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P08518

- RPB2_YEAST

UniProt

P08518 - RPB2_YEAST

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Protein

DNA-directed RNA polymerase II subunit RPB2

Gene

RPB2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single-stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it.

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi837 – 8371Magnesium; shared with RPB1
Metal bindingi1163 – 11631Zinc
Metal bindingi1166 – 11661Zinc
Metal bindingi1182 – 11821Zinc
Metal bindingi1185 – 11851Zinc

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1163 – 118523C4-typeAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. DNA-directed RNA polymerase activity Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. ribonucleoside binding Source: InterPro

GO - Biological processi

  1. transcription, RNA-templated Source: GOC
  2. transcription from RNA polymerase II promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-33668-MONOMER.
ReactomeiREACT_191540. mRNA Splicing - Minor Pathway.
REACT_229646. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_232590. Transcription-coupled NER (TC-NER).
REACT_235070. Dual incision reaction in TC-NER.
REACT_236803. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_240372. mRNA Capping.
REACT_247354. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_249293. RNA Polymerase II Transcription Initiation.
REACT_249645. Formation of the Early Elongation Complex.
REACT_250507. RNA Polymerase II Pre-transcription Events.
REACT_252915. RNA Pol II CTD phosphorylation and interaction with CE.
REACT_257112. RNA Polymerase II Promoter Escape.
REACT_261636. Processing of Capped Intron-Containing Pre-mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB2 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 2
Alternative name(s):
B150
DNA-directed RNA polymerase II 140 kDa polypeptide
Gene namesi
Name:RPB2
Synonyms:RPB150, RPO22
Ordered Locus Names:YOR151C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XV

Organism-specific databases

CYGDiYOR151c.
SGDiS000005677. RPB2.

Subcellular locationi

GO - Cellular componenti

  1. DNA-directed RNA polymerase II, core complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12241224DNA-directed RNA polymerase II subunit RPB2PRO_0000048091Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei919 – 9191Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP08518.
PaxDbiP08518.
PeptideAtlasiP08518.
PRIDEiP08518.

Expressioni

Gene expression databases

GenevestigatoriP08518.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RPB3P163705EBI-15767,EBI-15773
RPB5P204348EBI-15767,EBI-15781

Protein-protein interaction databases

BioGridi34547. 138 interactions.
DIPiDIP-14N.
IntActiP08518. 62 interactions.
MINTiMINT-654304.

