Reviewed,
UniProtKB/Swiss-Prot P14248 (RPB1_PLAFD)
Last modified
June 16, 2009.
Version 68.
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 EC=2.7.7.6 Alternative name(s): DNA-directed RNA polymerase III largest subunit | ||
| Gene names |
| ||
| Organism | Plasmodium falciparum (isolate CDC / Honduras) | ||
| Taxonomic identifier | 5836 [NCBI] | ||
| Taxonomic lineage | Eukaryota › Alveolata › Apicomplexa › Aconoidasida › Haemosporida › Plasmodium › Plasmodium (Laverania) |
Protein attributes
| Sequence length | 2452 AA. |
| Sequence status | Complete. |
| 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. |
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 |
| 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 – 2452 | 2452 | DNA-directed RNA polymerase II subunit RPB1 | PRO_0000073942 | |||||
Regions | |||||||||
| Domain | 1093 – 1128 | 36 | Leucine-zipper Potential | ||||||
| Repeat | 2251 – 2257 | 7 | 1 | ||||||
| Repeat | 2265 – 2271 | 7 | 2 | ||||||
| Repeat | 2290 – 2296 | 7 | 3; approximate | ||||||
| Repeat | 2297 – 2303 | 7 | 4 | ||||||
| Repeat | 2304 – 2310 | 7 | 5 | ||||||
| Repeat | 2311 – 2317 | 7 | 6 | ||||||
| Repeat | 2318 – 2324 | 7 | 7 | ||||||
| Repeat | 2325 – 2331 | 7 | 8 | ||||||
| Repeat | 2332 – 2338 | 7 | 9 | ||||||
| Repeat | 2339 – 2345 | 7 | 10 | ||||||
| Repeat | 2346 – 2352 | 7 | 11 | ||||||
| Repeat | 2361 – 2367 | 7 | 12; approximate | ||||||
| Zinc finger | 68 – 84 | 17 | C2H2-type By similarity | ||||||
| DNA binding | 378 – 411 | 34 | By similarity | ||||||
| DNA binding | 1182 – 1193 | 12 | Potential | ||||||
| Region | 970 – 982 | 13 | Bridging helix | ||||||
| Region | 1261 – 1290 | 30 | 6 X tandem repeats of [YLV]-D(3,4) | ||||||
| Region | 2061 – 2246 | 186 | Highly diverged heptapeptide repeats | ||||||
| Region | 2251 – 2367 | 117 | 12 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[SYK] | ||||||
| Compositional bias | 707 – 725 | 19 | Poly-Asn | ||||||
| Compositional bias | 1144 – 1159 | 16 | Poly-Asn | ||||||
| Compositional bias | 1258 – 1290 | 33 | Asp/Glu-rich (highly acidic) | ||||||
| Compositional bias | 1602 – 1612 | 11 | Asp/Glu-rich (highly acidic) | ||||||
| Compositional bias | 1687 – 1694 | 8 | Poly-Asn | ||||||
| Compositional bias | 1746 – 1759 | 14 | Asp/Glu-rich (highly acidic) | ||||||
| Compositional bias | 1806 – 1820 | 15 | Asp/Glu-rich (highly acidic) | ||||||
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 | 203 | 1 | Zinc 2 By similarity | ||||||
| Metal binding | 514 | 1 | Magnesium 1; catalytic By similarity | ||||||
| Metal binding | 514 | 1 | Magnesium 2; shared with RPB2 By similarity | ||||||
| Metal binding | 516 | 1 | Magnesium 1; catalytic By similarity | ||||||
| Metal binding | 516 | 1 | Magnesium 2; shared with RPB2 By similarity | ||||||
| Metal binding | 518 | 1 | Magnesium 1; catalytic By similarity | ||||||
Sequences
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References
| [1] | "An enlarged largest subunit of Plasmodium falciparum RNA polymerase II defines conserved and variable RNA polymerase domains." Li W.B., Bzik D.J., Gu H., Tanaka M., Fox B.A., Inselburg J. Nucleic Acids Res. 17:9621-9636(1989) [PubMed: 2690004] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. |
Cross-references
Sequence databases | |
|---|---|
| X16561 Genomic DNA. Translation: CAA34560.1. | |
| PIR | RNZQ2L. S07485. |
3D structure databases | |
| HSSP | HSSP built from PDB template 1K83 based on UniProtKB P04050. |
| ModBase | Search... |
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. G3DSA:3.90.1120.10. RNA_pol_Rpb1_1. 1 hit. G3DSA:3.30.1360.90. RNA_pol_Rpb1_7. 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. 2 hits. PF04990. RNA_pol_Rpb1_7. 1 hit. PF05001. RNA_pol_Rpb1_R. 11 hits. [Graphical view] |
| SMART | SM00663. RPOLA_N. 1 hit. [Graphical view] |
| PROSITE | PS00115. RNA_POL_II_REPEAT. 9 hits. [Graphical view] |
| ProtoNet | Search... |
Entry information
| Entry name | RPB1_PLAFD | ||||||||
| Accession | Primary (citable) accession number: P14248 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
