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Protein

DNA-directed RNA polymerase II subunit RPB2

Gene

RpII140

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript 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 polymerase 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. It is composed of mobile elements that move relative to each other. RPB2 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 (By similarity).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi794 – 7941Magnesium; shared with RPB1By similarity
Metal bindingi1121 – 11211ZincBy similarity
Metal bindingi1124 – 11241ZincBy similarity
Metal bindingi1139 – 11391ZincBy similarity
Metal bindingi1142 – 11421ZincBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1121 – 114222C4-typeAdd
BLAST

GO - Molecular functioni

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

GO - Biological processi

  • transcription from RNA polymerase II promoter Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-DME-112382. Formation of RNA Pol II elongation complex.
R-DME-113418. Formation of the Early Elongation Complex.
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-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 RPB2 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 2
Short name:
RNA polymerase II subunit B2
Alternative name(s):
DNA-directed RNA polymerase II 140 kDa polypeptide
Gene namesi
Name:RpII140
ORF Names:CG3180
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 3R

Organism-specific databases

FlyBaseiFBgn0262955. RpII140.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase II, core complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11761176DNA-directed RNA polymerase II subunit RPB2PRO_0000048084Add
BLAST

Proteomic databases

PaxDbiP08266.

Expressioni

Gene expression databases

BgeeiP08266.
GenevisibleiP08266. DM.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi66798. 6 interactions.
DIPiDIP-17498N.
IntActiP08266. 4 interactions.
MINTiMINT-1578011.
STRINGi7227.FBpp0082353.

Structurei

3D structure databases

ProteinModelPortaliP08266.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1121 – 114222C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
GeneTreeiENSGT00760000119346.
InParanoidiP08266.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG7JT6VC.
PhylomeDBiP08266.

Family and domain databases

Gene3Di2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProiIPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007646. RNA_pol_Rpb2_4.
IPR007647. RNA_pol_Rpb2_5.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
[Graphical view]
PANTHERiPTHR20856. PTHR20856. 1 hit.
PfamiPF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF04566. RNA_pol_Rpb2_4. 1 hit.
PF04567. RNA_pol_Rpb2_5. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]
PROSITEiPS01166. RNA_POL_BETA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P08266-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMYDNEEELY EEENAEEISH ELWQEACWIV INAYFDEKGL VRQQLDSFDE
60 70 80 90 100
FIQMSVQRIV EDSPAIELQA EAQHTSGEVE TPPRFSLKFE QIYLSKPTHW
110 120 130 140 150
EKDGSPSPMM PNEARLRNLT YSAPLYVDIT KTKNVEGLDP VETQHQKTFI
160 170 180 190 200
GKIPIMLRST YCLLSQLTDR DLTELNECPL DPGGYFIING SEKVLIAQEK
210 220 230 240 250
MATNTVYVFS MKDGKYAFKT EIRSCLEHSS RPTSTLWVNM MARGSQNIKK
260 270 280 290 300
SAIGQRIIAI LPYIKQEIPI MIVFRALGFV ADRDILEHII YDFDDPEMME
310 320 330 340 350
MVKPSLDEAF VVQEQNVALN FIGARGARPG VTKDKRIKYA KEILQKEMLP
360 370 380 390 400
HVGVSDFCET KKAYFLGYMV HRLLLASLGR RELDDRDHYG NKRLDLAGPL
410 420 430 440 450
LAFLFRGLFK NLMKEVRMYT QKFIDRGKDF NLELAIKTNI ITDGLRYSLA
460 470 480 490 500
TGNWGDQKKA HQARAGVSQV LNRLTFASTL SHLRRVNSPI GRDGKLAKPR
510 520 530 540 550
QLHNTLWGML CPAETPEGAA VGLVKNLALM AYISVGSQPS PILEFLEEWS
560 570 580 590 600
MENLEEIAPS AIADATKIFV NGCWVGIHRD PEQLMATLRK LRRQMDIIVS
610 620 630 640 650
EVSMIRDIRD REIRIYTDAG RICRPLLIVE NGSLLLKKTH VEMLKERDYN
660 670 680 690 700
NYSWQVLVAS GVVEYIDTLE EETVMIAMSP YDLKQDKDYA YCTTYTHCEI
710 720 730 740 750
HPAMILGVCA SIIPFPDHNQ SPRNTYQSAM GKQAMGVYIT NFHVRMDTLA
760 770 780 790 800
HVLYYPMKPL VTTRSMEYLR FRELPAGINS IVAILCYTGY NQEDSVILNA
810 820 830 840 850
SAVERGFFRS VFYRSYKDSE NKRVGDQEEN FEKPHRGTCQ GMRNAHYDKL
860 870 880 890 900
DDDGIIAPGI RVSGDDVVIG KTITLPENDD ELDSNTKRFS KRDASTFLRN
910 920 930 940 950
SETGIVDQVM LTLNSEGYKF CKIRVRSVRI PQIGDKFASR HGQKGTCGIQ
960 970 980 990 1000
YRQEDMAFTC EGLAPDIIIN PHAIPSRMTI GHLIECLQGK LGSNKGEIGD
1010 1020 1030 1040 1050
ATPFNDAVNV QKISTFLQEY GYHLRGNEVM YNGHTGRKIN AQVFLGPTYY
1060 1070 1080 1090 1100
QRLKHMVDDK IHSRARGPVQ ILVRQPMEGR ARDGGLRFGE MERDCQISHG
1110 1120 1130 1140 1150
AAQFLRERLF EVSDPYRVHI CNFCGLIAIA NLRNNTFECK GCKNKTQISQ
1160 1170
VRLPYAAKLL FQELMSMNIA PRLMVT
Length:1,176
Mass (Da):134,043
Last modified:December 1, 2000 - v2
Checksum:i224821B335BED7F0
GO

