We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

RNA polymerase

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:07, 21 February 2024) (edit) (undo)
 
(90 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3m3y.png|left|200px|thumb|Crystal Structure of RNA polymerase [[3m3y]]]]
+
<StructureSection load='' size='350' side='right' caption='Yeast RNA polymerase II elongation complex C complexed with DNA and RNA and Zn+2 (grey) and Mg+2 (green) ions [[3m3y]]. Subunit B1 (grey), B2 (green), B3 (pink), B9 (wheat), B11 (rust), ABC1 (magenta), ABC2 (cyan), ABC3 (red), ABC4 (aqua), ABC5 (blue) (PDB code [[3m3y]]).' scene='RNA_polymerase/Cv/1'>
-
{{STRUCTURE_3m3y| PDB=3m3y | SIZE=300| SCENE=RNA_polymerase/Cv/1 |right|CAPTION=Yeast RNA polymerase complexed with DNA and RNA [[3m3y]] }}
+
__TOC__
-
{{TOC limit|limit=2}}
+
==Function==
 +
'''RNA polymerase''' (RNAP, '''DNA primase''', dnaG) catalyzes the addition of nucleotides to RNA during transcription.<br />
 +
'''DNA-dependent RNA polymerase''' catalyzes the transcription of RNA from a DNA template. The DNA-dependent eukaryote RNAP<ref>PMID:18573085</ref> are divided to<br />
 +
'''RNAP I''' (or '''Pol I''') which transcribes ribosomal RNA<ref>PMID:14969726</ref>; <br />
 +
'''RNAP II''' (or '''Pol II''') transcribes DNA and most snRNA and microRNA<ref>PMID:15114340</ref>; See [[RNA Polymerase II]].<br />
 +
'''RNAP III''' (or '''Pol III''') transcribes tRNA and 5S ribosomal RNA<ref>PMID:1452</ref>.<br />
 +
'''DNA primase''' (DNAP) is RNAP which catalyzes the synthesis of the RNA primer which complements an ssDNA template and initiates DNA synthesis<ref>PMID:11395402</ref>. The large subunit of promase is called '''p58C'''.<br />
 +
'''dnaG''' is a bacterial DNA primase<ref>PMID:23430154</ref>.<br />
 +
For DNA-dependent RNA polymerase see<br />
 +
* [[Molecular Playground/T7 RNAP Conformations]]<br />
 +
* [[User:Luis E Ramirez-Tapia/T7 RNA polymerase]]<br />
 +
* [[Molecular Playground/T7 RNA Polymerase (7 mer int)]].<br />
 +
* [[T7 RNA Polymerase]].<br />
 +
* [[Molecular Playground/Human mtRNA pol]].<br />
 +
* [[Beta-Prime Subunit of Bacterial RNA Polymerase]]<br />
 +
* [[Transcription and RNA Processing]].<br />
 +
* [[Rifampicin]]
-
'''RNA polymerase''' (RNAP, '''DNA primase''', dnaG) catalyzes the addition of nucleotides to RNA during transcription. DNA primase (DNAP) is RNAP which catalyzes the synthesis of the RNA primer which complements an ssDNA template and initiates DNA synthesis. dnaG is a bacterial primase.
+
'''RNA-dependent RNA polymerase''' or '''cap-snatching endonuclease''' or '''replicase''' catalyzes the replication of RNA from a RNA template<ref>PMID:12016304</ref>. An example is the '''Influenza virus RNA polymerase''' which is composed of 3 subunits. Subunit '''PA''' is involved in cap-snatching. Subunit '''PB1''' is involved in RNA synthesis. Subunit '''PB2''' is involved in RNA replication and transcription. It is implicated in endonuclease cleavage of RNA primers. <scene name='1qln/Rockets_steitz_colors/1'>View of the nucleic acid</scene> ([[1qln]]; blue: nontemplate strand; cyan: template strand; red:RNA).<br />
 +
See also [[RNA-directed RNA polymerase]].<br />
 +
For RNA-dependent RNA polymerase from Hepatitis C virus - NS5B - see<br />
 +
* [[NS5B]].<br />
 +
* [[User:Michael Strong/H1N1/PB2]]<br />
 +
* [[User:Michael Strong/H1N1/PB2/MSA]]<br />
 +
* [[User:Michael Strong/H1N1/PA]]<br />
 +
* [[User:Michael Strong/H1N1/PA/MSA]]
 +
*[[Sofosbuvir]]
-
== 3D Structures of RNA polymerase ==
+
For RNA-dependent RNA polymerase from murine norovirus see<br />
 +
* [[Ribavirin1]].<br />
-
===DNA-dependent RNAP===
+
'''Poly(A) RNA polymerase''' catalyzes the addition of long poly(A) tails to mRNA without a template<ref>PMID:15047805</ref>.
-
[[2y0s]] – RNAP – ''Sulfolobus shibata''<br />
+
== 3D Structures of RNA polymerase ==
-
[[3q22]], [[3q23]], [[3q24]] – RNAP + DNA – Enterobacteria phage N4<br />
+
[[RNA polymerase 3D structures]]
-
[[3p8b]] – PfRNAP subunit ε’’ + transcription antitermination protein – ''Pyrococcus furiosus''<br />
+
-
[[3lpe]] - RNAP subunit ε’’ + transcription antitermination protein – ''Methanocaldococcus jannaschii''<br />
+
-
[[3aoh]], [[3aoi]] - TtRNAP subunits α,β,β’,ω + DNA +RNA + GFH1 – ''Thermus thermophilus''<br />
+
-
[[3mlq]] - TtRNAP subunit β + transcription-repair coupling factor<br />
+
-
[[3lti]] – EcRNAP subunit β fragment – ''Escherichia coli''<br />
+
-
[[3mmp]] - EcRNAP subunit β + EF-TU<br />
+
-
[[3k4g]] - EcRNAP subunit α<br />
+
-
[[3lu0]] - EcRNAP subunits α,β,β’,ω – Electron diffraction<br />
+
-
[[3iyd]] - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + catabolite gene activator + DNA<br />
+
-
[[2l0i]] – yRNAP C-terminal + RTT103 – yeast – NMR<br />
+
-
[[2krc]] - BsRNAP subunit δ N-terminal – ''Bacillus subtilis'' – NMR<br />
+
-
[[3ihq]] - BsRNAP subunit α +regulatory protein SPX<br />
+
-
 
