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Protein

DNA-directed RNA polymerase II subunit RPB2

Gene

rpb2

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission 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. 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 bindingi826 – 8261Magnesium; shared with RPB1By similarity
Metal bindingi1152 – 11521ZincBy similarity
Metal bindingi1155 – 11551ZincBy similarity
Metal bindingi1170 – 11701ZincBy similarity
Metal bindingi1173 – 11731ZincBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1152 – 117322C4-typeAdd
BLAST

GO - Molecular functioni

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

GO - Biological processi

  • chromatin silencing by small RNA Source: PomBase
  • transcription from RNA polymerase II promoter Source: PomBase
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-SPO-113418. Formation of the Early Elongation Complex.
R-SPO-674695. RNA Polymerase II Pre-transcription Events.
R-SPO-6781823. Formation of TC-NER Pre-Incision Complex.
R-SPO-6782135. Dual incision in TC-NER.
R-SPO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SPO-72086. mRNA Capping.
R-SPO-72165. mRNA Splicing - Minor Pathway.
R-SPO-73776. RNA Polymerase II Promoter Escape.
R-SPO-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SPO-75953. RNA Polymerase II Transcription Initiation.
R-SPO-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SPO-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 138 kDa polypeptide
Gene namesi
Name:rpb2
ORF Names:SPAC23G3.01, SPAC521.06
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAC23G3.01.
PomBaseiSPAC23G3.01. rpb2.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: PomBase
  • DNA-directed RNA polymerase II, core complex Source: PomBase
  • nuclear chromatin Source: PomBase
  • nuclear pericentric heterochromatin Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12101210DNA-directed RNA polymerase II subunit RPB2PRO_0000048090Add
BLAST

Proteomic databases

MaxQBiQ02061.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi277951. 18 interactions.
IntActiQ02061. 2 interactions.
MINTiMINT-1214536.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65B/N1-1210[»]
ProteinModelPortaliQ02061.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ02061.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1152 – 117322C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000222962.
InParanoidiQ02061.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG7RRFGC.
PhylomeDBiQ02061.

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. 2 hits.
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.

Q02061-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSYEDYQYNE TLTQEDCWTV ISSFFEETSL ARQQLFSFDE FVQNTMQEIV
60 70 80 90 100
DDDSTLTLDQ YAQHTGAQGD VTRRYEINFG QIYLSRPTMT EADGSTTTMF
110 120 130 140 150
PQEARLRNLT YSSPLYVDMR KKVMVAADSN VPIGEEEWLV EEEDEEPSKV
160 170 180 190 200
FIGKIPIMLR STFCILNGVS DSELYDLNEC PYDQGGYFII NGSEKVIIAQ
210 220 230 240 250
ERSAANIVQV FKKAAPSPIA YVAEIRSALE RGSRLISSMQ IKLMARNTEN
260 270 280 290 300
SGQTIRATLP YIRSDIPIVI VFRALGVVPD RDILEHICYD PNDFQMLEMM
310 320 330 340 350
KPCIEEAFVI QDKDIALDYI GKRGSTTGVT REKRLRYAHD ILQKELLPHI
360 370 380 390 400
TTMEGFETRK AFFLGYMIHR MLLCALERRE PDDRDHFGKK RLDLAGPLLA
410 420 430 440 450
SLFRMLFRKM TRDVYKYMQK CVETNREFNL TLAVKSNIIT NGLRYSLATG
460 470 480 490 500
NWGDQKRSMV NRVGVSQVLN RYTFASTLSH LRRTNTPIGR DGKLAKPRQL
510 520 530 540 550
HNTHWGMVCP AETPEGQACG LVKNLSLMSY VSVGSPSAPI IEFLEEWGLE
560 570 580 590 600
TLEDYNPSAS PNATKVFVNG VWLGVHRDPA HLTETLRSLR RRLDISAEVS
610 620 630 640 650
IVRDIREKEL RLFTDAGRIC RPLFIVDNNP NSERRGELCI RKEHIQQLIE
660 670 680 690 700
DKDRYDIDPE QRFGWTALVS SGLIEYLDAE EEETVMIAMS PEDLEASRQM
710 720 730 740 750
QAGYEVKEEL DPAQRVKPAP NPHVHAWTHC EIHPAMILGI LASIIPFPDH
760 770 780 790 800
NQSPRNTYQS AMGKQAMGVY LTNYQVRMDT MANILYYPQK PLATTRSMEY
810 820 830 840 850
LKFRELPAGQ NAIVAILCYS GYNQEDSIIM NQASIDRGLF RSIFYRTYTD
860 870 880 890 900
QEKKIGMTVM EEFERPVRST TLRMKHGTYD KLEDDGLIAP GTRVSGEDII
910 920 930 940 950
IGKTAPIPLD HEELGQRTQL HAKRDVSTPL RSTESGIVDQ VMVTTNQEGL
960 970 980 990 1000
KFVKVRMRST RIPQIGDKFA SRHGQKGTIG MTYRHEDMPF SAQGIVPDII
1010 1020 1030 1040 1050
INPHAIPSRM TVAHLVECQL SKVSALSGFE GDATPFTDVT VEAVSKLLRS
1060 1070 1080 1090 1100
HGFQSRGFEV MYHGHTGRKL VAQVFLGPTY YQRLKHLVDD KIHARARGPV
1110 1120 1130 1140 1150
QILTRQPVEG RSRDGGLRFG EMERDCQISH GCSSVLRERL FDCSDAYRVI
1160 1170 1180 1190 1200
VCDICGLIAI ASYKKDSYEC RSCQNRTRFS QVYLPYAAKL LFQELMSMNI
1210
APRLFTKNHK
Length:1,210
Mass (Da):137,849
Last modified:August 14, 2001 - v2
Checksum:iC5D3794A743494CC
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti727 – 7271W → R in BAA02600 (PubMed:8441660).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13337 Genomic DNA. Translation: BAA02600.1.
CU329670 Genomic DNA. Translation: CAB86470.1.
PIRiS35548.
T50175.
RefSeqiNP_593101.2. NM_001018498.2.

