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Protein

DNA-directed RNA polymerase II subunit RPB2

Gene

rpb-2

Organism
Caenorhabditis elegans
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)DescriptionActionsGraphical viewLength
Metal bindingi798Magnesium; shared with RPB1By similarity1
Metal bindingi1125ZincBy similarity1
Metal bindingi1128ZincBy similarity1
Metal bindingi1143ZincBy similarity1
Metal bindingi1146ZincBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1125 – 1146C4-typeAdd BLAST22

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-CEL-112387. Elongation arrest and recovery.
R-CEL-113418. Formation of the Early Elongation Complex.
R-CEL-5578749. Transcriptional regulation by small RNAs.
R-CEL-674695. RNA Polymerase II Pre-transcription Events.
R-CEL-6781823. Formation of TC-NER Pre-Incision Complex.
R-CEL-6782135. Dual incision in TC-NER.
R-CEL-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-CEL-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-CEL-6803529. FGFR2 alternative splicing.
R-CEL-6807505. RNA polymerase II transcribes snRNA genes.
R-CEL-72086. mRNA Capping.
R-CEL-72163. mRNA Splicing - Major Pathway.
R-CEL-72165. mRNA Splicing - Minor Pathway.
R-CEL-73776. RNA Polymerase II Promoter Escape.
R-CEL-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-CEL-75953. RNA Polymerase II Transcription Initiation.
R-CEL-75955. RNA Polymerase II Transcription Elongation.
R-CEL-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-CEL-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
Gene namesi
Name:rpb-2
ORF Names:C26E6.4
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome III

Organism-specific databases

WormBaseiC26E6.4; CE01162; WBGene00016140; rpb-2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000480831 – 1193DNA-directed RNA polymerase II subunit RPB2Add BLAST1193

Proteomic databases

EPDiQ10578.
PaxDbiQ10578.
PeptideAtlasiQ10578.
PRIDEiQ10578.

PTM databases

iPTMnetiQ10578.

Expressioni

Gene expression databases

BgeeiWBGene00016140.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi40901. 4 interactors.
STRINGi6239.C26E6.4.2.

Structurei

3D structure databases

ProteinModelPortaliQ10578.
SMRiQ10578.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1125 – 1146C4-typeAdd BLAST22

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
GeneTreeiENSGT00860000133929.
HOGENOMiHOG000222962.
InParanoidiQ10578.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG091G00RQ.
PhylomeDBiQ10578.

Family and domain databases

CDDicd00653. RNA_pol_B_RPB2. 1 hit.
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.

