ray3.80C/O1-318[»]
2JA8X-ray3.80C1-318[»]
2NVQX-ray2.90C1-318[»]
2NVTX-ray3.36C1-318[»]
2NVXX-ray3.60C1-318[»]
2NVYX-ray3.40C1-318[»]
2NVZX-ray4.30C1-318[»]
2R7ZX-ray3.80C1-318[»]
2R92X-ray3.80C1-318[»]
2R93X-ray4.00C1-318[»]
2VUMX-ray3.40C1-318[»]
2YU9X-ray3.40C1-318[»]
3CQZX-ray2.80C1-318[»]
3FKIX-ray3.88C1-318[»]
3GTGX-ray3.78C1-318[»]
3GTJX-ray3.42C1-318[»]
3GTKX-ray3.80C1-318[»]
3GTLX-ray3.38C1-318[»]
3GTMX-ray3.80C1-318[»]
3GTOX-ray4.00C1-318[»]
3GTPX-ray3.90C1-318[»]
3GTQX-ray3.80C1-318[»]
3H3VX-ray4.00D1-318[»]
3HOUX-ray3.20C/O1-318[»]
3HOVX-ray3.50C1-318[»]
3HOWX-ray3.60C2-318[»]
3HOXX-ray3.65C2-318[»]
3HOYX-ray3.40C2-318[»]
3HOZX-ray3.65C2-318[»]
3I4MX-ray3.70C1-318[»]
3I4NX-ray3.90C1-318[»]
3J1Nelectron microscopy16.00C1-268[»]
3K1FX-ray4.30C1-318[»]
3K7AX-ray3.80C1-318[»]
3M3YX-ray3.18C1-318[»]
3M4OX-ray3.57C1-318[»]
3PO2X-ray3.30C1-318[»]
3PO3X-ray3.30C1-318[»]
3QT1X-ray4.30C1-318[»]
3RZDX-ray3.30C1-318[»]
3RZOX-ray3.00C1-318[»]
3S14X-ray2.85C1-318[»]
3S15X-ray3.30C1-318[»]
3S16X-ray3.24C1-318[»]
3S17X-ray3.20C1-318[»]
3S1MX-ray3.13C1-318[»]
3S1NX-ray3.10C1-318[»]
3S1QX-ray3.30C1-318[»]
3S1RX-ray3.20C1-318[»]
3S2DX-ray3.20C1-318[»]
3S2HX-ray3.30C1-318[»]
4A3BX-ray3.50C1-318[»]
4A3CX-ray3.50C1-318[»]
4A3DX-ray3.40C1-318[»]
4A3EX-ray3.40C1-318[»]
4A3FX-ray3.50C1-318[»]
4A3GX-ray3.50C1-318[»]
4A3IX-ray3.80C1-318[»]
4A3JX-ray3.70C1-318[»]
4A3KX-ray3.50C1-318[»]
4A3LX-ray3.50C1-318[»]
4A3MX-ray3.90C1-318[»]
4A93X-ray3.40C1-318[»]
4BBRX-ray3.40C1-318[»]
4BBSX-ray3.60C1-318[»]
4BXXX-ray3.28C1-318[»]
4BXZX-ray4.80C1-318[»]
4BY1X-ray3.60C1-318[»]
4BY7X-ray3.15C1-318[»]
ProteinModelPortalP16370.
SMRP16370. Positions 3-268.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34967. 193 interactions.
DIPDIP-837N.
IntActP16370. 32 interactions.
MINTMINT-613688.
STRING4932.YIL021W.

Proteomic databases

PaxDbP16370.
PeptideAtlasP16370.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYIL021W; YIL021W; YIL021W.
GeneID854791.
KEGGsce:YIL021W.

Organism-specific databases

CYGDYIL021w.
SGDS000001283. RPB3.

Phylogenomic databases

eggNOGCOG0202.
GeneTreeENSGT00640000091532.
HOGENOMHOG000230844.
KOK03011.
OMAHTDYWYE.
OrthoDBEOG776T14.

Enzyme and pathway databases

BioCycYEAST:G3O-31296-MONOMER.

Gene expression databases

GenevestigatorP16370.

Family and domain databases

Gene3D2.170.120.12. 1 hit.
InterProIPR001514. DNA-dir_RNA_pol_30-40kDasu_CS.
IPR011262. DNA-dir_RNA_pol_insert.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
IPR009025. RBP11-like_dimer.
[Graphical view]
PfamPF01000. RNA_pol_A_bac. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
SMARTSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMSSF55257. SSF55257. 1 hit.
SSF56553. SSF56553. 1 hit.
PROSITEPS00446. RNA_POL_D_30KD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP16370.
NextBio977585.
PROP16370.

Entry information

Entry nameRPB3_YEAST
AccessionPrimary (citable) accession number: P16370
Secondary accession number(s): D6VVQ8
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: February 1, 1995
Last modified: April 16, 2014
This is version 147 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IX

Yeast (Saccharomyces cerevisiae) chromosome IX: 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