RNA polymerase

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 7: Line 7:
'''RNAP III''' (or '''Pol III''') transcribes tRNA and 5S ribosomal RNA<ref>PMID:1452</ref>.<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>. <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>. <br />
-
'''dnaG''' is a bacterial primase<ref>PMID:23430154</ref>.<br />
+
'''dnaG''' is a bacterial DNA primase<ref>PMID:23430154</ref>.<br />
For DNA-dependent RNA polymerase see<br />
For DNA-dependent RNA polymerase see<br />
* [[Molecular Playground/T7 RNAP Conformations]]<br />
* [[Molecular Playground/T7 RNAP Conformations]]<br />
Line 32: Line 32:
{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
-
*Prokaryotic DNA-dependent RNAP
+
*'''Prokaryotic DNA-dependent RNAP'''
**[[2y0s]] – SsRNAP – ''Sulfolobus shibata''<br />
**[[2y0s]] – SsRNAP – ''Sulfolobus shibata''<br />
Line 69: Line 69:
**[[3nff]], [[3nfg]], [[3nfh]], [[3nfi]] – RNAP I fragments (mutant) – ''Candida glabrata''<br />
**[[3nff]], [[3nfg]], [[3nfh]], [[3nfi]] – RNAP I fragments (mutant) – ''Candida glabrata''<br />
-
*''Prokaryotic DNA-dependent RNAP complex with DNA/RNA''
+
*'''Prokaryotic DNA-dependent RNAP complex with DNA/RNA'''
**[[4v8s]] – SsRNAP + DNA<br />
**[[4v8s]] – SsRNAP + DNA<br />
Line 82: Line 82:
**[[4kn4]], [[4kn7]] - EcRNAP subunits α,β,β’,ω + RNA + antibiotic<br />
**[[4kn4]], [[4kn7]] - EcRNAP subunits α,β,β’,ω + RNA + antibiotic<br />
-
*''Prokaryotic DNA-dependent RNAP complex with protein''
+
*'''Prokaryotic DNA-dependent RNAP complex with protein'''
**[[3p8b]] – PfRNAP subunit ε’’ + transcription antitermination protein <br />
**[[3p8b]] – PfRNAP subunit ε’’ + transcription antitermination protein <br />
Line 114: Line 114:
-
*''Prokaryotic DNA-dependent RNAP complex with protein + DNA/RNA''
+
*'''Prokaryotic DNA-dependent RNAP complex with protein + DNA/RNA'''
**[[3aoh]], [[3aoi]] - TtRNAP subunits α,β,β’,ω + DNA + RNA + GFH1<br />
**[[3aoh]], [[3aoi]] - TtRNAP subunits α,β,β’,ω + DNA + RNA + GFH1<br />
Line 147: Line 147:
**[[1l9z]] - TaRNAP subunits α,β,β’,ω + σ factor + DNA<br />
**[[1l9z]] - TaRNAP subunits α,β,β’,ω + σ factor + DNA<br />
-
*''Prokaryotic DNA-dependent RNAP complex with small molecule''
+
*'''Prokaryotic DNA-dependent RNAP complex with small molecule'''
**[[1zyr]], [[2a68]], [[2a69]], [[2a6e]], [[2a6h]] - TtRNAP subunits α,β,β’,ω + antibiotic<br />
**[[1zyr]], [[2a68]], [[2a69]], [[2a6e]], [[2a6h]] - TtRNAP subunits α,β,β’,ω + antibiotic<br />
**[[1i6v]], [[1ynj]], [[1ynn]] - TaRNAP subunits α,β,β’,ω + antibiotic<br />
**[[1i6v]], [[1ynj]], [[1ynn]] - TaRNAP subunits α,β,β’,ω + antibiotic<br />
-
*Eukaryotic DNA-dependent RNAP I
+