Structurei

Secondary structure

1
1224
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi22 – 243Combined sources
Helixi29 – 4113Combined sources
Helixi42 – 443Combined sources
Helixi45 – 5612Combined sources
Helixi58 – 647Combined sources
Beta strandi69 – 713Combined sources
Beta strandi78 – 803Combined sources
Beta strandi96 – 1027Combined sources
Beta strandi105 – 1073Combined sources
Beta strandi109 – 1113Combined sources
Helixi114 – 1196Combined sources
Beta strandi125 – 1295Combined sources
Beta strandi141 – 1433Combined sources
Beta strandi166 – 1716Combined sources
Beta strandi176 – 1794Combined sources
Helixi180 – 1823Combined sources
Helixi186 – 1916Combined sources
Beta strandi202 – 2054Combined sources
Beta strandi208 – 2125Combined sources
Beta strandi214 – 2185Combined sources
Beta strandi224 – 2274Combined sources
Beta strandi232 – 24110Combined sources
Beta strandi245 – 2473Combined sources
Beta strandi253 – 2608Combined sources
Beta strandi264 – 2663Combined sources
Beta strandi269 – 2724Combined sources
Beta strandi277 – 2815Combined sources
Helixi282 – 2887Combined sources
Helixi294 – 3018Combined sources
Helixi308 – 32013Combined sources
Turni321 – 3233Combined sources
Helixi327 – 33610Combined sources
Beta strandi337 – 3393Combined sources
Helixi342 – 3443Combined sources
Helixi345 – 35814Combined sources
Beta strandi359 – 3613Combined sources
Turni362 – 3643Combined sources
Beta strandi367 – 3693Combined sources
Helixi371 – 38919Combined sources
Beta strandi390 – 3934Combined sources
Helixi401 – 4033Combined sources
Beta strandi404 – 4074Combined sources
Helixi409 – 43325Combined sources
Turni434 – 4363Combined sources
Helixi444 – 4474Combined sources
Helixi451 – 46313Combined sources
Beta strandi467 – 4693Combined sources
Helixi474 – 4763Combined sources
Beta strandi477 – 4793Combined sources
Beta strandi480 – 4823Combined sources
Helixi488 – 4958Combined sources
Beta strandi497 – 4993Combined sources
Turni510 – 5123Combined sources
Helixi516 – 5183Combined sources
Turni519 – 5213Combined sources
Helixi530 – 5323Combined sources
Turni533 – 5353Combined sources
Beta strandi536 – 5394Combined sources
Helixi552 – 5609Combined sources
Beta strandi563 – 5653Combined sources
Helixi566 – 5683Combined sources
Helixi571 – 5733Combined sources
Beta strandi574 – 5763Combined sources
Beta strandi578 – 5825Combined sources
Beta strandi585 – 5917Combined sources
Helixi593 – 60614Combined sources
Beta strandi607 – 6093Combined sources
Beta strandi614 – 6185Combined sources
Turni619 – 6224Combined sources
Beta strandi623 – 6275Combined sources
Beta strandi633 – 6419Combined sources
