P30876 · RPB2_HUMAN
- ProteinDNA-directed RNA polymerase II subunit RPB2
- GenePOLR2B
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids1174 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Catalytic core component of RNA polymerase II (Pol II), a DNA-dependent RNA polymerase which synthesizes mRNA precursors and many functional non-coding RNAs using the four ribonucleoside triphosphates as substrates (By similarity) (PubMed:27193682, PubMed:30190596, PubMed:9852112).
Pol II-mediated transcription cycle proceeds through transcription initiation, transcription elongation and transcription termination stages. During transcription initiation, Pol II pre-initiation complex (PIC) is recruited to DNA promoters, with focused-type promoters containing either the initiator (Inr) element, or the TATA-box found in cell-type specific genes and dispersed-type promoters that often contain hypomethylated CpG islands usually found in housekeeping genes. Once the polymerase has escaped from the promoter it enters the elongation phase during which RNA is actively polymerized, based on complementarity with the template DNA strand. Transcription termination involves the release of the RNA transcript and polymerase from the DNA (PubMed:27193682, PubMed:30190596, PubMed:9852112).
Forms Pol II active center together with the largest subunit POLR2A/RPB1. Appends one nucleotide at a time to the 3' end of the nascent RNA, with POLR2A/RPB1 most likely contributing a Mg2+-coordinating DxDGD motif and POLR2B/RPB2 participating in the coordination of a second Mg2+ ion and providing lysine residues believed to facilitate Watson-Crick base pairing between the incoming nucleotide and template base. Typically, Mg2+ ions direct a 5' nucleoside triphosphate to form a phosphodiester bond with the 3' hydroxyl of the preceding nucleotide of the nascent RNA, with the elimination of pyrophosphate. The reversible pyrophosphorolysis can occur at high pyrophosphate concentrations (By similarity) (PubMed:30190596, PubMed:9852112).
Can proofread the nascent RNA transcript by means of a 3' -> 5' exonuclease activity. If a ribonucleotide is mis-incorporated, backtracks along the template DNA and cleaves the phosphodiester bond releasing the mis-incorporated 5'-ribonucleotide (By similarity) (PubMed:8381534).
Pol II-mediated transcription cycle proceeds through transcription initiation, transcription elongation and transcription termination stages. During transcription initiation, Pol II pre-initiation complex (PIC) is recruited to DNA promoters, with focused-type promoters containing either the initiator (Inr) element, or the TATA-box found in cell-type specific genes and dispersed-type promoters that often contain hypomethylated CpG islands usually found in housekeeping genes. Once the polymerase has escaped from the promoter it enters the elongation phase during which RNA is actively polymerized, based on complementarity with the template DNA strand. Transcription termination involves the release of the RNA transcript and polymerase from the DNA (PubMed:27193682, PubMed:30190596, PubMed:9852112).
Forms Pol II active center together with the largest subunit POLR2A/RPB1. Appends one nucleotide at a time to the 3' end of the nascent RNA, with POLR2A/RPB1 most likely contributing a Mg2+-coordinating DxDGD motif and POLR2B/RPB2 participating in the coordination of a second Mg2+ ion and providing lysine residues believed to facilitate Watson-Crick base pairing between the incoming nucleotide and template base. Typically, Mg2+ ions direct a 5' nucleoside triphosphate to form a phosphodiester bond with the 3' hydroxyl of the preceding nucleotide of the nascent RNA, with the elimination of pyrophosphate. The reversible pyrophosphorolysis can occur at high pyrophosphate concentrations (By similarity) (PubMed:30190596, PubMed:9852112).
Can proofread the nascent RNA transcript by means of a 3' -> 5' exonuclease activity. If a ribonucleotide is mis-incorporated, backtracks along the template DNA and cleaves the phosphodiester bond releasing the mis-incorporated 5'-ribonucleotide (By similarity) (PubMed:8381534).
RNA-dependent RNA polymerase that catalyzes the extension of a non-coding RNA (ncRNA) at the 3'-end using the four ribonucleoside triphosphates as substrates. An internal ncRNA sequence near the 3'-end serves as a template in a single-round Pol II-mediated RNA polymerization reaction. May decrease the stability of ncRNAs that repress Pol II-mediated gene transcription.
Catalytic activity
- a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)This reaction proceeds in the forward and the backward directions.
- a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)This reaction proceeds in the forward direction.
- a 3'-end ribonucleotidyl-ribonucleotide-RNA + H2O = a 3'-end ribonucleotide-RNA + a ribonucleoside 5'-phosphate + H+This reaction proceeds in the forward direction.
Cofactor
Note: Two Mg2+ ions are coordinated by both the catalytic residues and the nucleic acid substrate to enhance substrate recognition and catalytic efficiency.
