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P04050

- RPB1_YEAST

UniProt

P04050 - RPB1_YEAST

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Protein

DNA-directed RNA polymerase II subunit RPB1

Gene

RPO21

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. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. 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. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single-stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA.

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi67 – 671Zinc 1
Metal bindingi70 – 701Zinc 1
Metal bindingi77 – 771Zinc 1
Metal bindingi80 – 801Zinc 1
Metal bindingi107 – 1071Zinc 2
Metal bindingi110 – 1101Zinc 2
Metal bindingi148 – 1481Zinc 2
Metal bindingi167 – 1671Zinc 2
Metal bindingi481 – 4811Magnesium 1; catalytic
Metal bindingi481 – 4811Magnesium 2; shared with RPB2
Metal bindingi483 – 4831Magnesium 1; catalytic
Metal bindingi483 – 4831Magnesium 2; shared with RPB2
Metal bindingi485 – 4851Magnesium 1; catalytic

GO - Molecular functioni

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

GO - Biological processi

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

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-29539-MONOMER.
ReactomeiREACT_191540. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB1 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 1
Short name:
RNA polymerase II subunit B1
Alternative name(s):
DNA-directed RNA polymerase III largest subunit
RNA polymerase II subunit B220
Gene namesi
Name:RPO21
Synonyms:RPB1, RPB220, SUA8
Ordered Locus Names:YDL140C
ORF Names:D2150
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

CYGDiYDL140c.
SGDiS000002299. RPO21.

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 – 17331733DNA-directed RNA polymerase II subunit RPB1PRO_0000073946Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki695 – 695Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Modified residuei1471 – 14711Phosphothreonine1 Publication

Post-translational modificationi

The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat. The phosphorylated form of Pol II appears to carry, on average, one phosphate per repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphataes, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed. Phosphorylation at 'Ser-5' occurs in promoter-proximal regions in early elongation. Phosphorylation at 'Ser-2' predominates in regions more distal to the promoter and triggers binding of the 3' RNA processing machinery. CTD kinases include KIN28 (as part of the TFKII complex, a subcomplex of the TFIIH holo complex), SSN3/SRB10 (as part of the SRB8-11 complex, a module of the Mediator complex), CTK1 (as part of CTD kinase), and probably BUR1 (as part of the BUR1-BUR2 kinase complex). Phosphatases include FCP1 and SSU72.4 Publications

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04050.
PaxDbiP04050.
PeptideAtlasiP04050.

Expressioni

Gene expression databases

GenevestigatoriP04050.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. Interacts with ASK10, ESS1, RTT103 and SHE2.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CDC73Q0669717EBI-15760,EBI-29913
CTR9P891054EBI-15760,EBI-5283
RTF1P530647EBI-15760,EBI-16303
SEN1Q004163EBI-15760,EBI-16945
SPT5P276923EBI-15760,EBI-17937

Protein-protein interaction databases

BioGridi31921. 301 interactions.
DIPiDIP-611N.
IntActiP04050. 43 interactions.
MINTiMINT-432838.

