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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: 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)DescriptionActionsGraphical viewLength
Metal bindingi67Zinc 1Combined sources2 Publications1
Metal bindingi70Zinc 1Combined sources2 Publications1
Metal bindingi77Zinc 1Combined sources2 Publications1
Metal bindingi80Zinc 1; via tele nitrogenCombined sources2 Publications1
Metal bindingi107Zinc 2Combined sources2 Publications1
Metal bindingi110Zinc 2Combined sources2 Publications1
Metal bindingi148Zinc 2Combined sources2 Publications1
Metal bindingi167Zinc 2Combined sources2 Publications1
Metal bindingi481Magnesium 1; catalyticCombined sources2 Publications1
Metal bindingi481Magnesium 2; shared with RPB2Combined sources2 Publications1
Metal bindingi483Magnesium 1; catalyticCombined sources2 Publications1
Metal bindingi483Magnesium 2; shared with RPB2Combined sources2 Publications1
Metal bindingi485Magnesium 1; catalyticCombined sources2 Publications1

GO - Molecular functioni

GO - Biological processi

  • transcription, RNA-templated Source: GOC
  • transcription from RNA polymerase II promoter Source: SGD
  • 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.
BRENDAi2.7.7.6. 984.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-SCE-72086. mRNA Capping.
R-SCE-72165. mRNA Splicing - Minor Pathway.
R-SCE-73776. RNA Polymerase II Promoter Escape.
R-SCE-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SCE-75953. RNA Polymerase II Transcription Initiation.
R-SCE-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

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
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL140C.
SGDiS000002299. RPO21.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic stress granule Source: SGD
  • DNA-directed RNA polymerase II, core complex Source: SGD
  • nucleus Source: CACAO
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000739461 – 1733DNA-directed RNA polymerase II subunit RPB1Add BLAST1733

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki695Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources1 Publication
Cross-linki1246Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Cross-linki1350Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei1471PhosphothreonineCombined sources1

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 SSU72.3 Publications

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04050.
PRIDEiP04050.
TopDownProteomicsiP04050.

PTM databases

iPTMnetiP04050.

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. 327 interactors.
DIPiDIP-611N.
IntActiP04050. 44 interactors.
MINTiMINT-432838.

