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Protein

DNA-directed RNA polymerase II subunit RPB1

Gene

RpII215

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

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. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single-stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. 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. During transcription elongation, Pol II moves on the template as the transcript elongates. 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 (By similarity).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi67Zinc 1By similarity1
Metal bindingi70Zinc 1By similarity1
Metal bindingi77Zinc 1By similarity1
Metal bindingi80Zinc 1By similarity1
Metal bindingi107Zinc 2By similarity1
Metal bindingi110Zinc 2By similarity1
Metal bindingi150Zinc 2By similarity1
Metal bindingi176Zinc 2By similarity1
Metal bindingi487Magnesium 1; catalyticBy similarity1
Metal bindingi487Magnesium 2; shared with RPB2By similarity1
Metal bindingi489Magnesium 1; catalyticBy similarity1
Metal bindingi489Magnesium 2; shared with RPB2By similarity1
Metal bindingi491Magnesium 1; catalyticBy similarity1

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • DNA-directed RNA polymerase activity Source: FlyBase
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • mitotic G2 DNA damage checkpoint Source: FlyBase
  • transcription from RNA polymerase II promoter Source: FlyBase
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-DME-112382. Formation of RNA Pol II elongation complex.
R-DME-112387. Elongation arrest and recovery.
R-DME-113418. Formation of the Early Elongation Complex.
R-DME-5578749. Transcriptional regulation by small RNAs.
R-DME-674695. RNA Polymerase II Pre-transcription Events.
R-DME-6781823. Formation of TC-NER Pre-Incision Complex.
R-DME-6782135. Dual incision in TC-NER.
R-DME-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-DME-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-DME-6803529. FGFR2 alternative splicing.
R-DME-6807505. RNA polymerase II transcribes snRNA genes.
R-DME-72086. mRNA Capping.
R-DME-72163. mRNA Splicing - Major Pathway.
R-DME-72165. mRNA Splicing - Minor Pathway.
R-DME-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-DME-73776. RNA Polymerase II Promoter Escape.
R-DME-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-DME-75953. RNA Polymerase II Transcription Initiation.
R-DME-75955. RNA Polymerase II Transcription Elongation.
R-DME-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-DME-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 B1
Alternative name(s):
DNA-directed RNA polymerase III largest subunit
Gene namesi
Name:RpII215
ORF Names:CG1554
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome X

Organism-specific databases

FlyBaseiFBgn0003277. RpII215.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase II, core complex Source: FlyBase
  • nucleus Source: FlyBase
  • polytene chromosome Source: FlyBase
  • polytene chromosome puff Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000739371 – 1887DNA-directed RNA polymerase II subunit RPB1Add BLAST1887

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 phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatase, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed.

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP04052.
PRIDEiP04052.

PTM databases

iPTMnetiP04052.

Expressioni

Gene expression databases

BgeeiFBgn0003277.
GenevisibleiP04052. DM.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.By similarity

Protein-protein interaction databases

BioGridi58510. 4 interactors.
DIPiDIP-22282N.
IntActiP04052. 13 interactors.
MINTiMINT-970158.
STRINGi7227.FBpp0073387.

Structurei

3D structure databases

ProteinModelPortaliP04052.
SMRiP04052.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati1579 – 158517
Repeati1586 – 15922; approximate7
Repeati1598 – 160437
Repeati1605 – 161147
Repeati1631 – 163757
Repeati1638 – 164467
Repeati1671 – 167777
Repeati1678 – 168487
Repeati1685 – 169197
Repeati1692 – 1698107
Repeati1699 – 1705117
Repeati1706 – 1712127
Repeati1713 – 1719137
Repeati1720 – 1726147
Repeati1727 – 1733157
Repeati1740 – 1746167
Repeati1754 – 1760177
Repeati1761 – 1767187
Repeati1777 – 1783197
Repeati1784 – 1790207
Repeati1791 – 1797217
Repeati1798 – 1804227
Repeati1811 – 1817237
Repeati1818 – 182424; approximate7
Repeati1825 – 1831257
Repeati1832 – 1838267
Repeati1839 – 1845277
Repeati1846 – 1852287
Repeati1853 – 1859297
Repeati1860 – 1866307
Repeati1868 – 1874317
Repeati1875 – 1881327

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni825 – 837Bridging helixAdd BLAST13
Regioni1579 – 1881C-terminal domain (CTD); 32 X 7 AA approximate tandem repeats of Y-[ST]-P-[STNVAPGN]-[STGMA]-[PSTR]-[SNAGCQKTLRIMH]Add BLAST303

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

eggNOGiKOG0260. Eukaryota.
COG0086. LUCA.
GeneTreeiENSGT00850000132392.
InParanoidiP04052.
KOiK03006.
OMAiDEDNGPY.
OrthoDBiEOG091G00CH.
PhylomeDBiP04052.