Structurei

Secondary structure

1
1733
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi16 – 183
Helixi24 – 296
Beta strandi32 – 343
Beta strandi39 – 413
Beta strandi43 – 453
Beta strandi46 – 483
Beta strandi51 – 544
Beta strandi56 – 583
Beta strandi62 – 643
Beta strandi67 – 693
Turni74 – 763
Beta strandi84 – 918
Helixi93 – 953
Helixi96 – 10510
Turni108 – 1103
Beta strandi113 – 1153
Beta strandi117 – 1193
Helixi120 – 1267
Beta strandi127 – 1293
Helixi131 – 14212
Beta strandi150 – 1523
Beta strandi160 – 1634
Beta strandi173 – 1775
Beta strandi181 – 1855
Beta strandi187 – 1904
Beta strandi198 – 2025
Helixi204 – 2118
Beta strandi212 – 2143
Helixi216 – 2216
Turni226 – 2283
Helixi231 – 2344
Beta strandi235 – 2395
Turni244 – 2463
Beta strandi253 – 2553
Beta strandi257 – 2604
Helixi261 – 28020
Turni281 – 2833
Helixi286 – 30419
Beta strandi307 – 3104
Beta strandi313 – 3164
Beta strandi318 – 3214
Helixi325 – 3295
Turni330 – 3356
Helixi338 – 3403
Beta strandi341 – 3444
Beta strandi347 – 3559
Beta strandi363 – 3675
Helixi368 – 3714
Beta strandi375 – 3795
Turni382 – 3843
Helixi385 – 39410
Turni395 – 3973
Beta strandi398 – 4003
Beta strandi402 – 4065
Helixi408 – 4103
Beta strandi412 – 4143
Turni415 – 4173
Turni419 – 4224
Beta strandi431 – 4355
Beta strandi441 – 4455
Helixi452 – 4543
Beta strandi455 – 47016
Helixi472 – 4743
Helixi475 – 4784
Beta strandi482 – 4843
Beta strandi486 – 4905
Helixi495 – 50410
Helixi507 – 5104
Beta strandi511 – 5133
Turni514 – 5174
Beta strandi518 – 5203
Helixi525 – 53511
Beta strandi536 – 5383
Beta strandi540 – 5423
Helixi543 – 55210
Beta strandi553 – 5553
Beta strandi567 – 5693
Beta strandi571 – 5733
Helixi574 – 5818
Beta strandi588 – 5903
Beta strandi596 – 5983
Beta strandi600 – 6023
Beta strandi604 – 6085
Beta strandi611 – 6155
Helixi619 – 6224
Beta strandi626 – 6283
Helixi629 – 6379
Helixi639 – 65820
Helixi666 – 6694
Helixi673 – 69927
Beta strandi706 – 7083
Helixi710 – 73627
Helixi742 – 7498
Beta strandi750 – 7523
Helixi755 – 7628
Beta strandi770 – 7745
Beta strandi778 – 7814
Beta strandi782 – 7843
Turni794 – 7985
Turni804 – 8063
Helixi810 – 84536
Beta strandi863 – 8675
Helixi868 – 8703
Helixi875 – 8773
Beta strandi878 – 8825
Helixi884 – 8863
Helixi890 – 8978
Beta strandi901 – 9033
Turni904 – 9063
Turni910 – 9123
Beta strandi913 – 9153
Helixi916 – 9194
Helixi923 – 94624
Turni947 – 9493
Beta strandi953 – 9586
Helixi960 – 97011
Beta strandi975 – 9773
Helixi983 – 99412
Helixi1005 – 10139
Helixi1016 – 102510
Helixi1028 – 10336
Helixi1039 – 105618
Helixi1064 – 107613
Beta strandi1079 – 10824
Helixi1086 – 10883
Beta strandi1089 – 10913
Beta strandi1092 – 10943
Helixi1097 – 11048
Turni1105 – 11073
Beta strandi1115 – 11206
Beta strandi1122 – 11265
Helixi1128 – 113811
Helixi1143 – 11453
Beta strandi1147 – 11548
Beta strandi1158 – 11603
Helixi1164 – 11663
Helixi1167 – 11715
Beta strandi1172 – 11743
Beta strandi1179 – 11824
Beta strandi1190 – 11978
Helixi1199 – 12046
Helixi1209 – 122012
Helixi1221 – 12233
Beta strandi1224 – 12285
Beta strandi1233 – 12353
Beta strandi1237 – 12426
Helixi1258 – 127013
Beta strandi1272 – 12754
Beta strandi1282 – 129211
Beta strandi1296 – 131015
Helixi1313 – 13164
Beta strandi1317 – 13226
Turni1324 – 13263
Beta strandi1328 – 13303
Helixi1332 – 13398
Helixi1341 – 135717
Turni1358 – 13603
Helixi1365 – 137410
Turni1375 – 13773
Beta strandi1378 – 13803
Beta strandi1384 – 13863
Beta strandi1388 – 13903
Beta strandi1392 – 13943
Helixi1396 – 13994
Turni1400 – 14023
Helixi1406 – 141510
Helixi1424 – 14296
Helixi1437 – 14393
Beta strandi1440 – 14456
Helixi1447 – 14504
Beta strandi1677 – 16804