Structurei

Secondary structure

11733
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi16 – 18Combined sources3
Helixi24 – 29Combined sources6
Beta strandi32 – 34Combined sources3
Beta strandi39 – 41Combined sources3
Beta strandi43 – 45Combined sources3
Beta strandi46 – 48Combined sources3
Beta strandi51 – 54Combined sources4
Beta strandi56 – 58Combined sources3
Beta strandi62 – 64Combined sources3
Beta strandi67 – 69Combined sources3
Turni74 – 76Combined sources3
Beta strandi84 – 91Combined sources8
Helixi93 – 95Combined sources3
Helixi96 – 105Combined sources10
Turni108 – 110Combined sources3
Beta strandi113 – 115Combined sources3
Beta strandi117 – 119Combined sources3
Helixi120 – 126Combined sources7
Beta strandi127 – 129Combined sources3
Helixi131 – 142Combined sources12
Beta strandi150 – 152Combined sources3
Beta strandi160 – 163Combined sources4
Beta strandi173 – 177Combined sources5
Beta strandi181 – 185Combined sources5
Beta strandi187 – 190Combined sources4
Beta strandi198 – 202Combined sources5
Helixi204 – 211Combined sources8
Beta strandi212 – 214Combined sources3
Helixi216 – 221Combined sources6
Turni226 – 228Combined sources3
Helixi231 – 234Combined sources4
Beta strandi235 – 239Combined sources5
Turni244 – 246Combined sources3
Beta strandi253 – 255Combined sources3
Beta strandi257 – 260Combined sources4
Helixi261 – 280Combined sources20
Turni281 – 283Combined sources3
Helixi286 – 304Combined sources19
Beta strandi307 – 310Combined sources4
Beta strandi313 – 316Combined sources4
Beta strandi318 – 321Combined sources4
Helixi325 – 329Combined sources5
Turni330 – 335Combined sources6
Helixi338 – 340Combined sources3
Beta strandi341 – 344Combined sources4
Beta strandi347 – 355Combined sources9
Beta strandi363 – 367Combined sources5
Helixi368 – 371Combined sources4
Beta strandi375 – 379Combined sources5
Turni382 – 384Combined sources3
Helixi385 – 394Combined sources10
Turni395 – 397Combined sources3
Beta strandi398 – 400Combined sources3
Beta strandi402 – 406Combined sources5
Helixi408 – 410Combined sources3
Beta strandi412 – 414Combined sources3
Turni415 – 417Combined sources3
Turni419 – 422Combined sources4
Beta strandi431 – 435Combined sources5
Beta strandi441 – 445Combined sources5
Helixi452 – 454Combined sources3
Beta strandi455 – 470Combined sources16
Helixi472 – 474Combined sources3
Helixi475 – 478Combined sources4
Beta strandi482 – 484Combined sources3
Beta strandi486 – 490Combined sources5
Helixi495 – 504Combined sources10
Helixi507 – 510Combined sources4
Beta strandi511 – 513Combined sources3
Turni514 – 517Combined sources4
Beta strandi518 – 520Combined sources3
Helixi525 – 535Combined sources11
Beta strandi536 – 538Combined sources3
Beta strandi540 – 542Combined sources3
Helixi543 – 552Combined sources10
Beta strandi553 – 555Combined sources3
Beta strandi567 – 569Combined sources3
Beta strandi571 – 573Combined sources3
Helixi574 – 581Combined sources8
Beta strandi588 – 590Combined sources3
Beta strandi596 – 598Combined sources3
Beta strandi600 – 602Combined sources3
Beta strandi604 – 608Combined sources5
Beta strandi611 – 615Combined sources5
Helixi619 – 622Combined sources4
Beta strandi626 – 628Combined sources3
Helixi629 – 637Combined sources9
Helixi639 – 658Combined sources20
Helixi666 – 669Combined sources4
Helixi673 – 699Combined sources27
Beta strandi706 – 708Combined sources3
Helixi710 – 736Combined sources27
Helixi742 – 749Combined sources8
Beta strandi750 – 752Combined sources3
Helixi755 – 762Combined sources8
Beta strandi770 – 774Combined sources5
Beta strandi778 – 781Combined sources4
Beta strandi782 – 784Combined sources3
Turni794 – 798Combined sources5
Turni804 – 806Combined sources3
Helixi810 – 845Combined sources36
Beta strandi863 – 867Combined sources5
Helixi868 – 870Combined sources3
Helixi875 – 877Combined sources3
Beta strandi878 – 882Combined sources5
Helixi884 – 886Combined sources3
Helixi890 – 897Combined sources8
Beta strandi901 – 903Combined sources3
Turni904 – 906Combined sources3
Turni910 – 912Combined sources3
Beta strandi913 – 915Combined sources3
Helixi916 – 919Combined sources4
Helixi923 – 946Combined sources24
Turni947 – 949Combined sources3
Beta strandi953 – 958Combined sources6
Helixi960 – 970Combined sources11
Beta strandi975 – 977Combined sources3
Helixi983 – 994Combined sources12
Helixi1005 – 1013Combined sources9
Helixi1016 – 1025Combined sources10
Helixi1028 – 1033Combined sources6
Helixi1039 – 1056Combined sources18
Helixi1064 – 1076Combined sources13
Beta strandi1079 – 1082Combined sources4
Helixi1086 – 1088Combined sources3
Beta strandi1089 – 1091Combined sources3
Beta strandi1092 – 1094Combined sources3
Helixi1097 – 1104Combined sources8
Turni1105 – 1107Combined sources3
Beta strandi1115 – 1120Combined sources6
Beta strandi1122 – 1126Combined sources5
Helixi1128 – 1138Combined sources11
Helixi1143 – 1145Combined sources3
Beta strandi1147 – 1154Combined sources8
Beta strandi1158 – 1160Combined sources3
Helixi1164 – 1166Combined sources3
Helixi1167 – 1171Combined sources5
Beta strandi1172 – 1174Combined sources3
Beta strandi1179 – 1182Combined sources4
Beta strandi1190 – 1197Combined sources8
Helixi1199 – 1204Combined sources6
Helixi1209 – 1220Combined sources12
Helixi1221 – 1223Combined sources3
Beta strandi1224 – 1228Combined sources5
Beta strandi1233 – 1235Combined sources3
Beta strandi1237 – 1242Combined sources6
Helixi1258 – 1270Combined sources13
Beta strandi1272 – 1275Combined sources4
Beta strandi1282 – 1292Combined sources11
Beta strandi1296 – 1310Combined sources15
Helixi1313 – 1316Combined sources4
Beta strandi1317 – 1322Combined sources6
Turni1324 – 1326Combined sources3
Beta strandi1328 – 1330Combined sources3
Helixi1332 – 1339Combined sources8
Helixi1341 – 1357Combined sources17
Turni1358 – 1360Combined sources3
Helixi1365 – 1374Combined sources10
Turni1375 – 1377Combined sources3
Beta strandi1378 – 1380Combined sources3
Beta strandi1384 – 1386Combined sources3
Beta strandi1388 – 1390Combined sources3
Beta strandi1392 – 1394Combined sources3
Helixi1396 – 1399Combined sources4
Turni1400 – 1402Combined sources3
Helixi1406 – 1415Combined sources10
Helixi1424 – 1429Combined sources6
Helixi1437 – 1439Combined sources3
Beta strandi1440 – 1445Combined sources6
Helixi1447 – 1450Combined sources4
Beta strandi1677 – 1680Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4V1Melectron microscopy6.60A1-1733[»]
4V1Nelectron microscopy7.80A1-1733[»]
4V1Oelectron microscopy9.70A1-1733[»]
4X67X-ray4.10A1-1733[»]
4X6AX-ray3.96A1-1733[»]
4Y52X-ray3.50A1-1733[»]
4Y7NX-ray3.30A1-1733[»]
5C3EX-ray3.70A1-1733[»]
5C44X-ray3.95A1-1733[»]
5C4AX-ray4.20A1-1733[»]
5C4JX-ray4.00A1-1733[»]
5C4XX-ray4.00A1-1733[»]
5FMFelectron microscopy6.00A1-1733[»]
5FYWelectron microscopy4.35A1-1733[»]
5FZ5electron microscopy8.80A1-1733[»]
5IP7X-ray3.52A2-1733[»]
5IP9X-ray3.90A2-1733[»]
5SVAelectron microscopy15.30A1-1733[»]
k1666-1690[»]
ProteinModelPortaliP04050.
SMRiP04050.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04050.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati1549 – 155517
Repeati1556 – 156227
Repeati1563 – 156937
Repeati1570 – 157647
Repeati1577 – 158357
Repeati1584 – 159067
Repeati1591 – 159777
Repeati1598 – 160487
Repeati1605 – 161197
Repeati1612 – 1618107
Repeati1619 – 1625117
Repeati1626 – 1632127
Repeati1633 – 1639137
Repeati1640 – 1646147
Repeati1647 – 1653157
Repeati1654 – 1660167
Repeati1661 – 1667177
Repeati1668 – 1674187
Repeati1675 – 1681197
Repeati1682 – 1688207
Repeati1689 – 1695217
Repeati1696 – 1702227
Repeati1703 – 1709237
Repeati1710 – 171624; approximate7

