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P08518

- RPB2_YEAST

UniProt

P08518 - RPB2_YEAST

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
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    • History
      Entry version 159 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    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. protein binding Source: IntAct
    5. ribonucleoside binding Source: InterPro

    GO - Biological processi

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

    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.

    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

    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. 135 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 – 243
    Helixi29 – 4113
    Helixi42 – 443
    Helixi45 – 5612
    Helixi58 – 647
    Beta strandi69 – 713
    Beta strandi78 – 803
    Beta strandi96 – 1027
    Beta strandi105 – 1073
    Beta strandi109 – 1113
    Helixi114 – 1196
    Beta strandi125 – 1295
    Beta strandi141 – 1433
    Beta strandi166 – 1716
    Beta strandi176 – 1794
    Helixi180 – 1823
    Helixi186 – 1916
    Beta strandi202 – 2054
    Beta strandi208 – 2125
    Beta strandi214 – 2185
    Beta strandi224 – 2274
    Beta strandi232 – 24110
    Beta strandi245 – 2473
    Beta strandi253 – 2608
    Beta strandi264 – 2663
    Beta strandi269 – 2724
    Beta strandi277 – 2815
    Helixi282 – 2887
    Helixi294 – 3018
    Helixi308 – 32013
    Turni321 – 3233
    Helixi327 – 33610
    Beta strandi337 – 3393
    Helixi342 – 3443
    Helixi345 – 35814
    Beta strandi359 – 3613
    Turni362 – 3643
    Beta strandi367 – 3693
    Helixi371 – 38919
    Beta strandi390 – 3934
    Helixi401 – 4033
    Beta strandi404 – 4074
    Helixi409 – 43325
    Turni434 – 4363
    Helixi444 – 4474
    Helixi451 – 46313
    Beta strandi467 – 4693
    Helixi474 – 4763
    Beta strandi477 – 4793
    Beta strandi480 – 4823
    Helixi488 – 4958
    Beta strandi497 – 4993
    Turni510 – 5123
    Helixi516 – 5183
    Turni519 – 5213
    Helixi530 – 5323
    Turni533 – 5353
    Beta strandi536 – 5394
    Helixi552 – 5609
    Beta strandi563 – 5653
    Helixi566 – 5683
    Helixi571 – 5733
    Beta strandi574 – 5763
    Beta strandi578 – 5825
    Beta strandi585 – 5917
    Helixi593 – 60614
    Beta strandi607 – 6093
    Beta strandi614 – 6185
    Turni619 – 6224
    Beta strandi623 – 6275
    Beta strandi633 – 6419
    Beta strandi646 – 6494
    Beta strandi650 – 6523
    Helixi655 – 66612
    Helixi681 – 6866
    Beta strandi689 – 6946
    Helixi695 – 6984
    Beta strandi703 – 7064
    Helixi707 – 7104
    Beta strandi725 – 7273
    Beta strandi739 – 7413
    Helixi745 – 7484
    Helixi753 – 7553
    Beta strandi756 – 7583
    Helixi759 – 7613
    Helixi764 – 77310
    Helixi774 – 7763
    Beta strandi779 – 7813
    Turni783 – 7875
    Beta strandi791 – 7988
    Beta strandi803 – 8053
    Helixi809 – 8124
    Turni813 – 8164
    Beta strandi821 – 8277
    Beta strandi829 – 8324
    Turni833 – 8375
    Beta strandi838 – 8425
    Helixi843 – 8475
    Turni848 – 8514
    Beta strandi853 – 8619
    Beta strandi866 – 8694
    Beta strandi873 – 8753
    Beta strandi880 – 8823
    Beta strandi886 – 8883
    Helixi890 – 8923
    Beta strandi895 – 8995
    Beta strandi904 – 9063
    Beta strandi910 – 9123
    Beta strandi914 – 9163
    Beta strandi935 – 9406
    Beta strandi947 – 95610
    Beta strandi958 – 9603
    Beta strandi962 – 97211
    Beta strandi979 – 9813
    Beta strandi983 – 9853
    Beta strandi987 – 9948
    Turni996 – 9983
    Beta strandi1009 – 10124
    Helixi1014 – 10163
    Turni1018 – 10214
    Helixi1023 – 103816
    Beta strandi1046 – 10494
    Helixi1052 – 10609
    Turni1061 – 10633
    Beta strandi1068 – 10703
    Beta strandi1071 – 10733
    Turni1075 – 10773
    Beta strandi1080 – 10845
    Beta strandi1085 – 109713
    Helixi1099 – 11013
    Beta strandi1104 – 11063
    Turni1113 – 11153
    Helixi1122 – 11243
    Beta strandi1128 – 11303
    Helixi1132 – 114110
    Helixi1144 – 11518
    Helixi1152 – 11565
    Beta strandi1159 – 11668
    Beta strandi1172 – 11743
    Turni1175 – 11784
    Beta strandi1179 – 11824
    Turni1183 – 11864
    Beta strandi1187 – 11959
    Helixi1198 – 120912
    Beta strandi1215 – 12184

