P16370 (RPB3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	318 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. 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.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Coding sequence diversity	Polymorphism
Ligand	Metal-binding Zinc
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	termination of RNA polymerase II transcription Inferred from mutant phenotype Ref.5. Source: SGD
Cellular_component	DNA-directed RNA polymerase II, core complex Inferred from direct assay PubMed 1331084PubMed 2183013PubMed 2186966. 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...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RPB11	P38902	3	EBI-15773,EBI-15806
RPB2	P08518	4	EBI-15773,EBI-15767

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 318

318

DNA-directed RNA polymerase II subunit RPB3

PRO_0000132748

Sites

Metal binding

86

1

Zinc

Metal binding

88

1

Zinc

Metal binding

92

1

Zinc

Metal binding

95

1

Zinc

Natural variations

Natural variant

30

1

A → D in mutant RPB3-1.

Experimental info

Mutagenesis

9

1

K → E: Transcript termination readthrough. Ref.5

Sequence conflict

175

1

A → G in AAA34889. Ref.1

Secondary structure

1

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318

Helix Strand Turn

Details...

Beta strand

5 – 7

3

Beta strand

11 – 13

3

Beta strand

15 – 18

4

Beta strand

21 – 25

5

Helix

27 – 39

13

Beta strand

43 – 54

12

Beta strand

56 – 58

3

Helix

60 – 68

9

Beta strand

72 – 74

3

Helix

77 – 79

3

Turn

83 – 85

3

Beta strand

86 – 90

5

Turn

93 – 95

3

Beta strand

96 – 104

9

Beta strand

107 – 109

3

Beta strand

111 – 114

4

Helix

115 – 117

3

Beta strand

118 – 120

3

Beta strand

128 – 132

5

Beta strand

137 – 139

3

Beta strand

142 – 147

6

Beta strand

152 – 162

11

Turn

164 – 166

3

Helix

168 – 170

3

Beta strand

173 – 180

8

Helix

184 – 186

3

Helix

197 – 200

4

Helix

205 – 207

3

Beta strand

208 – 210

3

Beta strand

215 – 217

3

Beta strand

228 – 234

7

Beta strand

236 – 238

3

Helix

240 – 265

26

Sequences

	Sequence		Length	Mass (Da)
	P16370 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: 8E1D1E6BB7B51D89	FASTA	318	35,298
	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

References

	« Hide 'large scale' referencesShow '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. , 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 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]	"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]	"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.
[7]	"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.
[8]	"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.
[9]	"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.
[10]	"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.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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).
[15]	"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.
[16]	"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.
[17]	"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.
[18]	"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.

PIR

S49961.

