RNA polymerase

From Proteopedia

Revision as of 10:43, 9 October 2013

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

• Molecular Playground/T7 RNAP Conformations
  
• User:Luis E Ramirez-Tapia/T7 RNA polymerase
  
• Molecular Playground/T7 RNA Polymerase (7 mer int).
  

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

• NS5B.
  

For DNA-dependent RNA polymerase see

• Molecular Playground/Human mtRNA pol.
  

For the Thermus thermophilus β' subunit see

• Beta-Prime Subunit of Bacterial RNA Polymerase
  

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

• User:Michael Strong/H1N1/PB2
  
• User:Michael Strong/H1N1/PB2/MSA
  
• User:Michael Strong/H1N1/PA
  
• User:Michael Strong/H1N1/PA/MSA

3D Structures of RNA polymerase

Update February 2013

DNA-dependent RNAP

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 - 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
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
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 – yRNAP II + RNA + DNA
4a3i – yRNAP II + DNA
2krc - BsRNAP subunit δ N-terminal – Bacillus subtilis – NMR
3ihq, 1z3e, 3gfk - BsRNAP subunit α +regulatory protein SPX
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

Eukaryotic DNA-dependent RNAP

3o2q, 3o2s – hRNAP II subunit α C-terminal + symplekin – human
1qkl - hRNAP II subunit RPB6
3j0k – hRNAP II + TFIIF – Cryo EM
2c35 - hRNAP II subunits RPB4 RPB7 (mutant) – NMR
2f3i - hRNAP II subunits RPB8 RPB17 RPABC3 – NMR
2ghq, 2ght - hRNAP II subunits RPB1 + hRNAP II C terminal
2q5e, 3l0b, 3l0c - hRNAP II C terminal
3pgl - hRNAP II C terminal + inhibitor
2xub, 2xv4 - hRNAP III subunits RPC3
2dk8 – RNAP III RPC34 domain - mouse – NMR
2dk5 – hRNAP III winged helix domain (mutant) – NMR
2yu3 - hRNAP III winged helix domain
3spa - hRNAP + polypeptide
3nff, 3nfg, 3nfh, 3nfi – RNAP I fragments (mutant) – Candida glabrata
2rf4 - yRNAP I subunit RPA4
1i6h - yRNAP II + DNA
1nik, 1nt9, 1wcm, 2b8k, 3fki, 3qt1, 1i3q, 1i50, 1dzf – yRNAP II
1y14 - yRNAP II subunits RPB4 RPB7
1pqv, 1y1v, 4bbr, 4bbs - yRNAP II + TFIIS
1y1y - yRNAP II + TFIIS + DNA +RNA
2vum - yRNAP II + inhibitor + DNA + RNA
3cqz, 1k83 - yRNAP II + inhibitor
1r5u, 3k7a, 3k1f - yRNAP II + TFIIB
1r9s, 2ja5, 2ja6, 2ja7, 2ja8, 2nvq, 2nvt, 2nvx, 2nvy, 2nvz, 3gtg, 3gtj, 3gtk, 3gtl, 3gtm, 3gto, 3gtp, 3gtq, 3hou, 3hov, 3how, 3hox, 3hoy, 3hoz, 3po2, 3po3, 3m3y, 3m4o, 3rzd, 3rzo, 3s14, 3s15, 3s16, 3s17, 3s1m, 3s1n, 3s1q, 3s1r, 3s2d, 3s2h - yRNAP II + RNA + DNA
1y1w, 1y77, 2r7z, 2r92, 2r93, 3h3v - yRNAP II + RNA
1twa, 1twc, 1twf, 1twg, 1twh - yRNAP II + nucleotide
2b63 - yRNAP II + nucleotide + RNA
2e2i, 2e2j - yRNAP II + nucleotide + DNA
2yu9, 3i4m, 3i4n - yRNAP II + nucleotide + DNA + RNA
2ckz - yRNAP III
1ef4 – MtRNAP subunit RPB10 – Methanothermobacter thermautotrophicus
1eik - MtRNAP subunit RPB5 – NMR

