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Reviewed, UniProtKB/Swiss-Prot P04052 (RPB1_DROME)

Last modified June 16, 2009. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    DNA-directed RNA polymerase II subunit RPB1
      Short name=RNA polymerase II subunit B1
    EC=2.7.7.6
Alternative name(s):
    DNA-directed RNA polymerase III largest subunit
Gene names
Name: RpII215
ORF Names: CG1554
OrganismDrosophila melanogaster (Fruit fly) [Complete proteome]
Taxonomic identifier7227 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Arthropoda › Hexapoda › Insecta › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Ephydroidea › Drosophilidae › Drosophila › Sophophora

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Protein attributes

Sequence length1887 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

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.

Catalytic activity

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

Subunit structure

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

Subcellular location

Nucleus By similarity.

Post-translational modification

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 heptapepdtide 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.

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 nucelotide 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.

Sequence similarities

Belongs to the RNA polymerase beta' chain family.

Contains 1 C2H2-type zinc finger.

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Binary interactions

With

Entry

#Exp.

IntAct

Notes

RpII15P369581EBI-173525,EBI-167046

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 18871887DNA-directed RNA polymerase II subunit RPB1
PRO_0000073937

Regions

Repeat1579 – 158571
Repeat1586 – 159272; approximate
Repeat1598 – 160473
Repeat1605 – 161174
Repeat1631 – 163775
Repeat1638 – 164476
Repeat1671 – 167777
Repeat1678 – 168478
Repeat1685 – 169179
Repeat1692 – 1698710
Repeat1699 – 1705711
Repeat1706 – 1712712
Repeat1713 – 1719713
Repeat1720 – 1726714
Repeat1727 – 1733715
Repeat1740 – 1746716
Repeat1754 – 1760717
Repeat1761 – 1767718
Repeat1777 – 1783719
Repeat1784 – 1790720
Repeat1791 – 1797721
Repeat1798 – 1804722
Repeat1811 – 1817723
Repeat1818 – 1824724; approximate
Repeat1825 – 1831725
Repeat1832 – 1838726
Repeat1839 – 1845727
Repeat1846 – 1852728
Repeat1853 – 1859729
Repeat1860 – 1866730
Repeat1868 – 1874731
Repeat1875 – 1881732
Zinc finger67 – 8317C2H2-type By similarity
Region825 – 83713Bridging helix
Region1579 – 188130332 X 7 AA approximate tandem repeats of Y-[ST]-P-[STNVAPGN]-[STGMA]-[PSTR]-[SNAGCQKTLRIMH]

Sites

Metal binding671Zinc 1 By similarity
Metal binding701Zinc 1 By similarity
Metal binding771Zinc 1 By similarity
Metal binding801Zinc 1 By similarity
Metal binding1071Zinc 2 By similarity
Metal binding1101Zinc 2 By similarity
Metal binding1501Zinc 2 By similarity
Metal binding1761Zinc 2 By similarity
Metal binding4871Magnesium 1; catalytic By similarity
Metal binding4871Magnesium 2; shared with RPB2 By similarity
Metal binding4891Magnesium 1; catalytic By similarity
Metal binding4891Magnesium 2; shared with RPB2 By similarity
Metal binding4911Magnesium 1; catalytic By similarity

Experimental info

Sequence conflict319 – 3246RAMQKS → GYAKV in AAA28863. Ref.5
Sequence conflict4501F → G in AAA28863. Ref.5
Sequence conflict455 – 4584TLHK → RCTT Ref.5
Sequence conflict463 – 47210GHRVKVLPWS → VTGESVASST Ref.5
Sequence conflict7411R → H in AAA28868. Ref.1
Sequence conflict1485 – 152440SMLGG…PPGHV → I in AAA28827. Ref.7
Sequence conflict1506 – 15083MTP → ELDSA in AAA28868. Ref.1
Sequence conflict18871D → DVRKGGRG in AAA28868. Ref.1

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Sequences

Sequence LengthMass (Da)Tools
P04052-1 [UniParc].