+
-
===Eukaryotic DNA-dependent RNAP===
+
-
 
+
-
[[3o2q]], [[3o2s]] – RNAP II subunit α C-terminal + symplekin – human<br />
+
-
[[3nff]], [[3nfg]], [[3nfh]], [[3nfi]] – RNAP I fragments (mutant) – ''Candida glabrata''<br />
+
-
[[3m3y]], [[3m4o]] – yRNAP I,II,III + RNA + DNA<br />
+
-
[[3k7a]], [[3k1f]] - yRNAP I,II,III + TFIIB
+
-
 
+
-
===RNA-dependent RNAP===
+
-
 
+
-
[[3phu]] – HfRNAP L RNA-directed – Hemorrhagic fever virus<br />
+
-
[[3phw]], [[2pt2]] – HfRNAP + ubiquitin<br />
+
-
[[3phx]] – HfRNAP + ISG15<br />
+
-
[[3pse]] - HfRNAP + ISG15 (mutant)<br />
+
-
[[2xwh]], [[2xxd]], [[2xhu]], [[2xhw]], [[3i5k]] – HvRNAP NS5B domain – Hepatitis virus<br />
+
-
[[2xym]], [[2xhv]], [[2xi2]] - HvRNAP NS5B domain (mutant)<br />
+
-
[[2xwy]], [[3mf5]], [[3hkw]], [[3hky]], [[3lkh]], [[3gnv]], [[3gnw]], [[3h98]], [[3g86]], [[3h59]] - HvRNAP NS5B domain + inhibitor<br />
+
-
[[3gyn]] - HvRNAP NS5B domain (mutant) + inhibitor<br />
+
-
[[2wrm]] – HvRNAP NS5B domain<br />
+
-
[[2xi3]] - HvRNAP NS5B domain (mutant) + nucleotide<br />
+
-
[[3ol6]] – PoRNAP (mutant) + RNA – Poliovirus<br />
+
-
[[3ol7]], [[3ol8]], [[3ol9]], [[3ola]], [[3olb]] - PoRNAP (mutant) + RNA + nucleotide<br />
+
-
[[2xi5]], [[2xi7]] – RNAP L N-terminal – Bunyavirus<br />
+
-
[[3jsb]] – RNAP (mutant) – Lymphocytic choriomengitis virus<br />
+
-
[[2wk4]] – RNAP (mutant) – Sapporo virus<br />
+
-
[[3klv]], [[3kmq]], [[3kms]], [[3kna]] – FmRNAP (mutant) + RNA – Foot-and-mouth virus<br />
+
-
[[3koa]] - FmRNAP (mutant) + RNA + nucleotide<br />
+
-
[[3hw3]], [[3hw6]] - IvRNAP subunit P2 (mutant) – Influenza virus<br />
+
-
[[3hw5]] - IvRNAP subunit P2 (mutant) + AMP<br />
+
-
 