Beta strandi646 – 6494Combined sources
Beta strandi650 – 6523Combined sources
Helixi655 – 66612Combined sources
Helixi681 – 6866Combined sources
Beta strandi689 – 6946Combined sources
Helixi695 – 6984Combined sources
Beta strandi703 – 7064Combined sources
Helixi707 – 7104Combined sources
Beta strandi725 – 7273Combined sources
Beta strandi739 – 7413Combined sources
Helixi745 – 7484Combined sources
Helixi753 – 7553Combined sources
Beta strandi756 – 7583Combined sources
Helixi759 – 7613Combined sources
Helixi764 – 77310Combined sources
Helixi774 – 7763Combined sources
Beta strandi779 – 7813Combined sources
Turni783 – 7875Combined sources
Beta strandi791 – 7988Combined sources
Beta strandi803 – 8053Combined sources
Helixi809 – 8124Combined sources
Turni813 – 8164Combined sources
Beta strandi821 – 8277Combined sources
Beta strandi829 – 8324Combined sources
Turni833 – 8375Combined sources
Beta strandi838 – 8425Combined sources
Helixi843 – 8475Combined sources
Turni848 – 8514Combined sources
Beta strandi853 – 8619Combined sources
Beta strandi866 – 8694Combined sources
Beta strandi873 – 8753Combined sources
Beta strandi880 – 8823Combined sources
Beta strandi886 – 8883Combined sources
Helixi890 – 8923Combined sources
Beta strandi895 – 8995Combined sources
Beta strandi904 – 9063Combined sources
Beta strandi910 – 9123Combined sources
Beta strandi914 – 9163Combined sources
Beta strandi935 – 9406Combined sources
Beta strandi947 – 95610Combined sources
Beta strandi958 – 9603Combined sources
Beta strandi962 – 97211Combined sources
Beta strandi979 – 9813Combined sources
Beta strandi983 – 9853Combined sources
Beta strandi987 – 9948Combined sources
Turni996 – 9983Combined sources
Beta strandi1009 – 10124Combined sources
Helixi1014 – 10163Combined sources
Turni1018 – 10214Combined sources
Helixi1023 – 103816Combined sources
Beta strandi1046 – 10494Combined sources
Helixi1052 – 10609Combined sources
Turni1061 – 10633Combined sources
Beta strandi1068 – 10703Combined sources
Beta strandi1071 – 10733Combined sources
Turni1075 – 10773Combined sources
Beta strandi1080 – 10845Combined sources
Beta strandi1085 – 109713Combined sources
Helixi1099 – 11013Combined sources
Beta strandi1104 – 11063Combined sources
Turni1113 – 11153Combined sources
Helixi1122 – 11243Combined sources
Beta strandi1128 – 11303Combined sources
Helixi1132 – 114110Combined sources
Helixi1144 – 11518Combined sources
Helixi1152 – 11565Combined sources
Beta strandi1159 – 11668Combined sources
Beta strandi1172 – 11743Combined sources
Turni1175 – 11784Combined sources
Beta strandi1179 – 11824Combined sources
Turni1183 – 11864Combined sources
Beta strandi1187 – 11959Combined sources