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10A1-1733[»]
1I50X-ray2.80A1-1733[»]
1I6HX-ray3.30A1-1733[»]
1K83X-ray2.80A1-1733[»]
1NIKX-ray4.10A1-1733[»]
1NT9X-ray4.20A1-1733[»]
1PQVX-ray3.80A1-1733[»]
1R5UX-ray4.50A1-1733[»]
1R9SX-ray4.25A1-1733[»]
1R9TX-ray3.50A1-1733[»]
1SFOX-ray3.61A1-1733[»]
1TWAX-ray3.20A1-1733[»]
1TWCX-ray3.00A1-1733[»]
1TWFX-ray2.30A1-1733[»]
1TWGX-ray3.30A1-1733[»]
1TWHX-ray3.40A1-1733[»]
1WCMX-ray3.80A1-1733[»]
1Y1VX-ray3.80A1-1733[»]
1Y1WX-ray4.00A1-1733[»]
1Y1YX-ray4.00A1-1733[»]
1Y77X-ray4.50A1-1733[»]
2B63X-ray3.80A1-1733[»]
2B8KX-ray4.15A1-1733[»]
2E2HX-ray3.95A1-1733[»]
2E2IX-ray3.41A1-1733[»]
2E2JX-ray3.50A1-1733[»]
2JA5X-ray3.80A1-1733[»]
2JA6X-ray4.00A1-1733[»]
2JA7X-ray3.80A/M1-1733[»]
2JA8X-ray3.80A1-1733[»]
2L0INMR-B1675-1688[»]
2LO6NMR-B1675-1688[»]
2NVQX-ray2.90A1-1733[»]
2NVTX-ray3.36A1-1733[»]
2NVXX-ray3.60A1-1733[»]
2NVYX-ray3.40A1-1733[»]
2NVZX-ray4.30A1-1733[»]
2R7ZX-ray3.80A1-1733[»]
2R92X-ray3.80A1-1733[»]
2R93X-ray4.00A1-1733[»]
2VUMX-ray3.40A1-1733[»]
2YU9X-ray3.40A1-1733[»]
3CQZX-ray2.80A1-1733[»]
3FKIX-ray3.88A1-1733[»]
3GTGX-ray3.78A1-1733[»]
3GTJX-ray3.42A1-1733[»]
3GTKX-ray3.80A1-1733[»]
3GTLX-ray3.38A1-1733[»]
3GTMX-ray3.80A1-1733[»]
3GTOX-ray4.00A1-1733[»]
3GTPX-ray3.90A1-1733[»]
3GTQX-ray3.80A1-1733[»]
3H3VX-ray4.00B1-1733[»]
3HOUX-ray3.20A/M1-1733[»]
3HOVX-ray3.50A1-1733[»]
3HOWX-ray3.60A1-1733[»]
3HOXX-ray3.65A1-1733[»]
3HOYX-ray3.40A1-1733[»]
3HOZX-ray3.65A1-1733[»]
3I4MX-ray3.70A1-1733[»]
3I4NX-ray3.90A1-1733[»]
3J0Kelectron microscopy36.00A1-1455[»]
3J1Nelectron microscopy16.00A1-1455[»]
3K1FX-ray4.30A1-1733[»]
3K7AX-ray3.80A1-1733[»]
3M3YX-ray3.18A1-1733[»]
3M4OX-ray3.57A1-1733[»]
3PO2X-ray3.30A1-1733[»]
3PO3X-ray3.30A1-1733[»]
3QT1X-ray4.30A1-1733[»]
3RZDX-ray3.30A1-1733[»]
3RZOX-ray3.00A1-1733[»]
3S14X-ray2.85A1-1733[»]
3S15X-ray3.30A1-1733[»]
3S16X-ray3.24A1-1733[»]
3S17X-ray3.20A1-1733[»]
3S1MX-ray3.13A1-1733[»]
3S1NX-ray3.10A1-1733[»]
3S1QX-ray3.30A1-1733[»]
3S1RX-ray3.20A1-1733[»]
3S2DX-ray3.20A1-1733[»]
3S2HX-ray3.30A1-1733[»]
4A3BX-ray3.50A1-1732[»]
4A3CX-ray3.50A1-1732[»]
4A3DX-ray3.40A1-1732[»]
4A3EX-ray3.40A1-1732[»]
4A3FX-ray3.50A1-1732[»]
4A3GX-ray3.50A1-1732[»]
4A3IX-ray3.80A1-1732[»]
4A3JX-ray3.70A1-1732[»]
4A3KX-ray3.50A1-1732[»]
4A3LX-ray3.50A1-1732[»]
4A3MX-ray3.90A1-1732[»]
4A93X-ray3.40A1-1732[»]
4BBRX-ray3.40A1-1733[»]
4BBSX-ray3.60A1-1733[»]
4BXXX-ray3.28A1-1733[»]
4BXZX-ray4.80A1-1733[»]
4BY1X-ray3.60A1-1733[»]
4BY7X-ray3.15A1-1733[»]
4GWQX-ray4.50H1619-1653[»]
ProteinModelPortaliP04050.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04050.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati1549 – 155571
Repeati1556 – 156272
Repeati1563 – 156973
Repeati1570 – 157674
Repeati1577 – 158375
Repeati1584 – 159076
Repeati1591 – 159777
Repeati1598 – 160478
Repeati1605 – 161179
Repeati1612 – 1618710
Repeati1619 – 1625711
Repeati1626 – 1632712
Repeati1633 – 1639713
Repeati1640 – 1646714
Repeati1647 – 1653715
Repeati1654 – 1660716
Repeati1661 – 1667717
Repeati1668 – 1674718
Repeati1675 – 1681719
Repeati1682 – 1688720
Repeati1689 – 1695721
Repeati1696 – 1702722
Repeati1703 – 1709723
Repeati1710 – 1716724; approximate

