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RNA polymerase

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Revision as of 11:41, 9 December 2014 by Michal Harel (Talk | contribs)
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Template:STRUCTURE 3m3y

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. Polymerase acidic protein (PAP) is an Influenza virus RNA polymerase. It is implicated in endonuclease cleavage of RNA primers. (1qln; blue: nontemplate strand; cyan: template strand; red:RNA). See also Transcription and RNA Processing.
For RNA polymerase from bacteriophage T7 see

For RNA-dependent RNA polymerase from Hepatitis C virus - NS5B - see

For DNA-dependent RNA polymerase see

For the Thermus thermophilus β' subunit see

For the influenza virus RNA-dependent RNA polymerase PB2 and PA homology model and sequence alignment see

3D Structures of RNA polymerase

Updated on 09-December-2014 {{#tree:id=OrganizedByTopic|openlevels=0|

  • DNA-dependent RNA polymerase
    • 2y0s – SsRNAP – Sulfolobus shibata
    • 4b1p – SsRNAP + DNA
    • 3q22, 3q23, 3q24, 4ff1, 4ff2, 4ff3, 4ff4 – RNAP + DNA – Enterobacteria phage N4
    • 3p8b – PfRNAP subunit ε’’ + transcription antitermination protein – Pyrococcus furiosus
    • 3qqc - PfRNAP subunits β,ε’’ + transcription antitermination protein
    • 1ryq - PfRNAP subunit ε’’
    • 3lpe - MjRNAP subunit ε’’ + transcription antitermination protein – Methanocaldococcus jannaschii
    • 1go3 – MjRNAP subunit RPB4, RPB7
    • 3aoh, 3aoi - TtRNAP subunits α,β,β’,ω + DNA +RNA + GFH1 – Thermus thermophilus
    • 2o5i, 2o5j, 4gzy, 4gzz - TtRNAP subunits α,β,β’,ω + DNA +RNA
    • 1iw7, 1smy - TtRNAP subunits α,β,β’,ω
    • 1zyr, 2a68, 2a69, 2a6e, 2a6h - TtRNAP subunits α,β,β’,ω + antibiotic
    • 2ppb - TtRNAP subunits α,β,β’,ω + antibiotic + DNA + RNA + substrate analog
    • 2be5 - TtRNAP subunits α,β,β’,ω + σ factor + inhibitor
    • 2cw0 - TtRNAP subunits α,β,β’,ω + σ factor
    • 4g7h, 4g7o, 4g7z - TtRNAP subunits α,β,β’,ω + σ factor + DNA
    • 3dxj, 3eql - TtRNAP subunits α,β,β’,ω + σ factor + antibiotic
    • 1doq - TtRNAP subunit α
    • 3mlq - TtRNAP subunit β + transcription-repair coupling factor
    • 3lti – EcRNAP subunit β fragment – Escherichia coli
    • 4iqz - EcRNAP subunit β’
    • 2lmc - EcRNAP subunit β + RNAP inhibitor
    • 3mmp - EcRNAP subunit β + EF-TU
    • 3t72 - EcRNAP subunit β + Pho box DNA + PhoB
    • 3k4g, 1coo - EcRNAP subunit α
    • 1lb2, 3n4m - EcRNAP subunit α + DNA + CAP
    • 1xs9 - EcRNAP subunit α + DNA + MARA
    • 3n97 - EcRNAP subunit α C terminal + DNA + σ factor
    • 1bdf - EcRNAP subunit α (mutant)
    • 3lu0 - EcRNAP subunits α,β,β’,ω – Electron diffraction
    • 4igc, 4jk1, 4jk2, 4jkr, 4kmu - EcRNAP subunits α,β,β’,ω + RNA
    • 4kn4, 4kn7 - EcRNAP subunits α,β,β’,ω + RNA + antibiotic
    • 4ljz, 4lk1 - EcRNAP subunits α,β,β’,ω + RNAP sigma factor
    • 4lk0, 4llg - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + RNAP inhibitor
    • 3iyd - EcRNAP subunits α,β,β’,ω + RNAP sigma factor + catabolite gene activator + DNA
    • 2l0i – yRNAP C-terminal + RTT103 – yeast – NMR
    • 1a1d – yRNAP subunit RPB8 – NMR
    • 4a3g, 4a93, 4a3b, 4a3c, 4a3d, 4a3e, 4a3f, 4a3j, 4a3k, 4a3l, 4a3m – yRNAP II + RNA + DNA
    • 4bxx, 4bxz, 4by1, 4by7 – yRNAP II + RNA + DNA + transcription factor Bye1
    • 4c2m, 4c3h, 4c3i, 4c3j – yRNAP
    • 4a3i – yRNAP II + DNA
    • 2krc - BsRNAP subunit δ N-terminal – Bacillus subtilis – NMR
    • 3ihq, 1z3e, 3gfk - BsRNAP subunit α +regulatory protein SPX
    • 2ly7 - BsRNAP subunit β − NMR
    • 2m4k - BsRNAP subunit δ − NMR
    • 2max - HpRNAP subunit α − Helicobacter pylori - NMR
