Primary Citation PubMed: 12000971
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Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases.
(2003) BMC Struct Biol 3
PubMed: 12553882 | PubMedCentral: PMC151600 | DOI: null
A search of the PDB database using the DALI program [ 61 ], with this β-barrel from Thermus thermophilus β' subunit submitted as a query (pdb: 1iw7, chain D region: 625–749), r... trieved the N-terminal domain of the CDC48-like AAA ATPases, formate dehydrogenases, aspartate decarboxylases and Barwin.
One of these corresponds to the catalytic, metal-coordinating domain, containing the DbDGD motif, in the β' subunit (residues: 626–750 of pdb id:1iw7 chain D), whereas the other one corresponds to the conserved core domain of the β subunit (residues:673–994 of pdb id: 1iw7 chain C).
Publication Year: 2003
Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
(2007) Nucleic Acids Res 35
PubMed: 17179178 | PubMedCentral: PMC1802627 | DOI: 10.1093/nar/gkl686
( B ) Spatial organization of the corresponding bacterial domain, based on the PDB crystallographic coordinates 1IW7 (47).
( C ) Equivalent view of the Thermus thermophilus holoenzyme, based on the PDB crystallographic coordinates 1IW7 ( 47 ).
Publication Year: 2007
Organization of an activator-bound RNA polymerase holoenzyme.
(2008) Mol Cell 32
PubMed: 18995832 | PubMedCentral: PMC2680985 | DOI: 10.1016/j.molcel.2008.09.015
The crystal structure of the RNAP core from the RNAP-σ A holoenzyme structure (Protein Data Bank [PDB] ID code 1IW7) was fitted into the reconstruction using manual docking followed by automat... d refinement procedures ( Wriggers et al., 1999 ) with an overall correlation coefficient of ∼0.7 ( Figures 1 C–1E).
In order to compare with the RNAP-σ A holoenzyme, the Tth RNAP-σ A (PDB ID code 1IW7) was fitted into the RNAP-σ 54 holoenzyme reconstruction.
Tth PDB ID code, 1IW7.
Publication Year: 2008
Bridge helix and trigger loop perturbations generate superactive RNA polymerases.
(2008) J Biol 7
PubMed: 19055851 | PubMedCentral: PMC2776397 | DOI: 10.1186/jbiol98
(a) Model of the T. thermophilus bridge helix kink (PDB 1IW7 ).
(b) Spatial relationship of the trigger loop base helices with the bridge helix in the kinked (PDB 1IW7 ) and straight (PDB 2O5J ) versions of T. thermophilus RNAP.
A bridge to transcription by RNA polymerase.
PubMed: 19090964 | PubMedCentral: PMC2776398 | DOI: 10.1186/jbiol99
BH from Tth RNAP holoenzyme without nucleic acids [PDB: 1iw7 ] (cyan) [ 8 ].
Structural and biochemical bases for the redox sensitivity of Mycobacterium tuberculosis RslA.
(2010) J Mol Biol 397
PubMed: 20184899 | PubMedCentral: PMC2877774 | DOI: 10.1016/j.jmb.2010.02.026
Modeling of the σ 4 L /RslA complex on RNAP (PDB ID 1IW7 ) also suggested steric clashes of RslA with the β flap–tip–helix of RNAP 21,22 ( Supplementary Fig. 3a and b )...
20 (b) Docking of the σ 4 L /RslA complex onto Thermus thermophilus holo-RNAP (PDB ID 1IW7 ).
Publication Year: 2010
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
(2010) PLoS Biol 8
PubMed: 20856905 | PubMedCentral: PMC2939025 | DOI: 10.1371/journal.pbio.1000483
Molecular Model of the Complete Eco Core RNAP In order to interpret the spEM map of Eco core RNAP, we generated a homology model of Eco core RNAP using the core component of the T. thermophilus ( Tth ... RNAP holoenzyme structure (PDB ID 1IW7)  as a template.
Transcriptional control in the prereplicative phase of T4 development.
(2010) Virol J 7
PubMed: 21029433 | PubMedCentral: PMC2988021 | DOI: 10.1186/1743-422X-7-289
C) Structures showing the interaction of T. thermophilus σ H5 with the β-flap tip [ 22 ] (left, accession # 1IW7) and the structure of MotA NTD [ 94 ] (right, accession # 1I1S) are sho... n.
The bridge helix coordinates movements of modules in RNA polymerase.
(2010) BMC Biol 8
PubMed: 21114873 | PubMedCentral: PMC2993669 | DOI: 10.1186/1741-7007-8-141
The looped-out bridge helix indicating the conformation in a nucleic-acid-free structure is from T. thermophilus RNA polymerase bound by σ A initiation factor (PDB 1iw7 ).
Accommodation of profound sequence differences at the interfaces of eubacterial RNA polymerase multi-protein assembly.