Last modified June 1, 2001. Version 4.
Checksum: 4EC68C7708A167A3

FASTA1,887209,168
        10         20         30         40         50         60 
MSTPTDSKAP LRQVKRVQFG ILSPDEIRRM SVTEGGVQFA ETMEGGRPKL GGLMDPRQGV 

        70         80         90        100        110        120 
IDRTSRCQTC AGNMTECPGH FGHIDLAKPV FHIGFITKTI KILRCVCFYC SKMLVSPHNP 

       130        140        150        160        170        180 
KIKEIVMKSR GQPRKRLAYV YDLCKGKTIC EGGEDMDLTK ENQQPDPNKK PGHGGCGHYQ 

       190        200        210        220        230        240 
PSIRRTGLDL TAEWKHQNED SQEKKIVVSA ERVWEILKHI TDEECFILGM DPKYARPDWM 

       250        260        270        280        290        300 
IVTVLPVPPL AVRPAVVMFG AAKNQDDLTH KLSDIIKANN ELRKNEASGA AAHVIQENIK 

       310        320        330        340        350        360 
MLQFHVATLV DNDMPGMPRA MQKSGKPLKA IKARLKGKEG RIRGNLMGKR VDFSARTVIT 

       370        380        390        400        410        420 
PDPNLRIDQV GVPRSIAQNL TFPELVTPFN IDRMQELVRR GNSQYPGAKY IVRDNGERID 

       430        440        450        460        470        480 
LRFHPKSSDL HLQCGYKVER HLRDDDLVIF NRQPTLHKMS MMGHRVKVLP WSTFRMNLSC 

       490        500        510        520        530        540 
TSPYNADFDG DEMNLHVPQS METRAEVENI HITPRQIITP QANKPVMGIV QDTLTAVRKM 

       550        560        570        580        590        600 
TKRDVFITRE QVMNLLMFLP TWDAKMPQPC ILKPRPLWTG KQIFSLIIPG NVNMIRTHST 

       610        620        630        640        650        660 
HPDEEDEGPY KWISPGDTKV MVEHGELIMG ILCKKSLGTS AGSLLHICFL ELGHDIAGRF 

       670        680        690        700        710        720 
YGNIQTVINN WLLFEGHSIG IGDTIADPQT YNEIQQAIKK AKDDVINVIQ KAHNMELEPT 

       730        740        750        760        770        780 
PGNTLRQTFE NKVNRILNDA RDKTGGSAKK SLTEYNNLKA MVVSGSKGSN INISQVIACV 

       790        800        810        820        830        840 
GQQNVEGKRI PYGFRKRTLP HFIKDDYGPE SRGFVENSYL AGLTPSEFYF HAMGGREGLI 

       850        860        870        880        890        900 
DTAVKTAETG YIQRRLIKAM ESVMVNYDGT VRNSVGQLIQ LRYGEDGLCG ELVEFQNMPT 

       910        920        930        940        950        960 
VKLSNKSFEK RFKFDWSNER LMKKVFTDDV IKEMTDSSEA IQELEAEWDR LVSDRDSLRQ 

       970        980        990       1000       1010       1020 
IFPNGESKVV LPCNLQRMIW NVQKIFHINK RLPTDLSPIR VIKGVKTLLE RCVIVTGNDR 

      1030       1040       1050       1060       1070       1080 
ISKQANENAT LLFQCLIRST LCTKYVSEEF RLSTEAFEWL VGEIETRFQQ AQANPGEMVG 

      1090       1100       1110       1120       1130       1140 
ALAAQSLGEP ATQMTLNTFH FAGVSSKNVT LGVPRLKEII NISKKPKAPS LTVFLTGGAA 

      1150       1160       1170       1180       1190       1200 
RDAEKAKNVL CRLEHTTLRK VTANTAIYYD PDPQRTVISE DQEFVNVYYE MPDFDPTRIS 

      1210       1220       1230       1240       1250       1260 
PWLLRIELDR KRMTDKKLTM EQIAEKINVG FGEDLNCIFN DDNADKLVLR IRIMNNEENK 

      1270       1280       1290       1300       1310       1320 
FQDEDEAVDK MEDDMFLRCI EANMLSDMTL QGIEAIGKVY MHLPQTDSKK RIVITETGEF 

      1330       1340       1350       1360       1370       1380 
KAIGEWLLET DGTSMMKVLS ERDVDPIRTS SNDICEIFQV LGIEAVRKSV EKEMNAVLQF 

      1390       1400       1410       1420       1430       1440 
YGLYVNYRHL ALLCDVMTAK GHLMAITRHG INRQDTGALM RCSFEETVDV LMDAAAHAET 

      1450       1460       1470       1480       1490       1500 
DPMRGVSENI IMGQLPKMGT GCFDLLLDAE KCRFGIEIPN TLGNSMLGGA AMFIGGGSTP 

      1510       1520       1530       1540       1550       1560 
SMTPPMTPWA NCNTPRYFSP PGHVSAMTPG GPSFSPSAAS DASGMSPSWS PAHPGSSPSS 

      1570       1580       1590       1600       1610       1620 
PGPSMSPYFP ASPSVSPSYS PTSPNYTASS PGGASPNYSP SSPNYSPTSP LYASPRYAST 