Helixi1198 – 120912Combined sources
Beta strandi1215 – 12184Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10B1-1224[»]
1I50X-ray2.80B1-1224[»]
1I6HX-ray3.30B1-1224[»]
1K83X-ray2.80B1-1224[»]
1NIKX-ray4.10B1-1224[»]
1NT9X-ray4.20B1-1224[»]
1PQVX-ray3.80B1-1224[»]
1R5UX-ray4.50B1-1224[»]
1R9SX-ray4.25B1-1224[»]
1R9TX-ray3.50B1-1224[»]
1SFOX-ray3.61B1-1224[»]
1TWAX-ray3.20B1-1224[»]
1TWCX-ray3.00B1-1224[»]
1TWFX-ray2.30B1-1224[»]
1TWGX-ray3.30B1-1224[»]
1TWHX-ray3.40B1-1224[»]
1WCMX-ray3.80B1-1224[»]
1Y1VX-ray3.80B1-1224[»]
1Y1WX-ray4.00B1-1224[»]
1Y1YX-ray4.00B1-1224[»]
1Y77X-ray4.50B1-1224[»]
2B63X-ray3.80B1-1224[»]
2B8KX-ray4.15B1-1224[»]
2E2HX-ray3.95B1-1224[»]
2E2IX-ray3.41B1-1224[»]
2E2JX-ray3.50B1-1224[»]
2JA5X-ray3.80B1-1224[»]
2JA6X-ray4.00B1-1224[»]
2JA7X-ray3.80B/N1-1224[»]
2JA8X-ray3.80B1-1224[»]
2NVQX-ray2.90B1-1224[»]
2NVTX-ray3.36B1-1224[»]
2NVXX-ray3.60B1-1224[»]
2NVYX-ray3.40B1-1224[»]
2NVZX-ray4.30B1-1224[»]
2R7ZX-ray3.80B1-1224[»]
2R92X-ray3.80B1-1224[»]
2R93X-ray4.00B1-1224[»]
2VUMX-ray3.40B1-1224[»]
2YU9X-ray3.40B1-1224[»]
3CQZX-ray2.80B1-1223[»]
3FKIX-ray3.88B1-1224[»]
3GTGX-ray3.78B1-1224[»]
3GTJX-ray3.42B1-1224[»]
3GTKX-ray3.80B1-1224[»]
3GTLX-ray3.38B1-1224[»]
3GTMX-ray3.80B1-1224[»]
3GTOX-ray4.00B1-1224[»]
3GTPX-ray3.90B1-1224[»]
3GTQX-ray3.80B1-1224[»]
3H3VX-ray4.00C1-1224[»]
3HOUX-ray3.20B/N1-1224[»]
3HOVX-ray3.50B1-1224[»]
3HOWX-ray3.60B1-1224[»]
3HOXX-ray3.65B1-1224[»]
3HOYX-ray3.40B1-1224[»]
3HOZX-ray3.65B1-1224[»]
3I4MX-ray3.70B1-1224[»]
3I4NX-ray3.90B1-1224[»]
3J0Kelectron microscopy36.00B1-1224[»]
3J1Nelectron microscopy16.00B1-1224[»]
3K1FX-ray4.30B1-1224[»]
3K7AX-ray3.80B1-1224[»]
3M3YX-ray3.18B1-1224[»]
3M4OX-ray3.57B1-1224[»]
3PO2X-ray3.30B1-1224[»]
3PO3X-ray3.30B1-1224[»]
3QT1X-ray4.30B1-1224[»]
3RZDX-ray3.30B1-1224[»]
3RZOX-ray3.00B1-1224[»]
3S14X-ray2.85B1-1224[»]
3S15X-ray3.30B1-1224[»]
3S16X-ray3.24B1-1224[»]
3S17X-ray3.20B1-1224[»]
3S1MX-ray3.13B1-1224[»]
3S1NX-ray3.10B1-1224[»]
3S1QX-ray3.30B1-1224[»]
3S1RX-ray3.20B1-1224[»]
3S2DX-ray3.20B1-1224[»]
3S2HX-ray3.30B1-1224[»]
4A3BX-ray3.50B1-1224[»]
4A3CX-ray3.50B1-1224[»]
4A3DX-ray3.40B1-1224[»]
4A3EX-ray3.40B1-1224[»]
4A3FX-ray3.50B1-1224[»]
4A3GX-ray3.50B1-1224[»]
4A3IX-ray3.80B1-1224[»]
4A3JX-ray3.70B1-1224[»]
4A3KX-ray3.50B1-1224[»]
4A3LX-ray3.50B1-1224[»]
4A3MX-ray3.90B1-1224[»]
4A93X-ray3.40B1-1224[»]
4BBRX-ray3.40B1-1224[»]
4BBSX-ray3.60B1-1224[»]
4BXXX-ray3.28B1-1224[»]
4BXZX-ray4.80B1-1224[»]
4BY1X-ray3.60B1-1224[»]
4BY7X-ray3.15B1-1224[»]
ProteinModelPortaliP08518.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08518.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni467 – 47812Fork loop 1Add
BLAST

