P04052 · RPB1_DROME
- ProteinDNA-directed RNA polymerase II subunit RPB1
- GenePolr2A
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1887 (go to sequence)
- Protein existenceInferred from homology
- Annotation score5/5
Function
function
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second 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. RPB1 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. At the start of transcription, a single-stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing (By similarity).
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 temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.
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 | 67 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 70 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 77 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 80 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 107 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 110 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 150 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 176 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 487 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 487 | Mg2+ 2 (UniProtKB | ChEBI); ligand shared with RPB2 | ||||
Sequence: D | ||||||
Binding site | 489 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 489 | Mg2+ 2 (UniProtKB | ChEBI); ligand shared with RPB2 | ||||
Sequence: D | ||||||
Binding site | 491 | Mg2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | nucleus | |
Cellular Component | polytene chromosome | |
Cellular Component | polytene chromosome puff | |
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 | |
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 RPB1
- EC number
- Short namesRNA polymerase II subunit B1
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Metazoa > Ecdysozoa > Arthropoda > Hexapoda > Insecta > Pterygota > Neoptera > Endopterygota > Diptera > Brachycera > Muscomorpha > Ephydroidea > Drosophilidae > Drosophila > Sophophora
Accessions
- Primary accessionP04052
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
PTM/Processing
Features
Showing features for chain, cross-link.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000073937 | 1-1887 | DNA-directed RNA polymerase II subunit RPB1 | |||
Sequence: MSTPTDSKAPLRQVKRVQFGILSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIVMKSRGQPRKRLAYVYDLCKGKTICEGGEDMDLTKENQQPDPNKKPGHGGCGHYQPSIRRTGLDLTAEWKHQNEDSQEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIVRDNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWDAKMPQPCILKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDEGPYKWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRYGEDGLCGELVEFQNMPTVKLSNKSFEKRFKFDWSNERLMKKVFTDDVIKEMTDSSEAIQELEAEWDRLVSDRDSLRQIFPNGESKVVLPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDEDEAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGCFDLLLDAEKCRFGIEIPNTLGNSMLGGAAMFIGGGSTPSMTPPMTPWANCNTPRYFSPPGHVSAMTPGGPSFSPSAASDASGMSPSWSPAHPGSSPSSPGPSMSPYFPASPSVSPSYSPTSPNYTASSPGGASPNYSPSSPNYSPTSPLYASPRYASTTPNFNPQSTGYSPSSSGYSPTSPVYSPTVQFQSSPSFAGSGSNIYSPGNAYSPSSSNYSPNSPSYSPTSPSYSPSSPSYSPTSPCYSPTSPSYSPTSPNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVKYSPTSPTYSPPSPSYDGSPGSPQYTPGSPQYSPASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTAPSHYSPTSPAYSPSSPTFEESED | ||||||
Cross-link | 1260 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) | ||||
Sequence: K |
Post-translational modification
The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatase, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed.
Following transcription stress, the elongating form of RNA polymerase II (RNA pol IIo) is polyubiquitinated via 'Lys-63'-linkages on Lys-1260 at DNA damage sites without leading to degradation: ubiquitination promotes RNA pol IIo backtracking to allow access by the transcription-coupled nucleotide excision repair (TC-NER) machinery. Subsequent DEF1-dependent polyubiquitination by the elongin complex via 'Lys-48'-linkages may lead to proteasome-mediated degradation; presumably at stalled RNA pol II where TC-NER has failed, to halt global transcription and enable 'last resort' DNA repair pathways.