Prokaryotic DNA-dependent RNAP

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 RNAP

3phu, 1khv, 1khw – HfRNAP L RNA-directed – Hemorrhagic fever virus
3phw, 2pt2, 3pt2 – HfRNAP + ubiquitin
3phx – HfRNAP + ISG15
3pse - HfRNAP + ISG15 (mutant)
2xwh, 2xxd, 2xhu, 2xhw, 3i5k, 1c2p, 1csj, 1quv, 1yuy, 1yv2, 1yvx, 1yvz, 3gsz, 4aep, 4aex – HvRNAP NS5B domain – Hepatitis virus
3vc8 - HvRNAP cytoplasmic domain C terminal
3vcb - HvRNAP cytoplasmic domain C terminal (mutant)
2xym, 2xhv, 2xi2, 4e76 - HvRNAP NS5B domain (mutant)
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 - HvRNAP NS5B domain + inhibitor
3gyn, 1os5, 3br9, 3bsa, 3bsc, 3cde, 3co9, 3cwj, 3d28, 3d5m, 3e51, 3frz, 3igv - HvRNAP NS5B domain (mutant) + inhibitor
2wrm – HvRNAP NS5B domain
2xi3 - HvRNAP NS5B domain (mutant) + nucleotide
1gx5, 1gx6 - HvRNAP NS5B domain + nucleotide
4e78, 4e7a - HvRNAP NS5B domain (mutant) + RNA
3ol6, 2jlg – PoRNAP (mutant) + RNA – Poliovirus
1rdr - PoRNAP
1tql, 2ijd, 2ijf - PoRNAP (mutant)
3ol7, 3ol8, 3ol9, 3ola, 3olb - PoRNAP (mutant) + RNA + nucleotide
2im1, 2im0, 2im2, 2im3, 2ily, 2ilz - PoRNAP (mutant) + nucleotide
2xi5, 2xi7 – RNAP L N-terminal – Bunyavirus
3jsb – RNAP (mutant) – Lymphocytic choriomengitis virus
2wk4, 2uut, 2uuw – SvRNAP (mutant) – Sapporo virus
2ckw - SvRNAP residues 1135-1649
3klv, 3kmq, 3kms, 3kna, 3nl0 – FmRNAP (mutant) + RNA – Foot-and-mouth virus
3nky - FmRNAP (mutant)
3koa - FmRNAP (mutant) + RNA + nucleotide
1wne – FmRNAP + RNA
2e9r, 2e9t, 2e9z, 2ec0 - FmRNAP + RNA + inhibitor
2d7s, 2f83 – FmRNAP + VPG protein
1hhs, 4a8o, 4b02 – P6RNAP – Bacteriophage φ-6
2jl9, 2jlf – P6RNAP (mutant)
1uvi, 1uvl, 1uvm, 1uvn, 4a8f, 4a8k, 4a8m, 4a8q, 4a8s, 4a8w, 4a8y – P6RNAP + RNA
2po4 – N4RNAP polymerase domain – Bacteriophage N4
3c2p, 3c3l, 3c46, 3q0a - N4RNAP polymerase domain + promoter DNA
1l9k – DevRNAP N terminal – Dengue virus
2j7u - DevRNAP polymerase domain
1oks – RNAP α subunit – Measles virus
1r4g - RNAP α subunit – Sendai virus – NMR
1s48, 1s49, 1s4f – DvRNAP residues 71-679 – Diarrhea virus
2cjq - DvRNAP polymerase domain
1sh0, 1sh2, 1sh3 - NvRNAP C terminal – Norwalk virus
3bsn, 3bso, 3h5x, 3h5y - NvRNAP + RNA + nucleotide
1vyi - RNAP α subunit C terminal – Rabies virus
2hcn, 2hcs, 2hfz – RNAP polymerase domain – West Nile virus
2pgg, 2pus – RNAP – Bursal disease virus
2r7o, 2r7q – SrRNAP – Simian rotavirus
4f5x – SrRNAP + Vp2 + Vp6
2yi8, 2yi9, 2yia, 2yib – RNAP – Infectious pancreatic necrosis virus
3n6l – EvRNAP – Human enterovirus
3n6m, 3n6n – EvRNAP + nucleotide
3nah, 3nai – MnvRNAP – Murine norovirus
3sfg – MnvRNAP + thio-uridine
3sfu – MnvRNAP + ribavirine
2r7r, 2r7s, 2r7t, 2r7u, 2r7v, 2r7w, 2r7x – SrRNAP + RNA
3cdu – CvRNAP + POP – Coxsakievirus
3ddk - CvRNAP
3cdw - CvRNAP + POP + VPG
3eva, 3evb, 3evc, 3evd, 3eve, 3evf, 3evg – RNAP N terminal + nucleotide – Yellow fever virus
2j7n, 2j7o – RNAP residues 381-1402 – Neurospora crassa

Influenza virus RNAP (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
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

3l9q – hDNAP large 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
4edg, 4edk, 4edr, 4edt, 4edv, 4ee1 – SaDNAP + nucleotide

Bacterial primase

2r6c – dnaG helicase binding domain + helicase – Bacillus stearothermophilus
2r6a - GsdnaG helicase binding domain + helicase – Geobacillus stearothermophilus
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

4rnp – T7RNAP
1aro – T7RNAP + T7 lysozyme
1cez, 1h38, 1qln, 2pi4, 2pi5 - T7RNAP + DNA
1msw, 1s0v, 1s76, 1s77, 3e2e, 3e3j - T7RNAP + DNA + RNA

Poly(A) RNA polymerase

3pq1 – hPAP (mutant)
3nyb – yPAP + AIR2
4e7x, 4e80, 4e8f, 4ep7, 4fh3 – fyPAP Cid1 – fission yeast
4fh5, 4fhp, 4fhv, 4fhw, 4fhy – fyPAP Cid1 + nucleotide
4fhx – fyPAP Cid1 (mutant) + nucleotide

• Created with the participation of Craig T Martin.