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni248 – 26013Lid loopAdd
BLAST
Regioni306 – 32318Rudder loopAdd
BLAST
Regioni810 – 82213Bridging helixAdd
BLAST
Regioni1549 – 171616824 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[A-S-N-G]Add
BLAST

Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0086.
GeneTreeiENSGT00730000110946.
HOGENOMiHOG000222975.
InParanoidiP04050.
KOiK03006.
OMAiIVFNRQP.
OrthoDBiEOG780RVQ.

Family and domain databases

InterProiIPR000722. RNA_pol_asu.
IPR000684. RNA_pol_II_repeat_euk.
IPR006592. RNA_pol_N.
IPR007080. RNA_pol_Rpb1_1.
IPR007066. RNA_pol_Rpb1_3.
IPR007083. RNA_pol_Rpb1_4.
IPR007081. RNA_pol_Rpb1_5.
IPR007075. RNA_pol_Rpb1_6.
IPR007073. RNA_pol_Rpb1_7.
[Graphical view]
PfamiPF04997. RNA_pol_Rpb1_1. 1 hit.
PF00623. RNA_pol_Rpb1_2. 1 hit.
PF04983. RNA_pol_Rpb1_3. 1 hit.
PF05000. RNA_pol_Rpb1_4. 1 hit.
PF04998. RNA_pol_Rpb1_5. 1 hit.
PF04992. RNA_pol_Rpb1_6. 1 hit.
PF04990. RNA_pol_Rpb1_7. 1 hit.
PF05001. RNA_pol_Rpb1_R. 16 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 22 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04050-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI
60 70 80 90 100
GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK
110 120 130 140 150
KVCECVCMHC GKLLLDEHNE LMRQALAIKD SKKRFAAIWT LCKTKMVCET
160 170 180 190 200
DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK LVGSWKKDRA TGDADEPELR
210 220 230 240 250
VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP VPPPPVRPSI
260 270 280 290 300
SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV
310 320 330 340 350
ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR
360 370 380 390 400
TVISGDPNLE LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP
410 420 430 440 450
GAKYVIRDSG DRIDLRYSKR AGDIQLQYGW KVERHIMDND PVLFNRQPSL
460 470 480 490 500
HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA DFDGDEMNLH VPQSEETRAE
510 520 530 540 550
LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF IELDQVLNML
560 570 580 590 600
YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP
610 620 630 640 650
KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ
660 670 680 690 700
KVVNFWLLHN GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN
710 720 730 740 750
LLTAKHGMTL RESFEDNVVR FLNEARDKAG RLAEVNLKDL NNVKQMVMAG
760 770 780 790 800
SKGSFINIAQ MSACVGQQSV EGKRIAFGFV DRTLPHFSKD DYSPESKGFV
810 820 830 840 850
ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV
860 870 880 890 900
HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD
910 920 930 940 950
LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG
960 970 980 990 1000
EANWPLPVNI RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL
1010 1020 1030 1040 1050
RGKNEIIQNA QRDAVTLFCC LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE
1060 1070 1080 1090 1100
AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT LNTFHFAGVA SKKVTSGVPR
1110 1120 1130 1140 1150
LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH TTLKSVTIAS
1160 1170 1180 1190 1200
EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA
1210 1220 1230 1240 1250
AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA
1260 1270 1280 1290 1300
ETEAEEDHML KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK
1310 1320 1330 1340 1350
EPEWVLETDG VNLSEVMTVP GIDPTRIYTN SFIDIMEVLG IEAGRAALYK
1360 1370 1380 1390 1400
EVYNVIASDG SYVNYRHMAL LVDVMTTQGG LTSVTRHGFN RSNTGALMRC
1410 1420 1430 1440 1450
SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA FDVMIDEESL
1460 1470 1480 1490 1500
VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS
1510 1520 1530 1540 1550
NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS
1560 1570 1580 1590 1600
PTSPAYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP
1610 1620 1630 1640 1650
TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT
1660 1670 1680 1690 1700
SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPNYSPTS
1710 1720 1730
PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR
Length:1,733
Mass (Da):191,612
Last modified:November 1, 1997 - v2
Checksum:iA45C1360FF99F968
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1514 – 15141A → V in CAA26904. (PubMed:3896517)Curated
Sequence conflicti1524 – 15241G → A in CAA26904. (PubMed:3896517)Curated
Sequence conflicti1601 – 16011T → M(PubMed:3896517)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti1653 – 16597Missing in strain: A364A.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03128 Genomic DNA. Translation: CAA26904.1.
X96876 Genomic DNA. Translation: CAA65619.1.
Z74188 Genomic DNA. Translation: CAA98713.1.
U27182 Genomic DNA. Translation: AAC49058.1.
BK006938 Genomic DNA. Translation: DAA11718.1.
PIRiS67686. RNBY2L.
RefSeqiNP_010141.1. NM_001180200.1.

Genome annotation databases

EnsemblFungiiYDL140C; YDL140C; YDL140C.
GeneIDi851415.
KEGGisce:YDL140C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X03128 Genomic DNA. Translation: CAA26904.1 .
X96876 Genomic DNA. Translation: CAA65619.1 .
Z74188 Genomic DNA. Translation: CAA98713.1 .
U27182 Genomic DNA. Translation: AAC49058.1 .
BK006938 Genomic DNA. Translation: DAA11718.1 .
PIRi S67686. RNBY2L.
RefSeqi NP_010141.1. NM_001180200.1.