Sequence cautioni

The sequence CAA29180.2 differs from that shown. Reason: Frameshift at position 43. The frameshift leads to an erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti72 – 721A → R in CAA29180 (PubMed:3116266).Curated
Sequence conflicti666 – 6672ID → MY in CAA29180 (PubMed:3116266).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05709 Genomic DNA. Translation: CAA29180.2. Frameshift.
AE014297 Genomic DNA. Translation: AAF55024.1.
BT003265 mRNA. Translation: AAO25022.1.
M62972 Genomic DNA. Translation: AAA28476.1.
PIRiA27826.
RefSeqiNP_001287323.1. NM_001300394.1.
NP_476706.1. NM_057358.4.
UniGeneiDm.6926.

Genome annotation databases

EnsemblMetazoaiFBtr0082892; FBpp0082353; FBgn0262955.
FBtr0344600; FBpp0310926; FBgn0262955.
GeneIDi41721.
KEGGidme:Dmel_CG3180.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05709 Genomic DNA. Translation: CAA29180.2. Frameshift.
AE014297 Genomic DNA. Translation: AAF55024.1.
BT003265 mRNA. Translation: AAO25022.1.
M62972 Genomic DNA. Translation: AAA28476.1.
PIRiA27826.
RefSeqiNP_001287323.1. NM_001300394.1.
NP_476706.1. NM_057358.4.
UniGeneiDm.6926.

3D structure databases

ProteinModelPortaliP08266.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi66798. 6 interactions.
DIPiDIP-17498N.
IntActiP08266. 4 interactions.
MINTiMINT-1578011.
STRINGi7227.FBpp0082353.

Proteomic databases

PaxDbiP08266.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0082892; FBpp0082353; FBgn0262955.
FBtr0344600; FBpp0310926; FBgn0262955.
GeneIDi41721.
KEGGidme:Dmel_CG3180.

Organism-specific databases

CTDi41721.
FlyBaseiFBgn0262955. RpII140.

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
GeneTreeiENSGT00760000119346.
InParanoidiP08266.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG7JT6VC.
PhylomeDBiP08266.

Enzyme and pathway databases

ReactomeiR-DME-112382. Formation of RNA Pol II elongation complex.
R-DME-113418. Formation of the Early Elongation Complex.
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-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

ChiTaRSiRpII140. fly.
GenomeRNAii41721.
NextBioi825231.
PROiP08266.

Gene expression databases

BgeeiP08266.
GenevisibleiP08266. DM.

Family and domain databases

Gene3Di2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProiIPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007646. RNA_pol_Rpb2_4.
IPR007647. RNA_pol_Rpb2_5.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
[Graphical view]
PANTHERiPTHR20856. PTHR20856. 1 hit.
PfamiPF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF04566. RNA_pol_Rpb2_4. 1 hit.
PF04567. RNA_pol_Rpb2_5. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]
PROSITEiPS01166. RNA_POL_BETA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "RNA polymerase II of Drosophila. Relation of its 140,000 Mr subunit to the beta subunit of Escherichia coli RNA polymerase."
    Falkenburg D., Dworniczak B., Faust D.M., Bautz E.K.F.
    J. Mol. Biol. 195:929-937(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Tissue: Embryo.
  2. "The genome sequence of Drosophila melanogaster."
    Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D.
    , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.
    Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Berkeley.
  3. Cited for: GENOME REANNOTATION.
    Strain: Berkeley.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: Berkeley.
    Tissue: Embryo.
  5. "Analysis of the promoter region of the housekeeping gene DmRP140 by sequence comparison of Drosophila melanogaster and Drosophila virilis."
    Sitzler S., Oldenburg I., Petersen G., Bautz E.K.F.
    Gene 100:155-162(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-69.
    Tissue: Embryo.

Entry informationi

Entry nameiRPB2_DROME
AccessioniPrimary (citable) accession number: P08266
Secondary accession number(s): Q04155, Q95027, Q9VFM7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: December 1, 2000
Last modified: May 11, 2016
This is version 145 of the entry and version 2 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 coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits (By similarity).By similarity

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.