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Gene expression databases
Interaction
Subunit
Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for region, compositional bias, repeat.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 156-178 | Disordered | ||||
Sequence: MDLTKENQQPDPNKKPGHGGCGH | ||||||
Region | 825-837 | Bridging helix | ||||
Sequence: PSEFYFHAMGGRE | ||||||
Region | 1528-1565 | Disordered | ||||
Sequence: TPGGPSFSPSAASDASGMSPSWSPAHPGSSPSSPGPSM | ||||||
Compositional bias | 1530-1553 | Polar residues | ||||
Sequence: GGPSFSPSAASDASGMSPSWSPAH | ||||||
Repeat | 1579-1585 | 1 | ||||
Sequence: YSPTSPN | ||||||
Compositional bias | 1579-1758 | Polar residues | ||||
Sequence: YSPTSPNYTASSPGGASPNYSPSSPNYSPTSPLYASPRYASTTPNFNPQSTGYSPSSSGYSPTSPVYSPTVQFQSSPSFAGSGSNIYSPGNAYSPSSSNYSPNSPSYSPTSPSYSPSSPSYSPTSPCYSPTSPSYSPTSPNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVKYSPTS | ||||||
Region | 1579-1881 | C-terminal domain (CTD); 32 X 7 AA approximate tandem repeats of Y-[ST]-P-[STNVAPGN]-[STGMA]-[PSTR]-[SNAGCQKTLRIMH] | ||||
Sequence: YSPTSPNYTASSPGGASPNYSPSSPNYSPTSPLYASPRYASTTPNFNPQSTGYSPSSSGYSPTSPVYSPTVQFQSSPSFAGSGSNIYSPGNAYSPSSSNYSPNSPSYSPTSPSYSPSSPSYSPTSPCYSPTSPSYSPTSPNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVKYSPTSPTYSPPSPSYDGSPGSPQYTPGSPQYSPASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTAPSHYSPTSPAYSPSSPT | ||||||
Region | 1579-1887 | Disordered | ||||
Sequence: YSPTSPNYTASSPGGASPNYSPSSPNYSPTSPLYASPRYASTTPNFNPQSTGYSPSSSGYSPTSPVYSPTVQFQSSPSFAGSGSNIYSPGNAYSPSSSNYSPNSPSYSPTSPSYSPSSPSYSPTSPCYSPTSPSYSPTSPNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVKYSPTSPTYSPPSPSYDGSPGSPQYTPGSPQYSPASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTAPSHYSPTSPAYSPSSPTFEESED | ||||||
Repeat | 1586-1592 | 2; approximate | ||||
Sequence: YTASSPG | ||||||
Repeat | 1598-1604 | 3 | ||||
Sequence: YSPSSPN | ||||||
Repeat | 1605-1611 | 4 | ||||
Sequence: YSPTSPL | ||||||
Repeat | 1631-1637 | 5 | ||||
Sequence: YSPSSSG | ||||||
Repeat | 1638-1644 | 6 | ||||
Sequence: YSPTSPV | ||||||
Repeat | 1671-1677 | 7 | ||||
Sequence: YSPSSSN | ||||||
Repeat | 1678-1684 | 8 | ||||
Sequence: YSPNSPS | ||||||
Repeat | 1685-1691 | 9 | ||||
Sequence: YSPTSPS | ||||||
Repeat | 1692-1698 | 10 | ||||
Sequence: YSPSSPS | ||||||
Repeat | 1699-1705 | 11 | ||||
Sequence: YSPTSPC | ||||||
Repeat | 1706-1712 | 12 | ||||
Sequence: YSPTSPS | ||||||
Repeat | 1713-1719 | 13 | ||||
Sequence: YSPTSPN | ||||||
Repeat | 1720-1726 | 14 | ||||
Sequence: YTPVTPS | ||||||
Repeat | 1727-1733 | 15 | ||||
Sequence: YSPTSPN | ||||||
Repeat | 1740-1746 | 16 | ||||
Sequence: YSPASPA | ||||||
Repeat | 1754-1760 | 17 | ||||
Sequence: YSPTSPT | ||||||
Repeat | 1761-1767 | 18 | ||||
Sequence: YSPPSPS | ||||||
Compositional bias | 1771-1887 | Polar residues | ||||
Sequence: SPGSPQYTPGSPQYSPASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTAPSHYSPTSPAYSPSSPTFEESED | ||||||
