Reviewed,
UniProtKB/Swiss-Prot A5DCV3 (RPB1_PICGU)
Last modified
November 24, 2009.
Version 15.
History...
Clusters with 100%,
90%,
50% identity |
 Documents (1) |
 Third-party data |
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Names and origin
| Protein names | Recommended name: DNA-directed RNA polymerase II subunit RPB1 Short name=RNA polymerase II subunit B1 Short name=RNA polymerase II subunit 1 EC=2.7.7.6 Alternative name(s): DNA-directed RNA polymerase III largest subunit | ||||
| Gene names |
| ||||
| Organism | Pichia guilliermondii (Yeast) (Candida guilliermondii) [Complete proteome] | ||||
| Taxonomic identifier | 4929 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Pichia |
Protein attributes
| Sequence length | 1579 AA. |
| Sequence status | Fragments. |
| Sequence processing | The displayed sequence is not processed. |
| Protein existence | Inferred from homology. |
General annotation (Comments)
| 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. |
| Catalytic activity | Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). |
| Subunit structure | Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits By similarity. |
| Subcellular location | Nucleus By similarity. |
| 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 heptapepdtide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphataes, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed 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 nucelotide 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. |
| Sequence similarities | Belongs to the RNA polymerase beta' chain family. Contains 1 C2H2-type zinc finger. |
| Sequence caution | The sequence EDK37008.1 differs from that shown. Reason: Frameshift at positions 1480 and 1528. The sequence EDK37010.1 differs from that shown. Reason: Frameshift at position 317. |
Ontologies
| Keywords | |
|---|---|
| Biological process | Transcription |
| Cellular component | DNA-directed RNA polymerase Nucleus |
| Domain | Repeat Zinc-finger |
| Ligand | DNA-binding Magnesium Metal-binding Zinc |
| Molecular function | Nucleotidyltransferase Transferase |
| PTM | Phosphoprotein |
| Technical term | Complete proteome |
| Gene Ontology (GO) | |
| Biological process | transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: InterPro |
| Cellular component | DNA-directed RNA polymerase II, core complex Inferred from electronic annotation. Source: InterPro |
| Molecular function | DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed RNA polymerase activityInferred from electronic annotation. Source: UniProtKB-KW magnesium ion bindingInferred from electronic annotation. Source: UniProtKB-KW zinc ion bindingInferred from electronic annotation. Source: UniProtKB-KW |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 1579 | 1579 | DNA-directed RNA polymerase II subunit RPB1 | PRO_0000295034 | |||||
Regions | |||||||||
| Repeat | 1385 – 1391 | 7 | 1 | ||||||
| Repeat | 1392 – 1398 | 7 | 2 | ||||||
| Repeat | 1399 – 1405 | 7 | 3 | ||||||
| Repeat | 1406 – 1412 | 7 | 4 | ||||||
| Repeat | 1413 – 1419 | 7 | 5 | ||||||
| Repeat | 1420 – 1426 | 7 | 6 | ||||||
| Repeat | 1427 – 1433 | 7 | 7 | ||||||
| Repeat | 1434 – 1440 | 7 | 8 | ||||||
| Repeat | 1441 – 1447 | 7 | 9 | ||||||
| Repeat | 1448 – 1454 | 7 | 10 | ||||||
| Repeat | 1455 – 1461 | 7 | 11 | ||||||
| Repeat | 1462 – 1468 | 7 | 12 | ||||||
| Repeat | 1469 – 1475 | 7 | 13 | ||||||
| Repeat | 1476 – 1482 | 7 | 14 | ||||||
| Repeat | 1483 – 1489 | 7 | 15 | ||||||
| Repeat | 1490 – 1496 | 7 | 16 | ||||||
| Repeat | 1497 – 1503 | 7 | 17; approximate | ||||||
| Repeat | 1504 – 1510 | 7 | 18 | ||||||
| Repeat | 1511 – 1517 | 7 | 19 | ||||||
| Repeat | 1518 – 1524 | 7 | 20 | ||||||
| Repeat | 1525 – 1531 | 7 | 21 | ||||||
| Repeat | 1532 – 1538 | 7 | 22 | ||||||
| Repeat | 1539 – 1545 | 7 | 23 | ||||||
| Repeat | 1546 – 1552 | 7 | 24 | ||||||