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1163 – 118523C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0085.
GeneTreeiENSGT00760000119346.
HOGENOMiHOG000222962.
InParanoidiP08518.
KOiK03010.
OMAiDSQMLEM.
OrthoDBiEOG7RRFGC.

Family and domain databases

Gene3Di2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProiIPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007646. RNA_pol_Rpb2_4.
IPR007647. RNA_pol_Rpb2_5.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
[Graphical view]
PANTHERiPTHR20856. PTHR20856. 1 hit.
PfamiPF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF04566. RNA_pol_Rpb2_4. 1 hit.
PF04567. RNA_pol_Rpb2_5. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]
PROSITEiPS01166. RNA_POL_BETA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P08518-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS
60 70 80 90 100
FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYEI SFGKIYVTKP
110 120 130 140 150
MVNESDGVTH ALYPQEARLR NLTYSSGLFV DVKKRTYEAI DVPGRELKYE
160 170 180 190 200
LIAEESEDDS ESGKVFIGRL PIMLRSKNCY LSEATESDLY KLKECPFDMG
210 220 230 240 250
GYFIINGSEK VLIAQERSAG NIVQVFKKAA PSPISHVAEI RSALEKGSRF
260 270 280 290 300
ISTLQVKLYG REGSSARTIK ATLPYIKQDI PIVIIFRALG IIPDGEILEH
310 320 330 340 350
ICYDVNDWQM LEMLKPCVED GFVIQDRETA LDFIGRRGTA LGIKKEKRIQ
360 370 380 390 400
YAKDILQKEF LPHITQLEGF ESRKAFFLGY MINRLLLCAL DRKDQDDRDH
410 420 430 440 450
FGKKRLDLAG PLLAQLFKTL FKKLTKDIFR YMQRTVEEAH DFNMKLAINA
460 470 480 490 500
KTITSGLKYA LATGNWGEQK KAMSSRAGVS QVLNRYTYSS TLSHLRRTNT
510 520 530 540 550
PIGRDGKLAK PRQLHNTHWG LVCPAETPEG QACGLVKNLS LMSCISVGTD
560 570 580 590 600
PMPIITFLSE WGMEPLEDYV PHQSPDATRV FVNGVWHGVH RNPARLMETL
610 620 630 640 650
RTLRRKGDIN PEVSMIRDIR EKELKIFTDA GRVYRPLFIV EDDESLGHKE
660 670 680 690 700
LKVRKGHIAK LMATEYQDIE GGFEDVEEYT WSSLLNEGLV EYIDAEEEES
710 720 730 740 750
ILIAMQPEDL EPAEANEEND LDVDPAKRIR VSHHATTFTH CEIHPSMILG
760 770 780 790 800
VAASIIPFPD HNQSPRNTYQ SAMGKQAMGV FLTNYNVRMD TMANILYYPQ
810 820 830 840 850
KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL
860 870 880 890 900
FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGTY DKLDDDGLIA
910 920 930 940 950
PGVRVSGEDV IIGKTTPISP DEEELGQRTA YHSKRDASTP LRSTENGIVD
960 970 980 990 1000
QVLVTTNQDG LKFVKVRVRT TKIPQIGDKF ASRHGQKGTI GITYRREDMP
1010 1020 1030 1040 1050
FTAEGIVPDL IINPHAIPSR MTVAHLIECL LSKVAALSGN EGDASPFTDI
1060 1070 1080 1090 1100
TVEGISKLLR EHGYQSRGFE VMYNGHTGKK LMAQIFFGPT YYQRLRHMVD
1110 1120 1130 1140 1150
DKIHARARGP MQVLTRQPVE GRSRDGGLRF GEMERDCMIA HGAASFLKER
1160 1170 1180 1190 1200
LMEASDAFRV HICGICGLMT VIAKLNHNQF ECKGCDNKID IYQIHIPYAA
1210 1220
KLLFQELMAM NITPRLYTDR SRDF
Length:1,224
Mass (Da):138,751
Last modified:November 1, 1997 - v2
Checksum:iBABD03212C0A583E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1003 – 10064AEGI → RRRY in AAA68096. (PubMed:3547406)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15693 Genomic DNA. Translation: AAA68096.1.
U55020 Genomic DNA. Translation: AAC49637.1.
Z75059 Genomic DNA. Translation: CAA99357.1.
AF527884 Genomic DNA. Translation: AAP57849.1.
BK006948 Genomic DNA. Translation: DAA10924.1.
PIRiA25884.
RefSeqiNP_014794.3. NM_001183570.3.