    • 1qyp – RNAP II C terminal – Thermococcus celer – NMR
    • 3ef0, 3ef1 - SpRNAP II subunit α C terminal – Schizosaccharomyces pombe
    • 3h0g – SpRNAP II
    • 3ayh - SpRNAP III subunit Rpc8+Rpc9
    • 4kbj – RNAP β subunit – Mycobacterium tuberculosis
    • 4noi – RNAP α subunit – Campylobacter jejuni
  • Eukaryotic DNA-dependent RNA polymerase
  • Prokaryotic DNA-dependent RNA polymerase
    • 1hqm – TaRNAP subunits α,β,β’,ω − Thermus aquaticus
    • 2gho - TaRNAP subunits α,β,β’
    • 1i6v, 1ynj, 1ynn - TaRNAP subunits α,β,β’,ω + antibiotic
    • 1l9u - TaRNAP subunits α,β,β’,ω + σ factor
    • 1l9z - TaRNAP subunits α,β,β’,ω + σ factor + DNA
    • 2auj, 2auk - TaRNAP subunit β’
    • 1xpp – RNAP subunit L – Thermoplasma acidophilum
    • 2jzb – RNAP subunit α + NUSA transcription elongation factor – Yersinia pseudotuberculosis
    • 2waq, 2wb1, 4ayb, 2y0s – SsRNAP - Sulfolobus shibata
    • 4b1o – SsRNAP + DNA
    • 3e7h – RNAP subunit β – Vibrio cholerae
  • RNA-dependent RNA polymerase
  • Influenza virus RNA polymerase (Polymerase acidic protein - PAP)
    • 3hw3, 3hw4, 3hw5 - IvRNAP subunit P2 (mutant) + Mn + nucleotide – Influenza virus
    • 3hw6 - IvRNAP subunit P2 (mutant) + Mn
    • [[3cm8 - IvPAP subunit P2 + RNA-directed RNA polymerase subunit P2 peptide
    • 4e5e - IvPAP residues 1-50, 73-196 + Mn
    • 4e5f, 4e5g, 4e5h, 4e5i, 4e5j, 4e5l - IvPAP residues 1-50, 73-196 + Mn + inhibitor
    • 2znl - IvRNAP subunit P1 + PAP subunit P2
    • 2ztt, 3a1g - IvRNAP subunit P1 + PAP N terminal
    • 2w69 - IvRNAP subunit PA
    • 4iuj - IvRNAP subunit P2
    • 2gmo, 3cw4 - IvRNAP subunit P3
    • 2vqz - IvRNAP subunit P3 CAP-binding domain
    • 2vy6 - IvRNAP subunit P3 627- and NLS domains
    • 2vy7 - IvRNAP subunit P3 627-domain
    • 2vy8 - IvRNAP subunit P3 627-domain (mutant)
  • DNA primase
    • 4lik - hDNAP small subunit
    • 4lil - hDNAP small subunit + UTP
    • 3q36 – hDNAP large subunit
    • 4bpu - hDNAP small (mutant) + large subunit
    • 4bpw - hDNAP small (mutant) + large subunit + UTP
    • 4bpx - hDNAP small (mutant) + DNA polymerase α subunit
    • 4ehs – HpDNAP C terminal
    • 4lim - yDNAP small subunit
    • 3lgb - yDNAP large subunit
    • 3m1m – DNAP RNA polymerase domain – Sulfolobus islandicus
    • 1zt2, 2pa8, 2pmz, 3hkz - DNAP small + large subunit – Sulfolobus solfataricus
    • 2au3 – DNAP zinc-binding and RNA polymerase domains – Aquifex aeolicus
    • 1v33 - PhDNAP small subunit – Pyrocuccus horikoshii
    • 1v34 - PhDNAP small subunit + nucleotide
    • 1g71 - PfDNAP small subunit
    • 1q57 – T7DNAP/helicase (mutant) – Enterobacteria phage T7
    • 1nui – T7DNAP/helicase primase fragment (mutant)
    • 1cr0 - T7DNAP/helicase helicase domain
    • 1cr1, 1cr2, 1cr4 - T7DNAP/helicase helicase domain + nucleotide
    • 4e2k – SaDNAP – Staphylococcus aureus
    • 2lzn – SaDNAP C terminal – NMR
    • 4edg, 4edk, 4edr, 4edt, 4edv, 4ee1 – SaDNAP + nucleotide
  • Bacterial primase
    • 2r6a, 2r6c - GsdnaG helicase binding domain + helicase – Geobacillus stearothermophilus
    • 4m4w - GsdnaG helicase binding domain + helicase + DnaI
    • 1d0q - GsDNAP zinc-binding domain
    • 1z8s - GsdnaG dnaB binding domain - NMR
    • 2haj - EcdnaG catalytic domain - NMR
    • 3b39 – EcdnaG catalytic domain + DNA
    • 1t3w – EcdnaG C-terminal
    • 1eqn, 1dd9, 1dde – EcdnaG catalytic core
  • RNA polymerase from Bacteriophage T7
  • Poly(A) RNA polymerase

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Proteopedia Page Contributors and Editors (what is this?)

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

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