Activity regulation
Pol II enzymatic activities are inhibited by alpha-amanitin. 3'->5' exonuclease activity is stimulated by TFIIS, whereas pyrophosphorolysis is enhanced by TFIIF.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 409 | DNA promoter (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 456 | DNA template strand (UniProtKB | ChEBI) | ||||
Sequence: Q | ||||||
Binding site | 731 | RNA (UniProtKB | ChEBI) | ||||
Sequence: Q | ||||||
Binding site | 792 | Mg2+ (UniProtKB | ChEBI); ligand shared with POLR2A/RPB1 | ||||
Sequence: D | ||||||
Binding site | 841 | RNA (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 890 | RNA (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 942 | RNA (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 1078 | DNA template strand (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 1085 | DNA template strand (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 1119 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 1122 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 1137 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 1140 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | membrane | |
Cellular Component | nucleoplasm | |
Cellular Component | nucleus | |
Cellular Component | RNA polymerase II, core complex | |
Molecular Function | chromatin binding | |
Molecular Function | DNA binding | |
Molecular Function | DNA-directed 5'-3' RNA polymerase activity | |
Molecular Function | hydrolase activity | |
Molecular Function | metal ion binding | |
Molecular Function | ribonucleoside binding | |
Molecular Function | RNA binding | |
Molecular Function | RNA-dependent RNA polymerase activity | |
Biological Process | transcription by RNA polymerase II |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA-directed RNA polymerase II subunit RPB2
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionP30876
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Disease & Variants
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 812 variants from UniProt as well as other sources including ClinVar and dbSNP.
Organism-specific databases
Miscellaneous
Genetic variation databases
PTM/Processing
Features
Showing features for chain, modified residue (large scale data), modified residue.
Type | ID | Position(s) | Source | Description | |||
---|---|---|---|---|---|---|---|
Chain | PRO_0000048085 | 1-1174 | UniProt | DNA-directed RNA polymerase II subunit RPB2 | |||
Sequence: MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV | |||||||
Modified residue (large scale data) | 75 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 106 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 487 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue | 937 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue | 1052 | UniProt | N6-methyllysine | ||||
Sequence: K |
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Interaction
Subunit
Component of the RNA polymerase II (Pol II) core complex consisting of 12 subunits: a ten-subunit catalytic core composed of POLR2A/RPB1, POLR2B/RPB2, POLR2C/RPB3, POLR2I/RPB9, POLR2J/RPB11, POLR2E/RPABC1, POLR2F/RPABC2, POLR2H/RPABC3, POLR2K/RPABC4 and POLR2L/RPABC5 and a mobile stalk composed of two subunits POLR2D/RPB4 and POLR2G/RPB7, protruding from the core and functioning primarily in transcription initiation. Part of Pol II(G) complex, in which Pol II core associates with an additional subunit POLR2M; unlike conventional Pol II, Pol II(G) functions as a transcriptional repressor. Part of TBP-based Pol II pre-initiation complex (PIC), in which Pol II core assembles with general transcription factors and other specific initiation factors including GTF2E1, GTF2E2, GTF2F1, GTF2F2, TCEA1, ERCC2, ERCC3, GTF2H2, GTF2H3, GTF2H4, GTF2H5, GTF2A1, GTF2A2, GTF2B and TBP; this large multi-subunit PIC complex mediates DNA unwinding and targets Pol II core to the transcription start site where the first phosphodiester bond forms (PubMed:27193682, PubMed:30190596, PubMed:9852112).
Interacts with WDR82 (PubMed:14992727, PubMed:17998332).
Interacts with MEN1 (PubMed:14992727).
Interacts with WDR82 (PubMed:14992727, PubMed:17998332).
Interacts with MEN1 (PubMed:14992727).
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Features
Showing features for zinc finger.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Zinc finger | 1119-1140 | C4-type | ||||
Sequence: CNLCGIMAIANTRTHTYECRGC |
Sequence similarities
Belongs to the RNA polymerase beta chain family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,174
- Mass (Da)133,897
- Last updated1993-07-01 v1
- Checksum32BEDF7F95E4DE10
Computationally mapped potential isoform sequences
There are 4 potential isoforms mapped to this entry
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
X63563 EMBL· GenBank· DDBJ | CAA45124.1 EMBL· GenBank· DDBJ | mRNA | ||
AK289823 EMBL· GenBank· DDBJ | BAF82512.1 EMBL· GenBank· DDBJ | mRNA | ||
CH471057 EMBL· GenBank· DDBJ | EAX05519.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BC023503 EMBL· GenBank· DDBJ | AAH23503.2 EMBL· GenBank· DDBJ | mRNA | ||
AF055028 EMBL· GenBank· DDBJ | AAC09367.1 EMBL· GenBank· DDBJ | mRNA |