Genome annotation databases

EnsemblFungiiYOR151C; YOR151C; YOR151C.
GeneIDi854322.
KEGGisce:YOR151C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15693 Genomic DNA. Translation: AAA68096.1 .
U55020 Genomic DNA. Translation: AAC49637.1 .
Z75059 Genomic DNA. Translation: CAA99357.1 .
AF527884 Genomic DNA. Translation: AAP57849.1 .
BK006948 Genomic DNA. Translation: DAA10924.1 .
PIRi A25884.
RefSeqi NP_014794.3. NM_001183570.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1I3Q X-ray 3.10 B 1-1224 [» ]
1I50 X-ray 2.80 B 1-1224 [» ]
1I6H X-ray 3.30 B 1-1224 [» ]
1K83 X-ray 2.80 B 1-1224 [» ]
1NIK X-ray 4.10 B 1-1224 [» ]
1NT9 X-ray 4.20 B 1-1224 [» ]
1PQV X-ray 3.80 B 1-1224 [» ]
1R5U X-ray 4.50 B 1-1224 [» ]
1R9S X-ray 4.25 B 1-1224 [» ]
1R9T X-ray 3.50 B 1-1224 [» ]
1SFO X-ray 3.61 B 1-1224 [» ]
1TWA X-ray 3.20 B 1-1224 [» ]
1TWC X-ray 3.00 B 1-1224 [» ]
1TWF X-ray 2.30 B 1-1224 [» ]
1TWG X-ray 3.30 B 1-1224 [» ]
1TWH X-ray 3.40 B 1-1224 [» ]
1WCM X-ray 3.80 B 1-1224 [» ]
1Y1V X-ray 3.80 B 1-1224 [» ]
1Y1W X-ray 4.00 B 1-1224 [» ]
1Y1Y X-ray 4.00 B 1-1224 [» ]
1Y77 X-ray 4.50 B 1-1224 [» ]
2B63 X-ray 3.80 B 1-1224 [» ]
2B8K X-ray 4.15 B 1-1224 [» ]
2E2H X-ray 3.95 B 1-1224 [» ]
2E2I X-ray 3.41 B 1-1224 [» ]
2E2J X-ray 3.50 B 1-1224 [» ]
2JA5 X-ray 3.80 B 1-1224 [» ]
2JA6 X-ray 4.00 B 1-1224 [» ]
2JA7 X-ray 3.80 B/N 1-1224 [» ]
2JA8 X-ray 3.80 B 1-1224 [» ]
2NVQ X-ray 2.90 B 1-1224 [» ]
2NVT X-ray 3.36 B 1-1224 [» ]
2NVX X-ray 3.60 B 1-1224 [» ]
2NVY X-ray 3.40 B 1-1224 [» ]
2NVZ X-ray 4.30 B 1-1224 [» ]
2R7Z X-ray 3.80 B 1-1224 [» ]
2R92 X-ray 3.80 B 1-1224 [» ]
2R93 X-ray 4.00 B 1-1224 [» ]
2VUM X-ray 3.40 B 1-1224 [» ]
2YU9 X-ray 3.40 B 1-1224 [» ]
3CQZ X-ray 2.80 B 1-1223 [» ]
3FKI X-ray 3.88 B 1-1224 [» ]
3GTG X-ray 3.78 B 1-1224 [» ]
3GTJ X-ray 3.42 B 1-1224 [» ]
3GTK X-ray 3.80 B 1-1224 [» ]
3GTL X-ray 3.38 B 1-1224 [» ]
3GTM X-ray 3.80 B 1-1224 [» ]
3GTO X-ray 4.00 B 1-1224 [» ]
3GTP X-ray 3.90 B 1-1224 [» ]
3GTQ X-ray 3.80 B 1-1224 [» ]
3H3V X-ray 4.00 C 1-1224 [» ]
3HOU X-ray 3.20 B/N 1-1224 [» ]
3HOV X-ray 3.50 B 1-1224 [» ]
3HOW X-ray 3.60 B 1-1224 [» ]
3HOX X-ray 3.65 B 1-1224 [» ]
3HOY X-ray 3.40 B 1-1224 [» ]
3HOZ X-ray 3.65 B 1-1224 [» ]
3I4M X-ray 3.70 B 1-1224 [» ]
3I4N X-ray 3.90 B 1-1224 [» ]
3J0K electron microscopy 36.00 B 1-1224 [» ]
3J1N electron microscopy 16.00 B 1-1224 [» ]
3K1F X-ray 4.30 B 1-1224 [» ]
3K7A X-ray 3.80 B 1-1224 [» ]
3M3Y X-ray 3.18 B 1-1224 [» ]
3M4O X-ray 3.57 B 1-1224 [» ]
3PO2 X-ray 3.30 B 1-1224 [» ]
3PO3 X-ray 3.30 B 1-1224 [» ]
3QT1 X-ray 4.30 B 1-1224 [» ]
3RZD X-ray 3.30 B 1-1224 [» ]
3RZO X-ray 3.00 B 1-1224 [» ]
3S14 X-ray 2.85 B 1-1224 [» ]
3S15 X-ray 3.30 B 1-1224 [» ]
3S16 X-ray 3.24 B 1-1224 [» ]
3S17 X-ray 3.20 B 1-1224 [» ]
3S1M X-ray 3.13 B 1-1224 [» ]
3S1N X-ray 3.10 B 1-1224 [» ]
3S1Q X-ray 3.30 B 1-1224 [» ]
3S1R X-ray 3.20 B 1-1224 [» ]
3S2D X-ray 3.20 B 1-1224 [» ]
3S2H X-ray 3.30 B 1-1224 [» ]
4A3B X-ray 3.50 B 1-1224 [» ]
4A3C X-ray 3.50 B 1-1224 [» ]
4A3D X-ray 3.40 B 1-1224 [» ]
4A3E X-ray 3.40 B 1-1224 [» ]
4A3F X-ray 3.50 B 1-1224 [» ]
4A3G X-ray 3.50 B 1-1224 [» ]
4A3I X-ray 3.80 B 1-1224 [» ]
4A3J X-ray 3.70 B 1-1224 [» ]
4A3K X-ray 3.50 B 1-1224 [» ]
4A3L X-ray 3.50 B 1-1224 [» ]
4A3M X-ray 3.90 B 1-1224 [» ]
4A93 X-ray 3.40 B 1-1224 [» ]
4BBR X-ray 3.40 B 1-1224 [» ]
4BBS X-ray 3.60 B 1-1224 [» ]
4BXX X-ray 3.28 B 1-1224 [» ]
4BXZ X-ray 4.80 B 1-1224 [» ]
4BY1 X-ray 3.60 B 1-1224 [» ]
4BY7 X-ray 3.15 B 1-1224 [» ]
ProteinModelPortali P08518.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34547. 138 interactions.
DIPi DIP-14N.
IntActi P08518. 62 interactions.
MINTi MINT-654304.