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 A 1-1733 [» ]
1I50 X-ray 2.80 A 1-1733 [» ]
1I6H X-ray 3.30 A 1-1733 [» ]
1K83 X-ray 2.80 A 1-1733 [» ]
1NIK X-ray 4.10 A 1-1733 [» ]
1NT9 X-ray 4.20 A 1-1733 [» ]
1PQV X-ray 3.80 A 1-1733 [» ]
1R5U X-ray 4.50 A 1-1733 [» ]
1R9S X-ray 4.25 A 1-1733 [» ]
1R9T X-ray 3.50 A 1-1733 [» ]
1SFO X-ray 3.61 A 1-1733 [» ]
1TWA X-ray 3.20 A 1-1733 [» ]
1TWC X-ray 3.00 A 1-1733 [» ]
1TWF X-ray 2.30 A 1-1733 [» ]
1TWG X-ray 3.30 A 1-1733 [» ]
1TWH X-ray 3.40 A 1-1733 [» ]
1WCM X-ray 3.80 A 1-1733 [» ]
1Y1V X-ray 3.80 A 1-1733 [» ]
1Y1W X-ray 4.00 A 1-1733 [» ]
1Y1Y X-ray 4.00 A 1-1733 [» ]
1Y77 X-ray 4.50 A 1-1733 [» ]
2B63 X-ray 3.80 A 1-1733 [» ]
2B8K X-ray 4.15 A 1-1733 [» ]
2E2H X-ray 3.95 A 1-1733 [» ]
2E2I X-ray 3.41 A 1-1733 [» ]
2E2J X-ray 3.50 A 1-1733 [» ]
2JA5 X-ray 3.80 A 1-1733 [» ]
2JA6 X-ray 4.00 A 1-1733 [» ]
2JA7 X-ray 3.80 A/M 1-1733 [» ]
2JA8 X-ray 3.80 A 1-1733 [» ]
2L0I NMR - B 1675-1688 [» ]
2LO6 NMR - B 1675-1688 [» ]
2NVQ X-ray 2.90 A 1-1733 [» ]
2NVT X-ray 3.36 A 1-1733 [» ]
2NVX X-ray 3.60 A 1-1733 [» ]
2NVY X-ray 3.40 A 1-1733 [» ]
2NVZ X-ray 4.30 A 1-1733 [» ]
2R7Z X-ray 3.80 A 1-1733 [» ]
2R92 X-ray 3.80 A 1-1733 [» ]
2R93 X-ray 4.00 A 1-1733 [» ]
2VUM X-ray 3.40 A 1-1733 [» ]
2YU9 X-ray 3.40 A 1-1733 [» ]
3CQZ X-ray 2.80 A 1-1733 [» ]
3FKI X-ray 3.88 A 1-1733 [» ]
3GTG X-ray 3.78 A 1-1733 [» ]
3GTJ X-ray 3.42 A 1-1733 [» ]
3GTK X-ray 3.80 A 1-1733 [» ]
3GTL X-ray 3.38 A 1-1733 [» ]
3GTM X-ray 3.80 A 1-1733 [» ]
3GTO X-ray 4.00 A 1-1733 [» ]
3GTP X-ray 3.90 A 1-1733 [» ]
3GTQ X-ray 3.80 A 1-1733 [» ]
3H3V X-ray 4.00 B 1-1733 [» ]