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni248 – 260Lid loopAdd BLAST13
Regioni306 – 323Rudder loopAdd BLAST18
Regioni810 – 822Bridging helixAdd BLAST13
Regioni1549 – 1716C-terminal domain (CTD); 24 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[A-S-N-G]Add BLAST168

Domaini

The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.Curated

Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00860000133919.
HOGENOMiHOG000222975.
InParanoidiP04050.
KOiK03006.
OMAiASTYYKP.
OrthoDBiEOG092C01XQ.

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. 12 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)DescriptionActionsGraphical viewLength
Sequence conflicti1514A → V in CAA26904 (PubMed:3896517).Curated1
Sequence conflicti1524G → A in CAA26904 (PubMed:3896517).Curated1
Sequence conflicti1601T → M (PubMed:3896517).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti1653 – 1659Missing in strain: A364A. 7

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4V1Melectron microscopy6.60A1-1733[»]
4V1Nelectron microscopy7.80A1-1733[»]
4V1Oelectron microscopy9.70A1-1733[»]
4X67X-ray4.10A1-1733[»]
4X6AX-ray3.96A1-1733[»]
4Y52X-ray3.50A1-1733[»]
4Y7NX-ray3.30A1-1733[»]
5C3EX-ray3.70A1-1733[»]
5C44X-ray3.95A1-1733[»]
5C4AX-ray4.20A1-1733[»]
5C4JX-ray4.00A1-1733[»]
5C4XX-ray4.00A1-1733[»]
5FMFelectron microscopy6.00A1-1733[»]
5FYWelectron microscopy4.35A1-1733[»]
5FZ5electron microscopy8.80A1-1733[»]
5IP7X-ray3.52A2-1733[»]
5IP9X-ray3.90A2-1733[»]
5SVAelectron microscopy15.30A1-1733[»]
k1666-1690[»]
ProteinModelPortaliP04050.
SMRiP04050.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31921. 327 interactors.
DIPiDIP-611N.
IntActiP04050. 44 interactors.
MINTiMINT-432838.

PTM databases

iPTMnetiP04050.

Proteomic databases

MaxQBiP04050.
PRIDEiP04050.
TopDownProteomicsiP04050.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YDL140C.
SGDiS000002299. RPO21.

Phylogenomic databases

GeneTreeiENSGT00860000133919.
HOGENOMiHOG000222975.
InParanoidiP04050.
KOiK03006.
OMAiASTYYKP.
OrthoDBiEOG092C01XQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-29539-MONOMER.
BRENDAi2.7.7.6. 984.
ReactomeiR-SCE-113418. Formation of the Early Elongation Complex.
R-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-SCE-72086. mRNA Capping.
R-SCE-72165. mRNA Splicing - Minor Pathway.
R-SCE-73776. RNA Polymerase II Promoter Escape.
R-SCE-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SCE-75953. RNA Polymerase II Transcription Initiation.
R-SCE-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SCE-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

EvolutionaryTraceiP04050.
PROiP04050.

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. 12 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 22 hits.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 193 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.