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UniProtKB - P08518 (RPB2_YEAST)

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Protein

DNA-directed RNA polymerase II subunit RPB2

Gene

RPB2

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

Functioni

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

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

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi837Magnesium; shared with RPB11
Metal bindingi1163Zinc1
Metal bindingi1166Zinc1
Metal bindingi1182Zinc1
Metal bindingi1185Zinc1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1163 – 1185C4-typeAdd BLAST23

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

  • transcription, RNA-templated Source: GOC
  • transcription by RNA polymerase II Source: SGD
View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionNucleotidyltransferase, Transferase
Biological processTranscription
LigandMagnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-33668-MONOMER
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-6807505 RNA polymerase II transcribes snRNA 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
R-SCE-9018519 Estrogen-dependent gene expression

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 lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR151C
SGDiS000005677 RPB2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000480911 – 1224DNA-directed RNA polymerase II subunit RPB2Add BLAST1224

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei919PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP08518
PaxDbiP08518
PRIDEiP08518

PTM databases

iPTMnetiP08518

Interactioni

Subunit structurei

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

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi34547, 464 interactors
ComplexPortaliCPX-2662 DNA-directed RNA polymerase II complex
DIPiDIP-14N
IntActiP08518, 104 interactors
MINTiP08518
STRINGi4932.YOR151C

Structurei

Secondary structure

11224
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi22 – 24Combined sources3
Helixi29 – 41Combined sources13
Helixi42 – 44Combined sources3
Helixi45 – 56Combined sources12
Helixi58 – 64Combined sources7
Beta strandi69 – 71Combined sources3
Beta strandi78 – 80Combined sources3
Beta strandi96 – 102Combined sources7
Beta strandi105 – 107Combined sources3
Beta strandi109 – 111Combined sources3
Helixi114 – 119Combined sources6
Beta strandi125 – 129Combined sources5
Beta strandi141 – 143Combined sources3
Beta strandi166 – 171Combined sources6
Beta strandi176 – 179Combined sources4
Helixi180 – 182Combined sources3
Helixi186 – 191Combined sources6
Beta strandi202 – 205Combined sources4
Beta strandi208 – 212Combined sources5
Beta strandi214 – 218Combined sources5
Beta strandi224 – 227Combined sources4
Beta strandi232 – 241Combined sources10
Beta strandi245 – 247Combined sources3
Beta strandi253 – 260Combined sources8
Beta strandi264 – 266Combined sources3
Beta strandi269 – 272Combined sources4
Beta strandi277 – 281Combined sources5
Helixi282 – 288Combined sources7
Helixi294 – 301Combined sources8
Helixi308 – 320Combined sources13
Turni321 – 323Combined sources3
Helixi327 – 336Combined sources10
Beta strandi337 – 339Combined sources3
Helixi342 – 344Combined sources3
Helixi345 – 358Combined sources14
Beta strandi359 – 361Combined sources3
Turni362 – 364Combined sources3
Beta strandi367 – 369Combined sources3
Helixi371 – 389Combined sources19
Beta strandi390 – 393Combined sources4
Helixi401 – 403Combined sources3
Beta strandi404 – 407Combined sources4
Helixi409 – 433Combined sources25
Turni434 – 436Combined sources3
Helixi444 – 447Combined sources4
Helixi451 – 463Combined sources13
Beta strandi467 – 469Combined sources3
Helixi474 – 476Combined sources3
Beta strandi477 – 479Combined sources3
Beta strandi480 – 482Combined sources3
Helixi488 – 495Combined sources8
Beta strandi497 – 499Combined sources3
Turni501 – 505Combined sources5
Beta strandi511 – 513Combined sources3
Helixi516 – 518Combined sources3
Turni519 – 521Combined sources3
Helixi530 – 532Combined sources3
Turni533 – 535Combined sources3
Beta strandi536 – 539Combined sources4
Helixi552 – 560Combined sources9
Beta strandi563 – 565Combined sources3
Helixi566 – 568Combined sources3
Helixi571 – 573Combined sources3
Beta strandi574 – 576Combined sources3
Beta strandi578 – 582Combined sources5
Beta strandi585 – 591Combined sources7
Helixi593 – 606Combined sources14
Beta strandi607 – 609Combined sources3
Beta strandi614 – 618Combined sources5
Turni619 – 622Combined sources4
Beta strandi623 – 627Combined sources5
Beta strandi633 – 641Combined sources9
Beta strandi646 – 649Combined sources4
Beta strandi650 – 652Combined sources3
Helixi655 – 666Combined sources12
Helixi681 – 686Combined sources6
Beta strandi689 – 694Combined sources6
Helixi695 – 698Combined sources4
Beta strandi703 – 706Combined sources4
Helixi707 – 710Combined sources4
Beta strandi711 – 713Combined sources3
Beta strandi725 – 727Combined sources3
Beta strandi739 – 741Combined sources3
Helixi745 – 748Combined sources4
Helixi753 – 755Combined sources3
Beta strandi756 – 758Combined sources3
Helixi759 – 761Combined sources3
Helixi764 – 773Combined sources10
Helixi774 – 776Combined sources3
Beta strandi779 – 781Combined sources3
Turni783 – 787Combined sources5
Beta strandi791 – 798Combined sources8
Beta strandi803 – 805Combined sources3
Helixi809 – 812Combined sources4
Turni813 – 816Combined sources4
Beta strandi821 – 827Combined sources7
Beta strandi829 – 832Combined sources4
Turni833 – 837Combined sources5
Beta strandi838 – 842Combined sources5
Helixi843 – 847Combined sources5
Turni848 – 851Combined sources4
Beta strandi853 – 861Combined sources9
Beta strandi866 – 869Combined sources4
Beta strandi873 – 875Combined sources3
Beta strandi880 – 882Combined sources3
Beta strandi886 – 888Combined sources3
Helixi890 – 892Combined sources3
Beta strandi895 – 899Combined sources5
Beta strandi904 – 906Combined sources3
Beta strandi910 – 912Combined sources3
Beta strandi914 – 916Combined sources3
Beta strandi935 – 940Combined sources6
Beta strandi947 – 956Combined sources10
Beta strandi958 – 960Combined sources3
Beta strandi962 – 972Combined sources11
Beta strandi979 – 981Combined sources3
Beta strandi983 – 985Combined sources3
Beta strandi987 – 994Combined sources8
Turni996 – 998Combined sources3
Beta strandi1001 – 1005Combined sources5
Beta strandi1009 – 1012Combined sources4
Helixi1014 – 1016Combined sources3
Turni1018 – 1021Combined sources4
Helixi1023 – 1038Combined sources16
Beta strandi1046 – 1049Combined sources4
Helixi1052 – 1060Combined sources9
Turni1061 – 1063Combined sources3
Beta strandi1068 – 1070Combined sources3
Beta strandi1071 – 1073Combined sources3
Turni1075 – 1077Combined sources3
Beta strandi1080 – 1084Combined sources5
Beta strandi1085 – 1097Combined sources13
Helixi1099 – 1101Combined sources3
Beta strandi1104 – 1106Combined sources3
Turni1113 – 1115Combined sources3
Helixi1122 – 1124Combined sources3
Beta strandi1128 – 1130Combined sources3
Helixi1132 – 1141Combined sources10
Helixi1144 – 1151Combined sources8
Helixi1152 – 1156Combined sources5
Beta strandi1159 – 1166Combined sources8
Beta strandi1172 – 1174Combined sources3
Turni1175 – 1178Combined sources4
Beta strandi1179 – 1182Combined sources4
Turni1183 – 1186Combined sources4
Beta strandi1187 – 1195Combined sources9
Helixi1198 – 1209Combined sources12
Beta strandi1215 – 1218Combined sources4