Repeat | 1777-1783 | 19 | ||||
Sequence: YTPGSPQ | ||||||
Repeat | 1784-1790 | 20 | ||||
Sequence: YSPASPK | ||||||
Repeat | 1791-1797 | 21 | ||||
Sequence: YSPTSPL | ||||||
Repeat | 1798-1804 | 22 | ||||
Sequence: YSPSSPQ | ||||||
Repeat | 1811-1817 | 23 | ||||
Sequence: YSPTGST | ||||||
Repeat | 1818-1824 | 24; approximate | ||||
Sequence: YSATSPR | ||||||
Repeat | 1825-1831 | 25 | ||||
Sequence: YSPNMSI | ||||||
Repeat | 1832-1838 | 26 | ||||
Sequence: YSPSSTK | ||||||
Repeat | 1839-1845 | 27 | ||||
Sequence: YSPTSPT | ||||||
Repeat | 1846-1852 | 28 | ||||
Sequence: YTPTARN | ||||||
Repeat | 1853-1859 | 29 | ||||
Sequence: YSPTSPM | ||||||
Repeat | 1860-1866 | 30 | ||||
Sequence: YSPTAPS | ||||||
Repeat | 1868-1874 | 31 | ||||
Sequence: YSPTSPA | ||||||
Repeat | 1875-1881 | 32 | ||||
Sequence: YSPSSPT |
Domain
The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.
Sequence similarities
Belongs to the RNA polymerase beta' chain family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,887
- Mass (Da)209,168
- Last updated2001-06-01 v4
- Checksum4EC68C7708A167A3
Features
Showing features for sequence conflict, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 319-324 | in Ref. 5; AAA28863 | ||||
Sequence: RAMQKS → GYAKV | ||||||
Sequence conflict | 450 | in Ref. 5; AAA28863 | ||||
Sequence: F → G | ||||||
Sequence conflict | 455-458 | in Ref. 5 | ||||
Sequence: TLHK → RCTT | ||||||
Sequence conflict | 463-472 | in Ref. 5 | ||||
Sequence: GHRVKVLPWS → VTGESVASST | ||||||
Sequence conflict | 741 | in Ref. 1; AAA28868 | ||||
Sequence: R → H | ||||||
Sequence conflict | 1485-1524 | in Ref. 7; AAA28827 | ||||
Sequence: SMLGGAAMFIGGGSTPSMTPPMTPWANCNTPRYFSPPGHV → I | ||||||
Sequence conflict | 1506-1508 | in Ref. 1; AAA28868 | ||||
Sequence: MTP → ELDSA | ||||||
Compositional bias | 1530-1553 | Polar residues | ||||
Sequence: GGPSFSPSAASDASGMSPSWSPAH | ||||||
Compositional bias | 1579-1758 | Polar residues | ||||
Sequence: YSPTSPNYTASSPGGASPNYSPSSPNYSPTSPLYASPRYASTTPNFNPQSTGYSPSSSGYSPTSPVYSPTVQFQSSPSFAGSGSNIYSPGNAYSPSSSNYSPNSPSYSPTSPSYSPSSPSYSPTSPCYSPTSPSYSPTSPNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVKYSPTS | ||||||
Compositional bias | 1771-1887 | Polar residues | ||||
Sequence: SPGSPQYTPGSPQYSPASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTAPSHYSPTSPAYSPSSPTFEESED | ||||||
Sequence conflict | 1887 | in Ref. 1; AAA28868 | ||||
Sequence: D → DVRKGGRG |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
M27431 EMBL· GenBank· DDBJ | AAA28868.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AE014298 EMBL· GenBank· DDBJ | AAF48057.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M14203 EMBL· GenBank· DDBJ | AAA28864.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M11798 EMBL· GenBank· DDBJ | AAA28863.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M19537 EMBL· GenBank· DDBJ | AAA28827.1 EMBL· GenBank· DDBJ | Genomic DNA |