P08518 · RPB2_YEAST
- ProteinDNA-directed RNA polymerase II subunit RPB2
- GeneRPB2
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1224 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases 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. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single-stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it.
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.
Present with 18700 molecules/cell in log phase SD medium.
Catalytic activity
- a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 837 | Mg2+ (UniProtKB | ChEBI); ligand shared with RPB1 | ||||
Sequence: D | ||||||
Binding site | 1163 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 1166 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 1182 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 1185 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasmic stress granule | |
Cellular Component | mitochondrion | |
Cellular Component | nucleus | |
Cellular Component | RNA polymerase II, core complex | |
Molecular Function | DNA binding | |
Molecular Function | DNA-directed 5'-3' RNA polymerase activity | |
Molecular Function | metal ion binding | |
Molecular Function | mRNA binding | |
Molecular Function | ribonucleoside binding | |
Biological Process | RNA-templated transcription | |
Biological Process | transcription by RNA polymerase II | |
Biological Process | transcription elongation by RNA polymerase II | |
Biological Process | transcription initiation at RNA polymerase II promoter |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA-directed RNA polymerase II subunit RPB2
- EC number
- Short namesRNA polymerase II subunit 2
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageEukaryota > Fungi > Dikarya > Ascomycota > Saccharomycotina > Saccharomycetes > Saccharomycetales > Saccharomycetaceae > Saccharomyces
Accessions
- Primary accessionP08518
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000048091 | 1-1224 | DNA-directed RNA polymerase II subunit RPB2 | |||
Sequence: MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF | ||||||
Modified residue | 919 | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
Proteomic databases
PTM databases
Interaction
Subunit
Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P08518 | NPA3 P47122 | 3 | EBI-15767, EBI-25534 | |
BINARY | P08518 | RPB10 P22139 | 3 | EBI-15767, EBI-15802 | |
BINARY | P08518 | RPB3 P16370 | 6 | EBI-15767, EBI-15773 | |
BINARY | P08518 | RPB5 P20434 | 26 | EBI-15767, EBI-15781 | |
BINARY | P08518 | RPC40 P07703 | 2 | EBI-15767, EBI-15831 | |
BINARY | P08518 | RPO21 P04050 | 5 | EBI-15767, EBI-15760 | |
BINARY | P08518 | RPO26 P20435 | 3 | EBI-15767, EBI-15786 | |
BINARY | P08518 | SPN1 Q06505 | 3 | EBI-15767, EBI-32596 | |
BINARY | P08518 | TFG2 P41896 | 8 | EBI-15767, EBI-18916 |
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Features
Showing features for region, zinc finger.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 467-478 | Fork loop 1 | ||||
Sequence: GEQKKAMSSRAG | ||||||
Zinc finger | 1163-1185 | C4-type | ||||
Sequence: CGICGLMTVIAKLNHNQFECKGC |
Sequence similarities
Belongs to the RNA polymerase beta chain family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,224
- Mass (Da)138,751
- Last updated1997-11-01 v2
- ChecksumBABD03212C0A583E
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 1003-1006 | in Ref. 1; AAA68096 | ||||
Sequence: AEGI → RRRY |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
M15693 EMBL· GenBank· DDBJ | AAA68096.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
U55020 EMBL· GenBank· DDBJ | AAC49637.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
Z75059 EMBL· GenBank· DDBJ | CAA99357.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AF527884 EMBL· GenBank· DDBJ | AAP57849.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BK006948 EMBL· GenBank· DDBJ | DAA10924.1 EMBL· GenBank· DDBJ | Genomic DNA |