*'''Eukaryotic DNA-dependent RNAP I'''
**[[1a1d]] – yRNAP subunit RPB8 – yeast - NMR<br />
**[[1a1d]] – yRNAP subunit RPB8 – yeast - NMR<br />
Line 161: Line 161:
**[[5w66]], [[5w65]], [[5w64]], [[5w5y]] – yRNAP I + transcription initiation factor + DNA + RNA – Cryo EM<br />
**[[5w66]], [[5w65]], [[5w64]], [[5w5y]] – yRNAP I + transcription initiation factor + DNA + RNA – Cryo EM<br />
-
*Eukaryotic DNA-dependent RNAP II
+
*'''Eukaryotic DNA-dependent RNAP II'''
**[[1qkl]] - hRNAP II subunit RPB6 - human<br />
**[[1qkl]] - hRNAP II subunit RPB6 - human<br />
Line 179: Line 179:
**[[5u0s]] – fyRNAP II + mediator complex – Cryo EM<br />
**[[5u0s]] – fyRNAP II + mediator complex – Cryo EM<br />
-
*''Eukaryotic DNA-dependent RNAP II complex with DNA/RNA''
+
*'''Eukaryotic DNA-dependent RNAP II complex with DNA/RNA'''
**[[4boc]] – hRNAP + DNA<br />
**[[4boc]] – hRNAP + DNA<br />
Line 192: Line 192:
**[[2vum]] - yRNAP II + inhibitor + DNA + RNA<br />
**[[2vum]] - yRNAP II + inhibitor + DNA + RNA<br />
-
*''Eukaryotic DNA-dependent RNAP II complex with protein''
+
*'''Eukaryotic DNA-dependent RNAP II complex with protein'''
**[[3o2q]], [[3o2s]] – hRNAP II subunit α C-terminal + symplekin <br />
**[[3o2q]], [[3o2s]] – hRNAP II subunit α C-terminal + symplekin <br />
Line 208: Line 208:
**[[6exv]] – pRNAP II + RNA + DNA + amatoxin – Cryo EM<br />
**[[6exv]] – pRNAP II + RNA + DNA + amatoxin – Cryo EM<br />
-
*''Eukaryotic DNA-dependent RNAP II complex with small molecule''
+
*'''Eukaryotic DNA-dependent RNAP II complex with small molecule'''
**[[3pgl]] - hRNAP II C terminal + inhibitor<br />
**[[3pgl]] - hRNAP II C terminal + inhibitor<br />
Line 214: Line 214:
**[[1twa]], [[1twc]], [[1twf]], [[1twg]], [[1twh]] - yRNAP II + nucleotide<br />
**[[1twa]], [[1twc]], [[1twf]], [[1twg]], [[1twh]] - yRNAP II + nucleotide<br />
-
*Eukaryotic DNA-dependent RNAP III
+
*'''Eukaryotic DNA-dependent RNAP III'''
**[[2xub]], [[2xv4]] - hRNAP III subunits RPC3<br />
**[[2xub]], [[2xv4]] - hRNAP III subunits RPC3<br />
Line 230: Line 230:
**[[3ayh]] - fyRNAP III subunit Rpc8+Rpc9<br />
**[[3ayh]] - fyRNAP III subunit Rpc8+Rpc9<br />
-
*Eukaryotic DNA-dependent RNAP μ
+
*'''Eukaryotic DNA-dependent RNAP μ'''
**[[4lzd]] – hRNAP μ<br />
**[[4lzd]] – hRNAP μ<br />
Line 236: Line 236:
**[[5vzi]], [[5vzh]], [[5vzg]], [[5vzf]], [[5vze]], [[5vzd]], [[5vzc]], [[5vzb]], [[5vza]], [[5vz9]], [[5vz8]], [[5vz7]] – hRNAP μ (mutant) + DNA + nucleotide<br />
**[[5vzi]], [[5vzh]], [[5vzg]], [[5vzf]], [[5vze]], [[5vzd]], [[5vzc]], [[5vzb]], [[5vza]], [[5vz9]], [[5vz8]], [[5vz7]] – hRNAP μ (mutant) + DNA + nucleotide<br />
-
*Eukaryotic DNA-dependent RNAP mitochondrial
+
*'''Eukaryotic DNA-dependent RNAP mitochondrial'''