Genome annotation databases

EnsemblFungiiSPAC23G3.01.1; SPAC23G3.01.1:pep; SPAC23G3.01.
GeneIDi2541446.
KEGGispo:SPAC23G3.01.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13337 Genomic DNA. Translation: BAA02600.1.
CU329670 Genomic DNA. Translation: CAB86470.1.
PIRiS35548.
T50175.
RefSeqiNP_593101.2. NM_001018498.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65B/N1-1210[»]
ProteinModelPortaliQ02061.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277951. 18 interactions.
IntActiQ02061. 2 interactions.
MINTiMINT-1214536.

Proteomic databases

MaxQBiQ02061.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC23G3.01.1; SPAC23G3.01.1:pep; SPAC23G3.01.
GeneIDi2541446.
KEGGispo:SPAC23G3.01.

Organism-specific databases

EuPathDBiFungiDB:SPAC23G3.01.
PomBaseiSPAC23G3.01. rpb2.

Phylogenomic databases

HOGENOMiHOG000222962.
InParanoidiQ02061.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG7RRFGC.
PhylomeDBiQ02061.

Enzyme and pathway databases

ReactomeiR-SPO-113418. Formation of the Early Elongation Complex.
R-SPO-674695. RNA Polymerase II Pre-transcription Events.
R-SPO-6781823. Formation of TC-NER Pre-Incision Complex.
R-SPO-6782135. Dual incision in TC-NER.
R-SPO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SPO-72086. mRNA Capping.
R-SPO-72165. mRNA Splicing - Minor Pathway.
R-SPO-73776. RNA Polymerase II Promoter Escape.
R-SPO-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SPO-75953. RNA Polymerase II Transcription Initiation.
R-SPO-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SPO-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

EvolutionaryTraceiQ02061.
PROiQ02061.

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. 2 hits.
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. "Cloning and sequence determination of the Schizosaccharomyces pombe rpb2 gene encoding the subunit 2 of RNA polymerase II."
    Kawagishi M., Yamagishi M., Ishihama A.
    Nucleic Acids Res. 21:469-473(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.

Entry informationi

Entry nameiRPB2_SCHPO
AccessioniPrimary (citable) accession number: Q02061
Secondary accession number(s): Q9P7B1, Q9P7T2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: August 14, 2001
Last modified: June 8, 2016
This is version 135 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. 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.