| Repeat | 1553 – 1559 | 7 | 25; approximate | ||||||
| Repeat | 1560 – 1566 | 7 | 26; approximate | ||||||
| Zinc finger | 68 – 84 | 17 | C2H2-type By similarity | ||||||
| Region | 642 – 654 | 13 | Bridging helix By similarity | ||||||
| Region | 1385 – 1566 | 182 | 26 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[S-A-Q] | ||||||
| Compositional bias | 244 – 249 | 6 | Poly-Pro | ||||||
Sites | |||||||||
| Metal binding | 68 | 1 | Zinc 1 By similarity | ||||||
| Metal binding | 71 | 1 | Zinc 1 By similarity | ||||||
| Metal binding | 78 | 1 | Zinc 1 By similarity | ||||||
| Metal binding | 81 | 1 | Zinc 1 By similarity | ||||||
| Metal binding | 108 | 1 | Zinc 2 By similarity | ||||||
| Metal binding | 111 | 1 | Zinc 2 By similarity | ||||||
| Metal binding | 149 | 1 | Zinc 2 By similarity | ||||||
| Metal binding | 171 | 1 | Zinc 2 By similarity | ||||||
| Metal binding | 485 | 1 | Magnesium 1; catalytic By similarity | ||||||
| Metal binding | 485 | 1 | Magnesium 2; shared with RPB2 By similarity | ||||||
| Metal binding | 487 | 1 | Magnesium 1; catalytic By similarity | ||||||
| Metal binding | 487 | 1 | Magnesium 2; shared with RPB2 By similarity | ||||||
| Metal binding | 489 | 1 | Magnesium 1; catalytic By similarity | ||||||
Natural variations | |||||||||
| Natural variant | 198 | 1 | T → S in strain: MmRL 1635. Ref.2 | ||||||
Experimental info | |||||||||
| Non-adjacent residues | 566 – 567 | 2 | |||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Evolution of pathogenicity and sexual reproduction in eight Candida genomes." Butler G., Rasmussen M.D., Lin M.F., Santos M.A.S., Sakthikumar S., Munro C.A., Rheinbay E., Grabherr M., Forche A., Reedy J.L., Agrafioti I., Arnaud M.B., Bates S., Brown A.J.P., Brunke S., Costanzo M.C., Fitzpatrick D.A., de Groot P.W.J.  Cuomo C.A.Nature 459:657-662(2009) [PubMed: 19465905] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 6260 / CBS 566 / IFO 10279 / JCM 1539 / NRRL Y-324. |
| [2] | "Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis." Diezmann S., Cox C.J., Schoenian G., Vilgalys R.J., Mitchell T.G. J. Clin. Microbiol. 42:5624-5635(2004) [PubMed: 15583292] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 88-295, VARIANT SER-198. Strain: ATCC 46036 / CBS 2030 / IFO 10106 / NRRL Y-2075, MMRL 1635, MMRL 1636 and MMRL 1759. |
Cross-references
Sequence databases | |
|---|---|
| CH408155 Genomic DNA. Translation: EDK37008.1. Frameshift. CH408155 Genomic DNA. Translation: EDK37010.1. Frameshift. AY497711 Genomic DNA. Translation: AAT12588.1. AY497732 Genomic DNA. Translation: AAT12608.1. AY497733 Genomic DNA. Translation: AAT12609.1. AY497734 Genomic DNA. Translation: AAT12610.1. | |
3D structure databases | |
| ModBase | Search... |
Phylogenomic databases | |
| OrthoDB | EOG9SXPVX |
Enzyme and pathway databases | |
| BRENDA | 2.7.7.6. 3704. |
Family and domain databases | |
| InterPro | IPR000722. RNA_pol_asu. IPR000684. RNA_pol_II_repeat_euk. IPR006592. RNA_pol_N. IPR007080. RNA_pol_Rpb1_1. IPR007066. RNA_pol_Rpb1_3. IPR007083. RNA_pol_Rpb1_4. IPR007081. RNA_pol_Rpb1_5. IPR007075. RNA_pol_Rpb1_6. IPR007073. RNA_pol_Rpb1_7. [Graphical view] |
| Gene3D | G3DSA:2.40.40.30. RNA_pol_A. 1 hit. |
| Pfam | PF04997. RNA_pol_Rpb1_1. 1 hit. PF00623. RNA_pol_Rpb1_2. 1 hit. PF04983. RNA_pol_Rpb1_3. 1 hit. PF05000. RNA_pol_Rpb1_4. 1 hit. PF04998. RNA_pol_Rpb1_5. 1 hit. PF04992. RNA_pol_Rpb1_6. 1 hit. PF04990. RNA_pol_Rpb1_7. 1 hit. PF05001. RNA_pol_Rpb1_R. 15 hits. [Graphical view] |
| SMART | SM00663. RPOLA_N. 1 hit. [Graphical view] |
| PROSITE | PS00115. RNA_POL_II_REPEAT. 21 hits. [Graphical view] |
| ProtoNet | Search... |
Entry information
| Entry name | RPB1_PICGU | ||||||||
| Accession | Primary (citable) accession number: A5DCV3 Secondary accession number(s): A5DCV0 Q6JE98 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | FPAP (Fungal Proteome Annotation Project) | ||||||||