Q10578-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYDDEDEMVN DPMDGDYIDD SDEISAEAWQ EACWVVISAY FDEKGLVRQQ
60 70 80 90 100
LDSFDEFVQM NVQRIVEDSP PVELQSENQH LGTDMENPAK FSLKFNQIYL
110 120 130 140 150
SKPTHWEKDG APMPMMPNEA RLRNLTYASP LYVDITKVVT RDDSATEKVY
160 170 180 190 200
DKVFVGKVPV MLRSSYCMLS NMTDRDLTEL NECPLDPGGY FVINGSEKVL
210 220 230 240 250
IAQEKMATNT VYVFSMKDGK YAFKTECRSC LENSSRPTST MWVNMLARGG
260 270 280 290 300
GGGKKTAMGQ RIIGILPYIK QEIPIMIVFR ALGFVSDRDI LGHIIYDFND
310 320 330 340 350
PEMMEMVKPS LDEAFVIQEQ NVALNFIGAR GAKPGVTREQ RIKYAREILQ
360 370 380 390 400
KELLPHVGVS EHCETKKAFF IGYMVHRLLL AALGRRELDD RDHIGNKRLD
410 420 430 440 450
LAGPLLAFLF RSLFRNLLKE MRMTAQKYIN KNDDFALDVC VKTSTITRGL
460 470 480 490 500
TYSLATGNWG DQKKAHQSRA GVSQVLNRLT YTATLSHLRR ANSPIGREGK
510 520 530 540 550
LAKPRQLHNT QWGMVCPAET PEGQAVGLVK NLALMAYISV GSLPEPILEF
560 570 580 590 600
LEEWSMENLE EVSPSAIADA TKIFVNGAWV GIHREPDQLM TTLKKLRRQM
610 620 630 640 650
DIIVSEVSMV RDIRDREIRI YTDAGRVCRP LLIVENQKLA LKKRHIDQLK
660 670 680 690 700
EAADEANKYT WSDLVGGGVV ELIDSMEEET SMIAMMPEDL RSGGYCDTHT
710 720 730 740 750
HCEIHPAMIL GVCASIIPFP DHNQSPRNTY QSAMGKQAMG VYTTNFHVRM
760 770 780 790 800
DTLAHVLYYP QKPLVTTRSM EYLRFNELPA GINAIVAILS YSGYNQEDSV
810 820 830 840 850
IMNNSAIDRG LFRSVFYRSY RDNEANLDNA NEELIEKPTR EKCSGMRHSL
860 870 880 890 900
YDKLDEDGII SPGMRVSGDD VIIGKTVALP DIDDDLDASG KKYPKRDAST
910 920 930 940 950
FLRSSETGIV DQVMLSLNSD GNKFVKIRMR SVRLPQIGDK FASRHGQKGT
960 970 980 990 1000
MGIMYRQEDM PFTAEGLTPD IIINPHAVPS RMTIGHLIEC LQGKLSANKG
1010 1020 1030 1040 1050
EIGDATPFND TVNVQKISGL LCEYGYHLRG NEVMYNGHTG KKLTTQIFFG
1060 1070 1080 1090 1100
PTYYQRLKHM VDDKIHSRAR GPIQMMNRQP MEGRARDGGL RFGEMERDCQ
1110 1120 1130 1140 1150
ISHGATQFLR ERLFEVSDPY HVYVCNNCGL IVVANLRTNS FECKACRNKT
1160 1170 1180 1190
QVSAVRIPYA CKLLFQELMS MSIAPRLMVK PRQSKRSKHQ SEA
Length:1,193
Mass (Da):134,905
Last modified:November 1, 1997 - v2
Checksum:iB8A85E74E9CC7EBE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO080680 Genomic DNA. Translation: CCD65728.1.
U10333 mRNA. Translation: AAA50224.1.
PIRiE88445.
T43701.
RefSeqiNP_498047.1. NM_065646.4.
UniGeneiCel.7716.

Genome annotation databases

EnsemblMetazoaiC26E6.4; C26E6.4; WBGene00016140.
GeneIDi175668.
KEGGicel:CELE_C26E6.4.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO080680 Genomic DNA. Translation: CCD65728.1.
U10333 mRNA. Translation: AAA50224.1.
PIRiE88445.
T43701.
RefSeqiNP_498047.1. NM_065646.4.
UniGeneiCel.7716.

3D structure databases

ProteinModelPortaliQ10578.
SMRiQ10578.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi40901. 4 interactors.
STRINGi6239.C26E6.4.2.

PTM databases

iPTMnetiQ10578.

Proteomic databases

EPDiQ10578.
PaxDbiQ10578.
PeptideAtlasiQ10578.
PRIDEiQ10578.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiC26E6.4; C26E6.4; WBGene00016140.
GeneIDi175668.
KEGGicel:CELE_C26E6.4.

Organism-specific databases

CTDi175668.
WormBaseiC26E6.4; CE01162; WBGene00016140; rpb-2.

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
GeneTreeiENSGT00860000133929.
HOGENOMiHOG000222962.
InParanoidiQ10578.
KOiK03010.
OMAiRTQPHFE.
OrthoDBiEOG091G00RQ.
PhylomeDBiQ10578.

Enzyme and pathway databases

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

Miscellaneous databases

PROiQ10578.

Gene expression databases

BgeeiWBGene00016140.

Family and domain databases

CDDicd00653. RNA_pol_B_RPB2. 1 hit.
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...

Entry informationi

Entry nameiRPB2_CAEEL
AccessioniPrimary (citable) accession number: Q10578
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: November 30, 2016
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis 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. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  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.