RefSeq

NP_012243.3. NM_001179371.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1I3Q	X-ray	3.10	C	1-318	[»]
1I50	X-ray	2.80	C	1-318	[»]
1I6H	X-ray	3.30	C	1-318	[»]
1K83	X-ray	2.80	C	1-318	[»]
1NIK	X-ray	4.10	C	1-318	[»]
1NT9	X-ray	4.20	C	1-318	[»]
1PQV	X-ray	3.80	C	1-318	[»]
1R5U	X-ray	4.50	C	1-318	[»]
1R9S	X-ray	4.25	C	1-318	[»]
1R9T	X-ray	3.50	C	1-318	[»]
1SFO	X-ray	3.61	C	1-318	[»]
1TWA	X-ray	3.20	C	1-318	[»]
1TWC	X-ray	3.00	C	1-318	[»]
1TWF	X-ray	2.30	C	1-318	[»]
1TWG	X-ray	3.30	C	1-318	[»]
1TWH	X-ray	3.40	C	1-318	[»]
1WCM	X-ray	3.80	C	1-318	[»]
1Y1V	X-ray	3.80	C	1-318	[»]
1Y1W	X-ray	4.00	C	1-318	[»]
1Y1Y	X-ray	4.00	C	1-318	[»]
1Y77	X-ray	4.50	C	1-318	[»]
2B63	X-ray	3.80	C	1-318	[»]
2B8K	X-ray	4.15	C	1-318	[»]
2E2H	X-ray	3.95	C	1-318	[»]
2E2I	X-ray	3.41	C	1-318	[»]
2E2J	X-ray	3.50	C	1-318	[»]
2JA5	X-ray	3.80	C	1-318	[»]
2JA6	X-ray	4.00	C	1-318	[»]
2JA7	X-ray	3.80	C/O	1-318	[»]
2JA8	X-ray	3.80	C	1-318	[»]
2NVQ	X-ray	2.90	C	1-318	[»]
2NVT	X-ray	3.36	C	1-318	[»]
2NVX	X-ray	3.60	C	1-318	[»]
2NVY	X-ray	3.40	C	1-318	[»]
2NVZ	X-ray	4.30	C	1-318	[»]
2R7Z	X-ray	3.80	C	1-318	[»]
2R92	X-ray	3.80	C	1-318	[»]
2R93	X-ray	4.00	C	1-318	[»]
2VUM	X-ray	3.40	C	1-318	[»]
2YU9	X-ray	3.40	C	1-318	[»]
3CQZ	X-ray	2.80	C	1-318	[»]
3FKI	X-ray	3.88	C	1-318	[»]
3GTG	X-ray	3.78	C	1-318	[»]
3GTJ	X-ray	3.42	C	1-318	[»]
3GTK	X-ray	3.80	C	1-318	[»]
3GTL	X-ray	3.38	C	1-318	[»]
3GTM	X-ray	3.80	C	1-318	[»]
3GTO	X-ray	4.00	C	1-318	[»]
3GTP	X-ray	3.90	C	1-318	[»]
3GTQ	X-ray	3.80	C	1-318	[»]
3H3V	X-ray	4.00	D	1-318	[»]
3HOU	X-ray	3.20	C/O	1-318	[»]
3HOV	X-ray	3.50	C	1-318	[»]
3HOW	X-ray	3.60	C	2-318	[»]
3HOX	X-ray	3.65	C	2-318	[»]
3HOY	X-ray	3.40	C	2-318	[»]
3HOZ	X-ray	3.65	C	2-318	[»]
3I4M	X-ray	3.70	C	1-318	[»]
3I4N	X-ray	3.90	C	1-318	[»]
3J1N	electron microscopy	16.00	C	1-268	[»]
3K1F	X-ray	4.30	C	1-318	[»]
3K7A	X-ray	3.80	C	1-318	[»]
3M3Y	X-ray	3.18	C	1-318	[»]
3M4O	X-ray	3.57	C	1-318	[»]
3PO2	X-ray	3.30	C	1-318	[»]
3PO3	X-ray	3.30	C	1-318	[»]
3QT1	X-ray	4.30	C	1-318	[»]
3RZD	X-ray	3.30	C	1-318	[»]
3RZO	X-ray	3.00	C	1-318	[»]
3S14	X-ray	2.85	C	1-318	[»]
3S15	X-ray	3.30	C	1-318	[»]
3S16	X-ray	3.24	C	1-318	[»]
3S17	X-ray	3.20	C	1-318	[»]
3S1M	X-ray	3.13	C	1-318	[»]
3S1N	X-ray	3.10	C	1-318	[»]
3S1Q	X-ray	3.30	C	1-318	[»]
3S1R	X-ray	3.20	C	1-318	[»]
3S2D	X-ray	3.20	C	1-318	[»]
3S2H	X-ray	3.30	C	1-318	[»]
4A3B	X-ray	3.50	C	1-318	[»]
4A3C	X-ray	3.50	C	1-318	[»]
4A3D	X-ray	3.40	C	1-318	[»]
4A3E	X-ray	3.40	C	1-318	[»]
4A3F	X-ray	3.50	C	1-318	[»]
4A3G	X-ray	3.50	C	1-318	[»]
4A3I	X-ray	3.80	C	1-318	[»]
4A3J	X-ray	3.70	C	1-318	[»]
4A3K	X-ray	3.50	C	1-318	[»]
4A3L	X-ray	3.50	C	1-318	[»]
4A3M	X-ray	3.90	C	1-318	[»]
4A93	X-ray	3.40	C	1-318	[»]
4BBR	X-ray	3.40	C	1-318	[»]
4BBS	X-ray	3.60	C	1-318	[»]

ProteinModelPortal

P16370.

SMR

P16370. Positions 3-268.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-837N.

IntAct

P16370. 27 interactions.

MINT

MINT-613688.

STRING

4932.YIL021W.

Proteomic databases

PaxDb

P16370.

PeptideAtlas

P16370.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YIL021W; YIL021W; YIL021W.

GeneID

854791.

KEGG

sce:YIL021W.

Organism-specific databases

CYGD

YIL021w.

SGD

S000001283. RPB3.

Phylogenomic databases

eggNOG

COG0202.

GeneTree

ENSGT00640000091532.

HOGENOM

HOG000230844.

KO

K03011.

OMA

NQPTVKI.

OrthoDB

EOG4DV8VZ.

Enzyme and pathway databases

BioCyc

YEAST:G3O-31296-MONOMER.

Gene expression databases

Genevestigator

P16370.

GermOnline

YIL021W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

2.170.120.12. 1 hit.

InterPro

IPR001514. DNA-dir_RNA_pol_30-40kDasu_CS.
IPR011261. DNA-dir_RNA_pol_dimersation.
IPR011262. DNA-dir_RNA_pol_insert.
IPR009025. DNA-dir_RNA_pol_RBP11-like.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
[Graphical view]

Pfam

PF01000. RNA_pol_A_bac. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]

SMART

SM00662. RPOLD. 1 hit.
[Graphical view]

SUPFAM

SSF56553. RNAP_insert. 1 hit.
SSF55257. RNAP_RBP11-like. 1 hit.

PROSITE

PS00446. RNA_POL_D_30KD. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P16370.

NextBio

977585.

Entry information

Entry name

RPB3_YEAST

Accession

Primary (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:	May 29, 2013
This is version 139 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program