**[[4boc]] – hRNAP + DNA<br />
**[[4boc]] – hRNAP + DNA<br />
Line 242: Line 242:
**[[3spa]] - hRNAP + polypeptide <br />
**[[3spa]] - hRNAP + polypeptide <br />
-
*''Eukaryotic DNA primase''
+
*'''Eukaryotic DNA primase'''
**[[4lik]], [[4mhk]] - hDNAP small subunit<br />
**[[4lik]], [[4mhk]] - hDNAP small subunit<br />
Line 255: Line 255:
**[[3lgb]] - yDNAP large subunit<br />
**[[3lgb]] - yDNAP large subunit<br />
-
*''Eukaryotic DNA primase complex''
+
*'''Eukaryotic DNA primase complex'''
**[[4lil]] - hDNAP small subunit + UTP<br />
**[[4lil]] - hDNAP small subunit + UTP<br />
Line 263: Line 263:
**[[5exr]] - hDNAP small + large subunits + DNA polymerase α catalytic subunit<br />
**[[5exr]] - hDNAP small + large subunits + DNA polymerase α catalytic subunit<br />
-
*''Bacterial DNA primase''
+
*'''Bacterial DNA primase'''
**[[1d0q]] - GsDNAP zinc-binding domain - ''Geobacillus stearothermophilus''<br />
**[[1d0q]] - GsDNAP zinc-binding domain - ''Geobacillus stearothermophilus''<br />
Line 282: Line 282:
**[[5guj]] – BsdnaG RNAP domain <br />
**[[5guj]] – BsdnaG RNAP domain <br />
-
*''Bacterial DNA primase complex''
+
*'''Bacterial DNA primase complex'''
**[[2r6a]], [[2r6c]] - GsdnaG helicase binding domain + helicase – ''Geobacillus stearothermophilus''<br />
**[[2r6a]], [[2r6c]] - GsdnaG helicase binding domain + helicase – ''Geobacillus stearothermophilus''<br />
Line 290: Line 290:
**[[1v34]] - PhDNAP small subunit + UTP<br />
**[[1v34]] - PhDNAP small subunit + UTP<br />
**[[4edg]], [[4edk]], [[4edr]], [[4edt]], [[4edv]], [[4ee1]] – SaDNAP + nucleotide<br />
**[[4edg]], [[4edk]], [[4edr]], [[4edt]], [[4edv]], [[4ee1]] – SaDNAP + nucleotide<br />
-
*''RNA polymerase from Bacteriophage T7''
+
 
 +
*'''RNA polymerase from Bacteriophage T7'''
**[[1q57]] – T7DNAP/helicase (mutant) – Enterobacteria phage T7<br />
**[[1q57]] – T7DNAP/helicase (mutant) – Enterobacteria phage T7<br />
Line 301: Line 302:
**[[1msw]], [[1s0v]], [[1s76]], [[1s77]], [[3e2e]], [[3e3j]] - T7RNAP + DNA + RNA<br />
**[[1msw]], [[1s0v]], [[1s76]], [[1s77]], [[3e2e]], [[3e3j]] - T7RNAP + DNA + RNA<br />
-
*RNA-dependent RNAP
+
*'''RNA-dependent RNAP'''
**[[3phu]], [[1khv]], [[1khw]] – HfRNAP L RNA-directed – Hemorrhagic fever virus<br />
**[[3phu]], [[1khv]], [[1khw]] – HfRNAP L RNA-directed – Hemorrhagic fever virus<br />
Line 358: Line 359:
**[[5u0c]] - ZvRNAP NS5 – Zika virus<br />
**[[5u0c]] - ZvRNAP NS5 – Zika virus<br />
-
*''RNA-dependent RNAP complex with RNA''
+
*'''RNA-dependent RNAP complex with RNA'''