      1630       1640       1650       1660       1670       1680 
TPNFNPQSTG YSPSSSGYSP TSPVYSPTVQ FQSSPSFAGS GSNIYSPGNA YSPSSSNYSP 

      1690       1700       1710       1720       1730       1740 
NSPSYSPTSP SYSPSSPSYS PTSPCYSPTS PSYSPTSPNY TPVTPSYSPT SPNYSASPQY 

      1750       1760       1770       1780       1790       1800 
SPASPAYSQT GVKYSPTSPT YSPPSPSYDG SPGSPQYTPG SPQYSPASPK YSPTSPLYSP 

      1810       1820       1830       1840       1850       1860 
SSPQHSPSNQ YSPTGSTYSA TSPRYSPNMS IYSPSSTKYS PTSPTYTPTA RNYSPTSPMY 

      1870       1880 
SPTAPSHYSP TSPAYSPSSP TFEESED

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References

« Hide 'large scale' references
[1]"Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila."
Jokerst R.S., Weeks J.R., Zehring W.A., Greenleaf A.L.
Mol. Gen. Genet. 215:266-275(1989) [PubMed: 2496296] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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. expand/collapse author list , 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: 10731132] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Berkeley.
[3]"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review."
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S., Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E., Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P., Bettencourt B.R., Celniker S.E., de Grey A.D.N.J. expand/collapse author list , Drysdale R.A., Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002) [PubMed: 12537572] [Abstract]
Cited for: GENOME REANNOTATION.
[4]"Sites of P element insertion and structures of P element deletions in the 5' region of Drosophila melanogaster RpII215."
Searles L.L., Greenleaf A.L., Kemp W.E., Voelker R.A.
Mol. Cell. Biol. 6:3312-3319(1986) [PubMed: 3025586] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-27.
[5]"Structure of the eukaryotic transcription apparatus: features of the gene for the largest subunit of Drosophila RNA polymerase II."
Biggs J., Searles L.L., Greenleaf A.L.
Cell 42:611-621(1985) [PubMed: 2992806] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-472.
[6]"Mapping of linear epitopes recognized by monoclonal antibodies with gene-fragment phage display libraries."
Petersen G., Song D., Hugle-Dorr B., Oldenburg I., Bautz E.K.
Mol. Gen. Genet. 249:425-431(1995) [PubMed: 8552047] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 778-827.
[7]"The C-terminal domain of the largest subunit of RNA polymerase II of Saccharomyces cerevisiae, Drosophila melanogaster, and mammals: a conserved structure with an essential function."
Allison L.A., Wong J.K.-C., Fitzpatrick V.D., Moyle M., Ingles C.J.
Mol. Cell. Biol. 8:321-329(1988) [PubMed: 3122024] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1441-1887.
+Additional computationally mapped references.

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Cross-references

Sequence databases

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.
PIRRNFF2L. S04457.
RefSeqNP_511124.1.
UniGeneDm.2925

3D structure databases

HSSPHSSP built from PDB template 1K83 based on UniProtKB P04050.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP:22282N.
IntActP04052. 5 interactions.

Genome annotation databases

EnsemblFBgn0003277. Drosophila melanogaster. [Contig view]
GeneID32100.
KEGGdme:Dmel_CG1554.
NMPDRfig|7227.3.peg.17442.

Organism-specific databases

FlyBaseFBgn0003277. RpII215.

Phylogenomic databases

HOGENOMP04052.
OMAP04052. TSPHYSP.

Enzyme and pathway databases

BioCycDMEL-XXX-02:DMEL-XXX-02-001503-MON.
BRENDA2.7.7.6. 48.

Gene expression databases

ArrayExpressP04052.
GermOnlineCG1554. Drosophila melanogaster.

Family and domain databases

InterProIPR000722. 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]
Gene3DG3DSA:2.40.40.30. RNA_pol_A. 1 hit.
G3DSA:3.90.1120.10. RNA_pol_Rpb1_1. 1 hit.
G3DSA:3.30.1360.90. RNA_pol_Rpb1_7. 1 hit.
PfamPF04997. 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. 18 hits.
[Graphical view]
SMARTSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEPS00115. RNA_POL_II_REPEAT. 11 hits.
[Graphical view]
ProtoNetSearch...

Other Resources

NextBio776837.

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Entry information

Entry nameRPB1_DROME
AccessionPrimary (citable) accession number: P04052
Secondary accession number(s): Q9VYX6
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: June 1, 2001
Last modified: June 16, 2009
This is version 102 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectDrosophila annotation project

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Relevant documents

Drosophila

Drosophila: entries, gene names and cross-references to FlyBase

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents