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Protein

DNA-directed RNA polymerase II subunit RPB2

Gene

Polr2b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 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 bindingi792 – 7921Magnesium; shared with RPB1By similarity
Metal bindingi1119 – 11191ZincBy similarity
Metal bindingi1122 – 11221ZincBy similarity
Metal bindingi1137 – 11371ZincBy similarity
Metal bindingi1140 – 11401ZincBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1119 – 114022C4-typeAdd
BLAST

GO - Molecular functioni

  1. chromatin binding Source: MGI
  2. DNA binding Source: InterPro
  3. DNA-directed RNA polymerase activity Source: UniProtKB-KW
  4. metal ion binding Source: UniProtKB-KW
  5. poly(A) RNA binding Source: MGI
  6. ribonucleoside binding Source: InterPro

GO - Biological processi

  1. 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

ReactomeiREACT_271571. mRNA Splicing - Minor Pathway.
REACT_279019. Dual incision reaction in TC-NER.
REACT_280637. Transcriptional regulation by small RNAs.
REACT_282911. RNA Polymerase II Pre-transcription Events.
REACT_283211. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_288316. Transcription-coupled NER (TC-NER).
REACT_292734. PIWI-interacting RNA (piRNA) biogenesis.
REACT_296420. RNA Pol II CTD phosphorylation and interaction with CE.
REACT_302527. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_307866. mRNA Splicing - Major Pathway.
REACT_308057. Formation of the Early Elongation Complex.
REACT_315215. RNA Polymerase II Transcription Elongation.
REACT_326102. Formation of RNA Pol II elongation complex.
REACT_329615. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_338828. mRNA Capping.
REACT_340895. Processing of Capped Intron-Containing Pre-mRNA.
REACT_342690. RNA Polymerase II Transcription Initiation.
REACT_349121. RNA Polymerase II Promoter Escape.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB2 (EC:2.7.7.6)
Alternative name(s):
DNA-directed RNA polymerase II 140 kDa polypeptide
DNA-directed RNA polymerase II subunit B
RNA polymerase II subunit 2
RNA polymerase II subunit B2
Gene namesi
Name:Polr2b
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:2388280. Polr2b.

Subcellular locationi

  1. Nucleus By similarity

GO - Cellular componenti

  1. DNA-directed RNA polymerase II, core complex Source: UniProtKB
  2. membrane Source: MGI
  3. nucleoplasm Source: MGI
  4. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11741174DNA-directed RNA polymerase II subunit RPB2PRO_0000048086Add
BLAST

Proteomic databases

MaxQBiQ8CFI7.
PaxDbiQ8CFI7.
PRIDEiQ8CFI7.

PTM databases

PhosphoSiteiQ8CFI7.

Expressioni

Gene expression databases

BgeeiQ8CFI7.
CleanExiMM_POLR2B.
ExpressionAtlasiQ8CFI7. baseline and differential.
GenevestigatoriQ8CFI7.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. Interacts with WDR82 (By similarity). Interacts with MEN1 (By similarity).By similarity

Protein-protein interaction databases

BioGridi231111. 8 interactions.
DIPiDIP-57023N.
IntActiQ8CFI7. 8 interactions.
MINTiMINT-4133069.

Structurei

3D structure databases

ProteinModelPortaliQ8CFI7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1119 – 114022C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0085.
GeneTreeiENSGT00760000119346.
HOGENOMiHOG000222962.
HOVERGENiHBG017744.
InParanoidiQ8CFI7.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG7JT6VC.
PhylomeDBiQ8CFI7.
TreeFamiTF103037.

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.

Q8CFI7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF
60 70 80 90 100
IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFEQ IYLSKPTHWE
110 120 130 140 150
RDGAPSPMMP NEARLRNLTY SAPLYVDITK TVIKEGEEQL QTQHQKTFIG
160 170 180 190 200
KIPIMLRSTY CLLNGLTDRD LCELNECPLD PGGYFIINGS EKVLIAQEKM
210 220 230 240 250
ATNTVYVFAK KDSKYAYTGE CRSCLENSSR PTSTIWVSML ARGGQGAKKS
260 270 280 290 300
AIGQRIVATL PYIKQEVPII IVFRALGFVS DRDILEHIIY DFEDPEMMEM
310 320 330 340 350
VKPSLDEAFV IQEQNVALNF IGSRGAKPGV TKEKRIKYAK EVLQKEMLPH
360 370 380 390 400
VGVSDFCETK KAYFLGYMVH RLLLAALGRR ELDDRDHYGN KRLDLAGPLL
410 420 430 440 450
AFLFRGMFKN LLKEVRIYAQ KFIDRGKDFN LELAIKTRII SDGLKYSLAT
460 470 480 490 500
GNWGDQKKAH QARAGVSQVL NRLTFASTLS HLRRLNSPIG RDGKLAKPRQ
510 520 530 540 550
LHNTLWGMVC PAETPEGHAV GLVKNLALMA YISVGSQPSP ILEFLEEWSM
560 570 580 590 600
ENLEEISPAA IADATKIFVN GCWVGIHKDP EQLMNTLRKL RRQMDIIVSE
610 620 630 640 650
VSMIRDIRER EIRIYTDAGR ICRPLLIVEK QKLLLKKRHI DQLKEREYNN
660 670 680 690 700
YSWQDLVASG VVEYIDTLEE ETVMLAMTPD DLQEKEVAYC STYTHCEIHP
710 720 730 740 750
SMILGVCASI IPFPDHNQSP RNTYQSAMGK QAMGVYITNF HVRMDTLAHV
760 770 780 790 800
LYYPQKPLVT TRSMEYLRFR ELPAGINSIV AIASYTGYNQ EDSVIMNRSA
810 820 830 840 850
VDRGFFRSVF YRSYKEQESK KGFDQEEVFE KPTRETCQGM RHAIYEKLDD
860 870 880 890 900
DGLIAPGVRV SGDDVIIGKT VTLPENEDEL ESTNRRYTKR DCSTFLRTSE
910 920 930 940 950
TGIVDQVMVT LNQEGYKFCK IRVRSVRIPQ IGDKFASRHG QKGTCGIQYR
960 970 980 990 1000
QEDMPFTCEG ITPDIIINPH AIPSRMTIGH LIECLQGKVS ANKGEIGDAT
1010 1020 1030 1040 1050
PFNDAVNVQK ISNLLSDYGY HLRGNEVLYN GFTGRKITSQ IFIGPTYYQR
1060 1070 1080 1090 1100
LKHMVDDKIH SRARGPIQIL NRQPMEGRSR DGGLRFGEME RDCQIAHGAA
1110 1120 1130 1140 1150
QFLRERLFEA SDPYQVHVCN LCGIMAIANT RTHTYECRGC RNKTQISLVR
1160 1170
MPYACKLLFQ ELMSMSIAPR MMSV
Length:1,174
Mass (Da):133,911
Last modified:August 31, 2004 - v2
Checksum:iF941FA6EC03E2160
GO

Sequence cautioni

The sequence AAH38472.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC038472 mRNA. Translation: AAH38472.1. Different initiation.
CCDSiCCDS51528.1.
RefSeqiNP_722493.2. NM_153798.2.
UniGeneiMm.273217.

Genome annotation databases

EnsembliENSMUST00000031167; ENSMUSP00000031167; ENSMUSG00000029250.
GeneIDi231329.
KEGGimmu:231329.
UCSCiuc008xwe.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC038472 mRNA. Translation: AAH38472.1. Different initiation.
CCDSiCCDS51528.1.
RefSeqiNP_722493.2. NM_153798.2.
UniGeneiMm.273217.

3D structure databases

ProteinModelPortaliQ8CFI7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi231111. 8 interactions.
DIPiDIP-57023N.
IntActiQ8CFI7. 8 interactions.
MINTiMINT-4133069.

PTM databases

PhosphoSiteiQ8CFI7.

Proteomic databases

MaxQBiQ8CFI7.
PaxDbiQ8CFI7.
PRIDEiQ8CFI7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000031167; ENSMUSP00000031167; ENSMUSG00000029250.
GeneIDi231329.
KEGGimmu:231329.
UCSCiuc008xwe.2. mouse.

Organism-specific databases

CTDi5431.
MGIiMGI:2388280. Polr2b.

Phylogenomic databases

eggNOGiCOG0085.
GeneTreeiENSGT00760000119346.
HOGENOMiHOG000222962.
HOVERGENiHBG017744.
InParanoidiQ8CFI7.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG7JT6VC.
PhylomeDBiQ8CFI7.
TreeFamiTF103037.

Enzyme and pathway databases

ReactomeiREACT_271571. mRNA Splicing - Minor Pathway.
REACT_279019. Dual incision reaction in TC-NER.
REACT_280637. Transcriptional regulation by small RNAs.
REACT_282911. RNA Polymerase II Pre-transcription Events.
REACT_283211. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
REACT_288316. Transcription-coupled NER (TC-NER).
REACT_292734. PIWI-interacting RNA (piRNA) biogenesis.
REACT_296420. RNA Pol II CTD phosphorylation and interaction with CE.
REACT_302527. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_307866. mRNA Splicing - Major Pathway.
REACT_308057. Formation of the Early Elongation Complex.
REACT_315215. RNA Polymerase II Transcription Elongation.
REACT_326102. Formation of RNA Pol II elongation complex.
REACT_329615. RNA Polymerase II Transcription Initiation And Promoter Clearance.
REACT_338828. mRNA Capping.
REACT_340895. Processing of Capped Intron-Containing Pre-mRNA.
REACT_342690. RNA Polymerase II Transcription Initiation.
REACT_349121. RNA Polymerase II Promoter Escape.

Miscellaneous databases

ChiTaRSiPolr2b. mouse.
NextBioi380519.
PROiQ8CFI7.
SOURCEiSearch...

Gene expression databases

BgeeiQ8CFI7.
CleanExiMM_POLR2B.
ExpressionAtlasiQ8CFI7. baseline and differential.
GenevestigatoriQ8CFI7.

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

  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Mammary tumor.

Entry informationi

Entry nameiRPB2_MOUSE
AccessioniPrimary (citable) accession number: Q8CFI7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 31, 2004
Last modified: April 1, 2015
This is version 102 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata 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

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.