+
-
===DNA primase===
+
-
 
+
-
[[3l9q]] – hDNAP large subunit<br />
+
-
[[3lgb]] - yDNAP large subunit<br />
+
-
[[3m1m]] – DNAP RNA polymerase domain – ''Sulfolobus islandicus''<br />
+
-
[[1zt2]] - DNAP small + large subunit – ''Sulfolobus solfataricus''<br />
+
-
[[2au3]] – DNAP zinc-binding and RNA polymerase domains – ''Aquifex aeolicus''<br />
+
-
[[1v33]] - PhDNAP small subunit – ''Pyrocuccus horikoshii''<br />
+
-
[[1v34]] - PhDNAP small subunit + nucleotide<br />
+
-
[[1g71]] - PfDNAP small subunit<br />
+
-
[[1q57]] – T7DNAP/helicase (mutant) – Enterobacteria phage T7<br />
+
-
[[1nui]] – T7DNAP/helicase primase fragment (mutant)<br />
+
-
[[1cr0]] - T7DNAP/helicase helicase domain<br />
+
-
[[1cr1]], [[1cr2]], [[1cr4]] - T7DNAP/helicase helicase domain + nucleotide<br />
+
-
===Bacterial primase===
+
</StructureSection>
-
[[2r6c]] – dnaG helicase binding domain + helicase – ''Bacillus stearothermophilus''<br />
+
== References ==
-
[[2r6a]] - GsdnaG helicase binding domain + helicase – ''Geobacillus stearothermophilus''<br />
+
<references/>
-
[[1d0q]] - GsDNAP zinc-binding domain<br />
+
[[Category:Topic Page]]
-
[[1z8s]] - GsdnaG dnaB binding domain - NMR<br />
+
*Created with the participation of [[User:Craig T Martin|Craig T Martin]].
-
[[2haj]] - EcdnaG catalytic domain - NMR<br />
+
-
[[3b39]] – EcdnaG catalytic domain + DNA<br />
+
-
[[1t3w]] – EcdnaG C-terminal<br />
+
-
[[1eqn]], [[1dd9]], [[1dde]] – EcdnaG catalytic core<br />
+

Current revision

Yeast RNA polymerase II elongation complex C complexed with DNA and RNA and Zn+2 (grey) and Mg+2 (green) ions 3m3y. Subunit B1 (grey), B2 (green), B3 (pink), B9 (wheat), B11 (rust), ABC1 (magenta), ABC2 (cyan), ABC3 (red), ABC4 (aqua), ABC5 (blue) (PDB code 3m3y).

Drag the structure with the mouse to rotate

References

  1. ↑ Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, Buchen C, Damsma GE, Dengl S, Geiger SR, Jasiak AJ, Jawhari A, Jennebach S, Kamenski T, Kettenberger H, Kuhn CD, Lehmann E, Leike K, Sydow JF, Vannini A. Structure of eukaryotic RNA polymerases. Annu Rev Biophys. 2008;37:337-52. doi: 10.1146/annurev.biophys.37.032807.130008. PMID:18573085 doi:http://dx.doi.org/10.1146/annurev.biophys.37.032807.130008
  2. ↑ Comai L. Mechanism of RNA polymerase I transcription. Adv Protein Chem. 2004;67:123-55. PMID:14969726 doi:http://dx.doi.org/10.1016/S0065-3233(04)67005-7
  3. ↑ Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol. 2004 May;11(5):394-403. PMID:15114340 doi:http://dx.doi.org/10.1038/nsmb763
  4. ↑ Longo DL, Herbert V. Radioassay for serum and red cell folate. J Lab Clin Med. 1976 Jan;87(1):138-51. PMID:1452
  5. ↑ Frick DN, Richardson CC. DNA primases. Annu Rev Biochem. 2001;70:39-80. PMID:11395402 doi:http://dx.doi.org/10.1146/annurev.biochem.70.1.39
  6. ↑ Naue N, Beerbaum M, Bogutzki A, Schmieder P, Curth U. The helicase-binding domain of Escherichia coli DnaG primase interacts with the highly conserved C-terminal region of single-stranded DNA-binding protein. Nucleic Acids Res. 2013 Apr;41(8):4507-17. doi: 10.1093/nar/gkt107. Epub 2013 Feb, 20. PMID:23430154 doi:http://dx.doi.org/10.1093/nar/gkt107
  7. ↑ Ahlquist P. RNA-dependent RNA polymerases, viruses, and RNA silencing. Science. 2002 May 17;296(5571):1270-3. PMID:12016304 doi:http://dx.doi.org/10.1126/science.1069132
  8. ↑ Fukushi S, Kojima S, Takai R, Hoshino FB, Oka T, Takeda N, Katayama K, Kageyama T. Poly(A)- and primer-independent RNA polymerase of Norovirus. J Virol. 2004 Apr;78(8):3889-96. PMID:15047805

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman, Karsten Theis

Retrieved from "http://52.214.119.220/wiki/index.php/RNA_polymerase"
Personal tools