**[[4e78]], [[4e7a]], [[4wta]], [[4wtc]], [[4wtd]], [[4wte]], [[4wtf]], [[4wtg]], [[4wti]], [[4wtj]], [[4wtk]], [[4wtl]], [[4wtm]] - HvRNAP Ns5b domain (mutant) + RNA<br />
**[[4e78]], [[4e7a]], [[4wta]], [[4wtc]], [[4wtd]], [[4wte]], [[4wtf]], [[4wtg]], [[4wti]], [[4wtj]], [[4wtk]], [[4wtl]], [[4wtm]] - HvRNAP Ns5b domain (mutant) + RNA<br />
Line 377: Line 378:
**[[4k4x]], [[4k4y]], [[4k4z]] – CvRNAP + RNA<br />
**[[4k4x]], [[4k4y]], [[4k4z]] – CvRNAP + RNA<br />
-
*''RNA-dependent RNAP complex with protein''
+
*'''RNA-dependent RNAP complex with protein'''
**[[3phw]], [[2pt2]], [[3pt2]] – HfRNAP + ubiquitin<br />
**[[3phw]], [[2pt2]], [[3pt2]] – HfRNAP + ubiquitin<br />
Line 391: Line 392:
**[[5jze]] – RNAP + ISG15 – Erve virus<br />
**[[5jze]] – RNAP + ISG15 – Erve virus<br />
-
*''RNA-dependent RNAP complex with small molecule''
+
*'''RNA-dependent RNAP complex with small molecule'''
**[[2xwy]], [[3mf5]], [[3hkw]], [[3hky]], [[3lkh]], [[3gnv]], [[3gnw]], [[3h98]], [[3g86]], [[3h59]], [[1nhu]], [[1nhv]], [[2brk]], [[2brl]], [[2gc8]], [[2giq]], 2gir]], [[2hai]], [[2hwh]], [[2hwi]], [[2i1r]], [[2ijn]], [[2jc0]], [[2jc1]], [[2qe2]], [[2qe5]], [[2wcx]], [[2who]], [[3ciz]], [[3cj0]], [[3cj2]], [[3cj3]], [[3cj4]], [[3cj5]], [[3cso]], [[3cvk]], [[3fqk]], [[3fql]], [[3gol]], [[3h5s]], [[3h5u]], [[3q0z]], [[3qgd]], [[3qge]], [[3qgf]], [[3qgg]], [[3qgh]], [[3qgi]], [[3ska]], [[3ske]], [[3skh]], 3uph]], [[3upi]], [[4dru]], [[3vqs]], [[3udl]], [[4eo6]], [[4eo8]], [[4eaw]], [[4gmc]], [[4ih5]], [[4ih6]], [[4ih7]], [[4iz0]], [[4jtz]], [[4jtw]], [[4jty]], [[4ju1]], [[4ju2]], [[4jjs]], [[4jju]], [[4j02]], [[4j04]], [[4j06]], [[4j08]], [[2yoj]], [[3tuq]], [[3tuv]], [[3u4o]], [[3u4r]], [[4mk7]], [[4mk8]], [[4mk9]], [[4mka]], [[4mkb]], [[4mz4]], [[4nld]], [[3tyq]], [[3tyv]], [[4mia]], [[4mib]], [[4oow]], [[4tlr]], [[5pzk]], [[5pzl]], [[5pzm]], [[5pzn]], [[5pzo]], [[5pzp]], [[5trh]], [[5tri]], [[5trj]] - HvRNAP Ns5b domain + inhibitor<br />
**[[2xwy]], [[3mf5]], [[3hkw]], [[3hky]], [[3lkh]], [[3gnv]], [[3gnw]], [[3h98]], [[3g86]], [[3h59]], [[1nhu]], [[1nhv]], [[2brk]], [[2brl]], [[2gc8]], [[2giq]], 2gir]], [[2hai]], [[2hwh]], [[2hwi]], [[2i1r]], [[2ijn]], [[2jc0]], [[2jc1]], [[2qe2]], [[2qe5]], [[2wcx]], [[2who]], [[3ciz]], [[3cj0]], [[3cj2]], [[3cj3]], [[3cj4]], [[3cj5]], [[3cso]], [[3cvk]], [[3fqk]], [[3fql]], [[3gol]], [[3h5s]], [[3h5u]], [[3q0z]], [[3qgd]], [[3qge]], [[3qgf]], [[3qgg]], [[3qgh]], [[3qgi]], [[3ska]], [[3ske]], [[3skh]], 3uph]], [[3upi]], [[4dru]], [[3vqs]], [[3udl]], [[4eo6]], [[4eo8]], [[4eaw]], [[4gmc]], [[4ih5]], [[4ih6]], [[4ih7]], [[4iz0]], [[4jtz]], [[4jtw]], [[4jty]], [[4ju1]], [[4ju2]], [[4jjs]], [[4jju]], [[4j02]], [[4j04]], [[4j06]], [[4j08]], [[2yoj]], [[3tuq]], [[3tuv]], [[3u4o]], [[3u4r]], [[4mk7]], [[4mk8]], [[4mk9]], [[4mka]], [[4mkb]], [[4mz4]], [[4nld]], [[3tyq]], [[3tyv]], [[4mia]], [[4mib]], [[4oow]], [[4tlr]], [[5pzk]], [[5pzl]], [[5pzm]], [[5pzn]], [[5pzo]], [[5pzp]], [[5trh]], [[5tri]], [[5trj]] - HvRNAP Ns5b domain + inhibitor<br />
Line 412: Line 413:
**[[5ltn]], [[5t2t]] - LcmvRNAP + inhibitor<br />
**[[5ltn]], [[5t2t]] - LcmvRNAP + inhibitor<br />
-
*Influenza virus polymerase acidic protein (or PA or subunit P2)
+
*'''Influenza virus polymerase acidic protein (or PA or subunit P2)'''
**[[3hw3]], [[3hw4]], [[3hw5]] - IvRNAP PA (mutant) + Mn + nucleotide – Influenza virus<br />
**[[3hw3]], [[3hw4]], [[3hw5]] - IvRNAP PA (mutant) + Mn + nucleotide – Influenza virus<br />
Line 428: Line 429:
**[[4iuj]] - IvRNAP PA residues 254-713<br />
**[[4iuj]] - IvRNAP PA residues 254-713<br />
-
*Influenza virus polymerase basic protein 2 (or RNAP subunit P3 or PB2)); Domains: cap-binding 318-483; Cap-binding and midlink 247-536; 627 538-693; NLS 694-753
+
*'''Influenza virus polymerase basic protein 2 (or RNAP subunit P3 or PB2))'''; Domains: cap-binding 318-483; Cap-binding and midlink 247-536; 627 538-693; NLS 694-753
**[[4enf]], [[4u6o]], [[4j2r]], [[2vqz]], [[5ef9]], [[5eg9]] – IvRNAP PB2 cap-binding domain<br />
**[[4enf]], [[4u6o]], [[4j2r]], [[2vqz]], [[5ef9]], [[5eg9]] – IvRNAP PB2 cap-binding domain<br />
Line 444: Line 445:
**[[2vy8]] - IvRNAP PB2 627 domain (mutant) <br />
**[[2vy8]] - IvRNAP PB2 627 domain (mutant) <br />
-
*Influenza virus RNAP PA+PB1
+
*'''Influenza virus RNAP PA+PB1'''
**[[2znl]] - IvRNAP PA + PB1<br />
**[[2znl]] - IvRNAP PA + PB1<br />
-
*Influenza virus RNAP PB1+PB2
+
*'''Influenza virus RNAP PB1+PB2'''
**[[2ztt]], [[3a1g]] - IvRNAP PB1 C terminal + RNAP PB2 N terminal<br />
**[[2ztt]], [[3a1g]] - IvRNAP PB1 C terminal + RNAP PB2 N terminal<br />
**[[3j9b]] - IvRNAP PB1+PB2 N terminal + RNA<br />
**[[3j9b]] - IvRNAP PB1+PB2 N terminal + RNA<br />
-
*Influenza virus RNAP PA+PB1+PB2
+
*'''Influenza virus RNAP PA+PB1+PB2'''
**[[4wsb]], [[5fmz]], [[5m3h]], [[5m3j]], [[5msg]], [[6f5o]], [[6evj]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA<br />
**[[4wsb]], [[5fmz]], [[5m3h]], [[5m3j]], [[5msg]], [[6f5o]], [[6evj]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + RNA<br />
Line 460: Line 461:
**[[6f5p]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + polyAla<br />
**[[6f5p]] - IvRNAP PB1 + IvRNAP PA + IvRNAP PB2 + polyAla<br />
-
*Poly(A) RNA polymerase
+
*'''Poly(A) RNA polymerase'''
**[[3pq1]] – hRNAP (mutant)<br />
**[[3pq1]] – hRNAP (mutant)<br />

Revision as of 10:18, 21 October 2018

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

3D Structures of RNA polymerase

Updated on 21-October-2018


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