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    GeneTreeiENSGT00750000117589.
    HOGENOMiHOG000222962.
    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

    MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS     50
    FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYEI SFGKIYVTKP 100
    MVNESDGVTH ALYPQEARLR NLTYSSGLFV DVKKRTYEAI DVPGRELKYE 150
    LIAEESEDDS ESGKVFIGRL PIMLRSKNCY LSEATESDLY KLKECPFDMG 200
    GYFIINGSEK VLIAQERSAG NIVQVFKKAA PSPISHVAEI RSALEKGSRF 250
    ISTLQVKLYG REGSSARTIK ATLPYIKQDI PIVIIFRALG IIPDGEILEH 300
    ICYDVNDWQM LEMLKPCVED GFVIQDRETA LDFIGRRGTA LGIKKEKRIQ 350
    YAKDILQKEF LPHITQLEGF ESRKAFFLGY MINRLLLCAL DRKDQDDRDH 400
    FGKKRLDLAG PLLAQLFKTL FKKLTKDIFR YMQRTVEEAH DFNMKLAINA 450
    KTITSGLKYA LATGNWGEQK KAMSSRAGVS QVLNRYTYSS TLSHLRRTNT 500
    PIGRDGKLAK PRQLHNTHWG LVCPAETPEG QACGLVKNLS LMSCISVGTD 550
    PMPIITFLSE WGMEPLEDYV PHQSPDATRV FVNGVWHGVH RNPARLMETL 600
    RTLRRKGDIN PEVSMIRDIR EKELKIFTDA GRVYRPLFIV EDDESLGHKE 650
    LKVRKGHIAK LMATEYQDIE GGFEDVEEYT WSSLLNEGLV EYIDAEEEES 700
    ILIAMQPEDL EPAEANEEND LDVDPAKRIR VSHHATTFTH CEIHPSMILG 750
    VAASIIPFPD HNQSPRNTYQ SAMGKQAMGV FLTNYNVRMD TMANILYYPQ 800
    KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL 850
    FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGTY DKLDDDGLIA 900
    PGVRVSGEDV IIGKTTPISP DEEELGQRTA YHSKRDASTP LRSTENGIVD 950
    QVLVTTNQDG LKFVKVRVRT TKIPQIGDKF ASRHGQKGTI GITYRREDMP 1000
    FTAEGIVPDL IINPHAIPSR MTVAHLIECL LSKVAALSGN EGDASPFTDI 1050
    TVEGISKLLR EHGYQSRGFE VMYNGHTGKK LMAQIFFGPT YYQRLRHMVD 1100
    DKIHARARGP MQVLTRQPVE GRSRDGGLRF GEMERDCMIA HGAASFLKER 1150
    LMEASDAFRV HICGICGLMT VIAKLNHNQF ECKGCDNKID IYQIHIPYAA 1200
    KLLFQELMAM NITPRLYTDR SRDF 1224
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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. 135 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 ENSGT00750000117589.
    HOGENOMi HOG000222962.
    KOi K03010.
    OMAi DSQMLEM.
    OrthoDBi EOG7RRFGC.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33668-MONOMER.
    Reactomei REACT_191540. mRNA Splicing - Minor Pathway.

    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

    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: October 1, 2014
    This is version 159 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