3D structure databases

ProteinModelPortaliP08518
SMRiP08518
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08518

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni467 – 478Fork loop 1Add BLAST12

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1163 – 1185C4-typeAdd BLAST23

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00920000149299
HOGENOMiHOG000222962
InParanoidiP08518
KOiK03010
OMAiKNLSLMC
OrthoDBiEOG092C06IY

Family and domain databases

CDDicd00653 RNA_pol_B_RPB2, 1 hit
Gene3Di2.40.270.10, 3 hits
2.40.50.150, 2 hits
3.90.1110.10, 1 hit
InterProiView protein in InterPro
IPR015712 DNA-dir_RNA_pol_su2
IPR007120 DNA-dir_RNAP_su2_dom
IPR037033 DNA-dir_RNAP_su2_hyb_sf
IPR007121 RNA_pol_bsu_CS
IPR007644 RNA_pol_bsu_protrusion
IPR007642 RNA_pol_Rpb2_2
IPR037034 RNA_pol_Rpb2_2_sf
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
PANTHERiPTHR20856 PTHR20856, 1 hit
PfamiView protein in Pfam
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
PROSITEiView protein in PROSITE
PS01166 RNA_POL_BETA, 1 hit

Sequencei

Sequence statusi: Complete.

P08518-1 [UniParc]FASTAAdd to basket

« Hide

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1003 – 1006AEGI → RRRY in AAA68096 (PubMed:3547406).Curated4

Sequence databases

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

Genome annotation databases

EnsemblFungiiYOR151C; YOR151C; YOR151C
GeneIDi854322
KEGGisce:YOR151C

Similar proteinsi

Entry informationi

Entry nameiRPB2_YEAST
AccessioniPrimary (citable) accession number: P08518
Secondary accession number(s): D6W2K8, Q12738, Q7Z9Y0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: November 1, 1997
Last modified: July 18, 2018
This is version 199 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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