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.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 11 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04052-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTPTDSKAP LRQVKRVQFG ILSPDEIRRM SVTEGGVQFA ETMEGGRPKL
60 70 80 90 100
GGLMDPRQGV IDRTSRCQTC AGNMTECPGH FGHIDLAKPV FHIGFITKTI
110 120 130 140 150
KILRCVCFYC SKMLVSPHNP KIKEIVMKSR GQPRKRLAYV YDLCKGKTIC
160 170 180 190 200
EGGEDMDLTK ENQQPDPNKK PGHGGCGHYQ PSIRRTGLDL TAEWKHQNED
210 220 230 240 250
SQEKKIVVSA ERVWEILKHI TDEECFILGM DPKYARPDWM IVTVLPVPPL
260 270 280 290 300
AVRPAVVMFG AAKNQDDLTH KLSDIIKANN ELRKNEASGA AAHVIQENIK
310 320 330 340 350
MLQFHVATLV DNDMPGMPRA MQKSGKPLKA IKARLKGKEG RIRGNLMGKR
360 370 380 390 400
VDFSARTVIT PDPNLRIDQV GVPRSIAQNL TFPELVTPFN IDRMQELVRR
410 420 430 440 450
GNSQYPGAKY IVRDNGERID LRFHPKSSDL HLQCGYKVER HLRDDDLVIF
460 470 480 490 500
NRQPTLHKMS MMGHRVKVLP WSTFRMNLSC TSPYNADFDG DEMNLHVPQS
510 520 530 540 550
METRAEVENI HITPRQIITP QANKPVMGIV QDTLTAVRKM TKRDVFITRE
560 570 580 590 600
QVMNLLMFLP TWDAKMPQPC ILKPRPLWTG KQIFSLIIPG NVNMIRTHST
610 620 630 640 650
HPDEEDEGPY KWISPGDTKV MVEHGELIMG ILCKKSLGTS AGSLLHICFL
660 670 680 690 700
ELGHDIAGRF YGNIQTVINN WLLFEGHSIG IGDTIADPQT YNEIQQAIKK
710 720 730 740 750
AKDDVINVIQ KAHNMELEPT PGNTLRQTFE NKVNRILNDA RDKTGGSAKK
760 770 780 790 800
SLTEYNNLKA MVVSGSKGSN INISQVIACV GQQNVEGKRI PYGFRKRTLP
810 820 830 840 850
HFIKDDYGPE SRGFVENSYL AGLTPSEFYF HAMGGREGLI DTAVKTAETG
860 870 880 890 900
YIQRRLIKAM ESVMVNYDGT VRNSVGQLIQ LRYGEDGLCG ELVEFQNMPT
910 920 930 940 950
VKLSNKSFEK RFKFDWSNER LMKKVFTDDV IKEMTDSSEA IQELEAEWDR
960 970 980 990 1000
LVSDRDSLRQ IFPNGESKVV LPCNLQRMIW NVQKIFHINK RLPTDLSPIR
1010 1020 1030 1040 1050
VIKGVKTLLE RCVIVTGNDR ISKQANENAT LLFQCLIRST LCTKYVSEEF
1060 1070 1080 1090 1100
RLSTEAFEWL VGEIETRFQQ AQANPGEMVG ALAAQSLGEP ATQMTLNTFH
1110 1120 1130 1140 1150
FAGVSSKNVT LGVPRLKEII NISKKPKAPS LTVFLTGGAA RDAEKAKNVL
1160 1170 1180 1190 1200
CRLEHTTLRK VTANTAIYYD PDPQRTVISE DQEFVNVYYE MPDFDPTRIS
1210 1220 1230 1240 1250
PWLLRIELDR KRMTDKKLTM EQIAEKINVG FGEDLNCIFN DDNADKLVLR
1260 1270 1280 1290 1300
IRIMNNEENK FQDEDEAVDK MEDDMFLRCI EANMLSDMTL QGIEAIGKVY
1310 1320 1330 1340 1350
MHLPQTDSKK RIVITETGEF KAIGEWLLET DGTSMMKVLS ERDVDPIRTS
1360 1370 1380 1390 1400
SNDICEIFQV LGIEAVRKSV EKEMNAVLQF YGLYVNYRHL ALLCDVMTAK
1410 1420 1430 1440 1450
GHLMAITRHG INRQDTGALM RCSFEETVDV LMDAAAHAET DPMRGVSENI
1460 1470 1480 1490 1500
IMGQLPKMGT GCFDLLLDAE KCRFGIEIPN TLGNSMLGGA AMFIGGGSTP
1510 1520 1530 1540 1550
SMTPPMTPWA NCNTPRYFSP PGHVSAMTPG GPSFSPSAAS DASGMSPSWS
1560 1570 1580 1590 1600
PAHPGSSPSS PGPSMSPYFP ASPSVSPSYS PTSPNYTASS PGGASPNYSP
1610 1620 1630 1640 1650
SSPNYSPTSP LYASPRYAST TPNFNPQSTG YSPSSSGYSP TSPVYSPTVQ
1660 1670 1680 1690 1700
FQSSPSFAGS GSNIYSPGNA YSPSSSNYSP NSPSYSPTSP SYSPSSPSYS
1710 1720 1730 1740 1750
PTSPCYSPTS PSYSPTSPNY TPVTPSYSPT SPNYSASPQY SPASPAYSQT
1760 1770 1780 1790 1800
GVKYSPTSPT YSPPSPSYDG SPGSPQYTPG SPQYSPASPK YSPTSPLYSP
1810 1820 1830 1840 1850
SSPQHSPSNQ YSPTGSTYSA TSPRYSPNMS IYSPSSTKYS PTSPTYTPTA
1860 1870 1880
RNYSPTSPMY SPTAPSHYSP TSPAYSPSSP TFEESED
Length:1,887
Mass (Da):209,168
Last modified:June 1, 2001 - v4
Checksum:i4EC68C7708A167A3
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti319 – 324RAMQKS → GYAKV in AAA28863 (PubMed:2992806).Curated6
Sequence conflicti450F → G in AAA28863 (PubMed:2992806).Curated1
Sequence conflicti455 – 458TLHK → RCTT (PubMed:2992806).Curated4
Sequence conflicti463 – 472GHRVKVLPWS → VTGESVASST (PubMed:2992806).Curated10
Sequence conflicti741R → H in AAA28868 (PubMed:2496296).Curated1
Sequence conflicti1485 – 1524SMLGG…PPGHV → I in AAA28827 (PubMed:3122024).CuratedAdd BLAST40
Sequence conflicti1506 – 1508MTP → ELDSA in AAA28868 (PubMed:2496296).Curated3
Sequence conflicti1887D → DVRKGGRG in AAA28868 (PubMed:2496296).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27431 Genomic DNA. Translation: AAA28868.1.
AE014298 Genomic DNA. Translation: AAF48057.1.
M14203 Genomic DNA. Translation: AAA28864.1.
M11798 Genomic DNA. Translation: AAA28863.1.
M19537 Genomic DNA. Translation: AAA28827.1.
PIRiS04457. RNFF2L.
RefSeqiNP_511124.1. NM_078569.3.
UniGeneiDm.2925.