3HOU X-ray 3.20 A/M 1-1733 [» ]
3HOV X-ray 3.50 A 1-1733 [» ]
3HOW X-ray 3.60 A 1-1733 [» ]
3HOX X-ray 3.65 A 1-1733 [» ]
3HOY X-ray 3.40 A 1-1733 [» ]
3HOZ X-ray 3.65 A 1-1733 [» ]
3I4M X-ray 3.70 A 1-1733 [» ]
3I4N X-ray 3.90 A 1-1733 [» ]
3J0K electron microscopy 36.00 A 1-1455 [» ]
3J1N electron microscopy 16.00 A 1-1455 [» ]
3K1F X-ray 4.30 A 1-1733 [» ]
3K7A X-ray 3.80 A 1-1733 [» ]
3M3Y X-ray 3.18 A 1-1733 [» ]
3M4O X-ray 3.57 A 1-1733 [» ]
3PO2 X-ray 3.30 A 1-1733 [» ]
3PO3 X-ray 3.30 A 1-1733 [» ]
3QT1 X-ray 4.30 A 1-1733 [» ]
3RZD X-ray 3.30 A 1-1733 [» ]
3RZO X-ray 3.00 A 1-1733 [» ]
3S14 X-ray 2.85 A 1-1733 [» ]
3S15 X-ray 3.30 A 1-1733 [» ]
3S16 X-ray 3.24 A 1-1733 [» ]
3S17 X-ray 3.20 A 1-1733 [» ]
3S1M X-ray 3.13 A 1-1733 [» ]
3S1N X-ray 3.10 A 1-1733 [» ]
3S1Q X-ray 3.30 A 1-1733 [» ]
3S1R X-ray 3.20 A 1-1733 [» ]
3S2D X-ray 3.20 A 1-1733 [» ]
3S2H X-ray 3.30 A 1-1733 [» ]
4A3B X-ray 3.50 A 1-1732 [» ]
4A3C X-ray 3.50 A 1-1732 [» ]
4A3D X-ray 3.40 A 1-1732 [» ]
4A3E X-ray 3.40 A 1-1732 [» ]
4A3F X-ray 3.50 A 1-1732 [» ]
4A3G X-ray 3.50 A 1-1732 [» ]
4A3I X-ray 3.80 A 1-1732 [» ]
4A3J X-ray 3.70 A 1-1732 [» ]
4A3K X-ray 3.50 A 1-1732 [» ]
4A3L X-ray 3.50 A 1-1732 [» ]
4A3M X-ray 3.90 A 1-1732 [» ]
4A93 X-ray 3.40 A 1-1732 [» ]
4BBR X-ray 3.40 A 1-1733 [» ]
4BBS X-ray 3.60 A 1-1733 [» ]
4BXX X-ray 3.28 A 1-1733 [» ]
4BXZ X-ray 4.80 A 1-1733 [» ]
4BY1 X-ray 3.60 A 1-1733 [» ]
4BY7 X-ray 3.15 A 1-1733 [» ]
4GWQ X-ray 4.50 H 1619-1653 [» ]
ProteinModelPortali P04050.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31921. 301 interactions.
DIPi DIP-611N.
IntActi P04050. 43 interactions.
MINTi MINT-432838.