(2012) Bioinformation 8
PubMed: 22359428 | PubMedCentral: PMC3282269 | DOI: null
Remarkably, prokaryotic ( Thermus thermophilus (PDB: 1IW7), Thermus aquaticus (PDB: 1HQM)) and eukaryotic ( Saccharomyces cerevisiae (PDB: 2E2I)) holo enzyme structures exhibit high degree of structur... l similarity, although their sequence similarity is low [ 8 ].
Next, the interface residues for the various subunits, extracted from the RNA polymerase holoenzyme complex of Thermus thermophilus (PDB ID: 1IW7), were mapped on to the sequences to get an idea of the extent of participation of every sequence domain in interface formation.
The RNA polymerase holoenzyme complex of Thermus thermophilus (PDB: 1IW7) solved at 2.6 Å was used as the template structure.
Figure 2 Insertions and deletions in the subunits of a) Helicobacter pylori b) Onion yellows phytoplasma and c) Mycoplasma pulmonis mapped onto the crystal structure of the macro-molecular assembly of RNA polymerase from Thermus thermophilus (PDB:1IW7).
Similarity is assessed using (a) %Total surface area involved in interface formation (b) Interface score for all pairwise interfaces in template (1IW7) and modeled structures.
Publication Year: 2012
Indirect read-out of the promoter DNA by RNA polymerase in the closed complex.
(2013) Nucleic Acids Res 41
PubMed: 23118489 | PubMedCentral: PMC3592454 | DOI: 10.1093/nar/gks1018
The homology model was built for residues 359–613 using RNA polymerase holoenzyme of T hermus thermophilus (PDB id: 1IW7) ( 12 ) as template, using Insight II (Accelrys Inc., San Diego, CA, US... ).
Publication Year: 2013
Computational simulation strategies for analysis of multisubunit RNA polymerases.
(2013) Chem Rev 113
PubMed: 23987500 | PubMedCentral: PMC3829680 | DOI: 10.1021/cr400046x
Table 1 Structures of RNAPs Used in Computational Simulations PDB ID resolution (Å) organism a protein nucleic acid nucleotide state TL b simulations c refs 1I6H 3.30 Sc 10 subunits T/R ... 0; pretranslocation open NMA (ENM) ( 13a ) 1I50 2.80 Sc 10 subunits open NMA (ENM) ( 13a ) 1HQM 3.30 Ta α 2 ββ′ω open NMA (ENM) ( 13a ) 1ARO 2.80 T7 T/N NMA (ENM) ( 13 ) 1CEZ 2.40 T7 NMA (ENM) ( 13 ) 1I6H 3.30 Sc 10 subunits T/N/R preinsertion open restricted MD ( 19 ) 1IW7 2.6 Tt α 2 ββ′ωσ initiation open BNM ( 15 ) 1R9T 3.5 Sc 10 subunits T/N/R ATP (E site) posttranslocation open BD ( 9 ) 1H38 2.9 T7 T/N/R preinsertion MD and umbrella sampling ( 22 ) 1S77 2.69 T7 T/N/R PP i pretranslocation MD and umbrella sampling ( 22 ) 2E2H 3.95 Sc 10 subunits T/N/R GTP posttranslocation closed MD, MSM,QM ( 7a , 16 , 17 , 21 , 29 ) 2E2J 3.5 Sc 10 subunits T/N/R GMPCPP posttranslocation open MD, MSM,QM ( 7a , 16 ) 2O5J 3.0 Tt α 2 ββ′ω T/N/R ATP posttranslocation closed MD ( 18 ) 2PPB 3.0 Tt α 2 ββ′ω T/N/R AMPCPP preinsertion open MD ( 18a , 18b ) 2NVZ 4.3 Sc 10 subunits T/N/R UTP posttranslocation closed QM ( 62 , 73 ) a Sc, Saccharomyces cerevisiae ; Ta, Thermus aquaticus ; T7, Enterobacteria phage T7; Tt, Thermus thermophilus .
Transcription inhibition by the depsipeptide antibiotic salinamide A.
(2014) Elife 3
PubMed: 24843001 | PubMedCentral: PMC4029172 | DOI: 10.7554/eLife.02451
Structure of bacterial RNAP (gray ribbons; black circle for active-center region; violet sphere for active-center Mg 2+ ; β' non-conserved region and σ omitted for clarity; PDB 1IW7), ... howing the sites of Sal-resistant substitutions (green surface; sequences from Figure 2C ; ‘Sal target’).
( B ) Superimposition of bridge helices of E. coli RNAP-Sal (black), E. coli RNAP (green; unbent BH-H N and BH-H C ), T. thermophilus RNAP (cyan; PDB 1IW7), T. thermophilus RPo (yellow; PDB 4G7H), T. thermophilus transcription elongation complex (pink; PDB 2O5J), and paused T. thermophilus transcription elongation complex (violet; PDB 4GZY).