Genome annotation databases

EnsemblMetazoaiFBtr0073542; FBpp0073387; FBgn0003277.
GeneIDi32100.
KEGGidme:Dmel_CG1554.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M27431 Genomic DNA. Translation: AAA28868.1.
AE014298 Genomic DNA. Translation: AAF48057.1.
M14203 Genomic DNA. Translation: AAA28864.1.
M11798 Genomic DNA. Translation: AAA28863.1.
M19537 Genomic DNA. Translation: AAA28827.1.
PIRiS04457. RNFF2L.
RefSeqiNP_511124.1. NM_078569.3.
UniGeneiDm.2925.

3D structure databases

ProteinModelPortaliP04052.
SMRiP04052.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi58510. 4 interactors.
DIPiDIP-22282N.
IntActiP04052. 13 interactors.
MINTiMINT-970158.
STRINGi7227.FBpp0073387.

PTM databases

iPTMnetiP04052.

Proteomic databases

PaxDbiP04052.
PRIDEiP04052.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0073542; FBpp0073387; FBgn0003277.
GeneIDi32100.
KEGGidme:Dmel_CG1554.

Organism-specific databases

CTDi32100.
FlyBaseiFBgn0003277. RpII215.

Phylogenomic databases

eggNOGiKOG0260. Eukaryota.
COG0086. LUCA.
GeneTreeiENSGT00850000132392.
InParanoidiP04052.
KOiK03006.
OMAiDEDNGPY.
OrthoDBiEOG091G00CH.
PhylomeDBiP04052.

Enzyme and pathway databases

ReactomeiR-DME-112382. Formation of RNA Pol II elongation complex.
R-DME-112387. Elongation arrest and recovery.
R-DME-113418. Formation of the Early Elongation Complex.
R-DME-5578749. Transcriptional regulation by small RNAs.
R-DME-674695. RNA Polymerase II Pre-transcription Events.
R-DME-6781823. Formation of TC-NER Pre-Incision Complex.
R-DME-6782135. Dual incision in TC-NER.
R-DME-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-DME-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-DME-6803529. FGFR2 alternative splicing.
R-DME-6807505. RNA polymerase II transcribes snRNA genes.
R-DME-72086. mRNA Capping.
R-DME-72163. mRNA Splicing - Major Pathway.
R-DME-72165. mRNA Splicing - Minor Pathway.
R-DME-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-DME-73776. RNA Polymerase II Promoter Escape.
R-DME-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-DME-75953. RNA Polymerase II Transcription Initiation.
R-DME-75955. RNA Polymerase II Transcription Elongation.
R-DME-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-DME-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

GenomeRNAii32100.
PROiP04052.

Gene expression databases

BgeeiFBgn0003277.
GenevisibleiP04052. DM.

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.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 11 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPB1_DROME
AccessioniPrimary (citable) accession number: P04052
Secondary accession number(s): Q9VYX6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: June 1, 2001
Last modified: November 30, 2016
This is version 167 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

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 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

Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. SIMILARITY comments
    Index of protein domains and families

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.