Proteomic databases

MaxQBi P04050.
PaxDbi P04050.
PeptideAtlasi P04050.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDL140C ; YDL140C ; YDL140C .
GeneIDi 851415.
KEGGi sce:YDL140C.

Organism-specific databases

CYGDi YDL140c.
SGDi S000002299. RPO21.

Phylogenomic databases

eggNOGi COG0086.
GeneTreei ENSGT00730000110946.
HOGENOMi HOG000222975.
InParanoidi P04050.
KOi K03006.
OMAi IVFNRQP.
OrthoDBi EOG780RVQ.

Enzyme and pathway databases

BioCyci YEAST:G3O-29539-MONOMER.
Reactomei REACT_191540. mRNA Splicing - Minor Pathway.

Miscellaneous databases

EvolutionaryTracei P04050.
NextBioi 968606.
PROi P04050.

Gene expression databases

Genevestigatori P04050.

Family and domain databases

InterProi IPR000722. RNA_pol_asu.
IPR000684. RNA_pol_II_repeat_euk.
IPR006592. RNA_pol_N.
IPR007080. RNA_pol_Rpb1_1.
IPR007066. RNA_pol_Rpb1_3.
IPR007083. RNA_pol_Rpb1_4.
IPR007081. RNA_pol_Rpb1_5.
IPR007075. RNA_pol_Rpb1_6.
IPR007073. RNA_pol_Rpb1_7.
[Graphical view ]
Pfami PF04997. RNA_pol_Rpb1_1. 1 hit.
PF00623. RNA_pol_Rpb1_2. 1 hit.
PF04983. RNA_pol_Rpb1_3. 1 hit.
PF05000. RNA_pol_Rpb1_4. 1 hit.
PF04998. RNA_pol_Rpb1_5. 1 hit.
PF04992. RNA_pol_Rpb1_6. 1 hit.
PF04990. RNA_pol_Rpb1_7. 1 hit.
PF05001. RNA_pol_Rpb1_R. 16 hits.
[Graphical view ]
SMARTi SM00663. RPOLA_N. 1 hit.
[Graphical view ]
PROSITEi PS00115. RNA_POL_II_REPEAT. 22 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases."
    Allison L.A., Moyle M., Shales M., Ingles C.J.
    Cell 42:599-610(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204626 / S288c / A364A.
  2. "Analysis of a 26,756 bp segment from the left arm of yeast chromosome IV."
    Woelfl S., Haneman V., Saluz H.P.
    Yeast 12:1549-1554(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(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. "The gene encoding the biotin-apoprotein ligase of Saccharomyces cerevisiae."
    Cronan J.E. Jr., Wallace J.C.
    FEMS Microbiol. Lett. 130:221-230(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1669-1733.
    Strain: ATCC 204508 / S288c.
  6. "Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations."
    West M.L., Corden J.L.
    Genetics 140:1223-1233(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF THE CTD.
  7. "Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases."
    Hengartner C.J., Myer V.E., Liao S.-M., Wilson C.J., Koh S.S., Young R.A.
    Mol. Cell 2:43-53(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION BY THE TFIIK COMPLEX AND THE SRB8-11 COMPLEX.
  8. "Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3'-End formation."
    Morris D.P., Phatnani H.P., Greenleaf A.L.
    J. Biol. Chem. 274:31583-31587(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ESS1.
  9. "An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae."
    Kobor M.S., Archambault J., Lester W., Holstege F.C.P., Gileadi O., Jansma D.B., Jennings E.G., Kouyoumdjian F., Davidson A.R., Young R.A., Greenblatt J.
    Mol. Cell 4:55-62(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEPHOSPHORYLATION BY FCP1.
  10. "Phosphorylation of the RNA polymerase II carboxy-terminal domain by the Bur1 cyclin-dependent kinase."
    Murray S., Udupa R., Yao S., Hartzog G., Prelich G.