Vassylyev DG , Sekine S , Laptenko O , Lee J , Vassylyeva MN , Borukhov S , Yokoyama S , 2002 , Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution , http://www.pdb.org/pdb/explore/explore.do?structureId=1iw7 , Publicly available at RCSB Protein Data Bank.
Publication Year: 2014
Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining.
(2014) IUCrJ 1
PubMed: 25075337 | PubMedCentral: PMC4086436 | DOI: 10.1107/S2052252514005442
In four structures of RNA polymerase [PDB entries 1iw7 (Vassylyev et al. , 2002 ▶ ), 1smy (Artsimovitch et al. , 2004 ▶ ), 2a68 and 2a69 (Artsimovitch et al. , 2005 ▶ )] there ... re 485, 362, 562 and 487 magnesium ions, respectively.
PubMed ID is not available.
Published in 2015
thermophilus (pdb: 1IW7), with the residues homologous to N45 in B .
Publication Year: 2015
Structures of the holoenzyme containing the group I σ factor σ A (also known as SigA), isolated from T. aquaticus and T. thermophilus , showed that three σ domains (σ d... mains 2, 3, and 4) arranged on the surface of the core enzyme whose function was to recognize the −35 and−10 elements (separated by ~17 bp DNA) (PDB: 1L9U, 1IW7) [ 32 , 33 ] ( Table 1 ).
Structure PDB code Reference Source Subunit and domain α subunit NTD 1BDF X [ 7 ] A α subunit NTD 4NOI X none F α subunit CTD 1COO N , 3K4G X [ 5 , 8 ] A α subunit CTD 1DOQ N [ 9 ] B α subunit CTD 2MAX N [ 10 ] E β subunit 2/i4 domains 3LTI X [ 11 ] A β subunit flap domain 2LY7 N none C β subunit 1/2 domains 4KBJ X [ 12 ] I β' subunit i2 domain 2AUJ X [ 13 ] B β' subunit i6 domain 2AUK X , 4IQZ X [ 13 ] A σ region 1.1 2K6X N [ 14 ] G, a σ 70 domain2 1SIG X [ 15 ] A, a σ A domains2 and 3 1KU2 X [ 16 ] B, a σ A domain4 1KU3 X [ 16 ] B, a σ A domain4–DNA (−35 element) 1KU7 X [ 16 ] B, a σ A domain4 1TTY N [ 17 ] G, a σ A domain2–DNA (−10 element) 3UGO X , 3UGP X [ 18 ] B, a σ A domain4–αCTD–DNA 3N97 X none B, a, A σ N RpoN–DNA (−24 element) 2O8K N , 2O9L N [ 19 ] D, d σ N core binding domain 2K9M N [ 20 ] D, d σ N RpoN domain 2AHQ N [ 21 ] D, d σ E domain4–DNA (−35 element) 2H27 X [ 22 ] A, c σ C domain2 2O7G X [ 23 ] I, c σ C domain4 2O8X X [ 23 ] I, c σ D domain4 3VFZ X [ 24 ] I, c δ subunit NTD 2KRC N , 4NC7 X , 4NC8 X , 2M4K N , 2KRC N [ 25 , 26 , 27 ] C ε subunit 4NJC X [ 28 ] C RNAP Core enzyme 1HQM X [ 29 , 30 ] B Core enzyme (Δω subunit) 2GHO X [ 31 ] B Holoenzyme 1L9U X , 1IW7 X , 2A6E X , 2CW0 X [ 32 , 33 , 34 ] B Holoenzyme 4YG2 X , 4LJZ X , 4MEY X [ 35 , 36 , 37 ] A Holoenzyme–DNA (−41 ~ −7) 1L9Z X [ 38 ] B Holoenzyme–DNA (−12 ~ +12) 4G7H X , 4G7O X [ 39 ] B de novo initiation complex 4Q4Z X , 4OIO X [ 40 , 41 ] B Initially transcribing complex 4Q5S X [ 40 ] B Elongation complex 2O5I X , 2O5J X [ 42 , 43 ] B Paused elongation complex 4GZY X , 4GZZ X [ 44 ] B Backtracked elongation complex 4WQS X [ 45 ] B A: Escherichia coli ; B: Thermus aquatics/Thermus thermophilus ; C: Bacillus subtilis/Bacilus stearothermophilus ; D: Aquifex aeolicus ; E: Helicobacter pylori ; F: Campylobacter jejuni ; G: Thermotoga maritime ; I: Mycobacterium tuberculosis ; a: group I σ factor; c: extracytoplasmic function (ECF) σ factor; d: σ N /σ 54 factor; X : X-ray crystallography method; N : NMR method.
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