Proteomic databases

MaxQBi P08518.
PaxDbi P08518.
PeptideAtlasi P08518.
PRIDEi P08518.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YOR151C ; YOR151C ; YOR151C .
GeneIDi 854322.
KEGGi sce:YOR151C.

Organism-specific databases

CYGDi YOR151c.
SGDi S000005677. RPB2.

Phylogenomic databases

eggNOGi COG0085.
GeneTreei ENSGT00760000119346.
HOGENOMi HOG000222962.
InParanoidi P08518.
KOi K03010.
OMAi DSQMLEM.
OrthoDBi EOG7RRFGC.

Enzyme and pathway databases

BioCyci YEAST:G3O-33668-MONOMER.
Reactomei REACT_191540. mRNA Splicing - Minor Pathway.
REACT_229646. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_232590. Transcription-coupled NER (TC-NER).
REACT_235070. Dual incision reaction in TC-NER.
REACT_236803. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_240372. mRNA Capping.
REACT_247354. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_249293. RNA Polymerase II Transcription Initiation.
REACT_249645. Formation of the Early Elongation Complex.
REACT_250507. RNA Polymerase II Pre-transcription Events.
REACT_252915. RNA Pol II CTD phosphorylation and interaction with CE.
REACT_257112. RNA Polymerase II Promoter Escape.
REACT_261636. Processing of Capped Intron-Containing Pre-mRNA.

Miscellaneous databases

EvolutionaryTracei P08518.
NextBioi 976360.
PROi P08518.

Gene expression databases

Genevestigatori P08518.

Family and domain databases

Gene3Di 2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProi IPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007646. RNA_pol_Rpb2_4.
IPR007647. RNA_pol_Rpb2_5.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
[Graphical view ]
PANTHERi PTHR20856. PTHR20856. 1 hit.
Pfami PF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF04566. RNA_pol_Rpb2_4. 1 hit.
PF04567. RNA_pol_Rpb2_5. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view ]
PROSITEi PS01166. RNA_POL_BETA. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Prokaryotic and eukaryotic RNA polymerases have homologous core subunits."
    Sweetser D., Nonet M., Young R.A.
    Proc. Natl. Acad. Sci. U.S.A. 84:1192-1196(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Analysis of a 35.6 kb region on the right arm of Saccharomyces cerevisiae chromosome XV."
    Bordonne R., Camasses A., Madania A., Poch O., Tarassov I.A., Winsor B., Martin R.P.
    Yeast 13:73-83(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: S288c / FY1678.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses."
    Kurtzman C.P., Robnett C.J.
    FEMS Yeast Res. 3:417-432(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 549-773.
    Strain: ATCC 18824 / CBS 1171 / DSM 70449 / IFO 10217 / NRRL Y-12632.
  6. "Mapping the active site of yeast RNA polymerase B (II)."
    Riva M., Carles C., Sentenac A., Grachev M.A., Mustaev A.A., Zaychikov E.F.
    J. Biol. Chem. 265:16498-16503(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 837-844.
  7. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-919, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  8. "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-919, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  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] [Europe PMC] [Abstract]
    Cited for: ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX.
  11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  12. "The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II."
    Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S.
    Nature 432:517-522(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RTT103.
  13. "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.
  14. "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.
  15. "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.
  16. "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.
  17. "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.
  18. "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.
  19. "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.
  20. "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).
  21. "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.
  22. "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.
  23. "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.
  24. "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.

Entry informationi

Entry nameiRPB2_YEAST
AccessioniPrimary (citable) accession number: P08518
Secondary accession number(s): D6W2K8, Q12738, Q7Z9Y0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: November 1, 1997
Last modified: November 26, 2014
This is version 161 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits.
Present with 18700 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

External Data

Dasty 3