    Mol. Cell. Biol. 21:4089-4096(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION BY THE BUR KINASE COMPLEX.
  11. "Ask10p mediates the oxidative stress-induced destruction of the Saccharomyces cerevisiae C-type cyclin Ume3p/Srb11p."
    Cohen T.J., Lee K., Rutkowski L.H., Strich R.
    Eukaryot. Cell 2:962-970(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ASK10.
  12. "A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
    Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
    Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-695.
  13. "C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats."
    Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M., Greenleaf A.L.
    J. Biol. Chem. 279:24957-24964(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION BY CTD KINASE.
  14. "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.
  15. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  16. "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 THR-1471, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud."
    Shen Z., St-Denis A., Chartrand P.
    Genes Dev. 24:1914-1926(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SHE2.
  18. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
    Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
    Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  19. "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.
  20. "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.
  21. "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.
  22. "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.
  23. "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.
  24. "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.
  25. "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.
  26. "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.
  27. "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).
  28. "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.
  29. "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.
  30. "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.
  31. "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 nameiRPB1_YEAST
AccessioniPrimary (citable) accession number: P04050
Secondary accession number(s): D6VRK8, Q12364, Q92315
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: November 1, 1997
Last modified: October 29, 2014
This is version 169 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Mutagenesis experiments demonstrate that the minimum viable CTD contains eight consensus Y-S-P-T-S-P-[A-S-N-G] heptapeptide repeats. Identical and simultaneous substitutions in a number of consecutive repeats are lethal: 'Ser-2' -> 'Ala-2' (14 repeats), 'Ser-5' -> 'Ala-5' (15 repeats), '2-Ser-Pro-Thr-Ser-5'-> '2-Ala-Pro-Thr-Ala-5' (10 repeats), 'Ser-2'-> 'Glu-2' (15 repeats), 'Ser-5' -> 'Glu-5' (12 repeats), '2-Ser-Pro-3' -> '2-Pro-Ser-3' (15 repeats) and 'Tyr-1' -> 'Phe-1' (12 repeats).
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 temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.

Keywords - Technical termi

3D-structure, Complete proteome, 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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3