Primary Citation PubMed: 10734094
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Structural basis of gate-DNA breakage and resealing by type II topoisomerases.
(2010) PLoS One 5
PubMed: 20596531 | PubMedCentral: PMC2893164 | DOI: 10.1371/journal.pone.0011338
The diagram is built using a model of the full-length topo IV which, in turn, is based on the crystal structure of the drug-free cleavage complex of topo IV from S. pneumoniae with cleaved DNA (report... d in this paper, 3KSA, covering the N-terminal domain of ParC, C-terminal domain of ParE and bound/cleaved G-segment) as well as the crystal structures of the C-terminal domain of GyrA from B. burgdorferi (1SUU) 1 (for C-terminal domain of ParC) and the N-terminal domain of GyrB from E. coli (1EI1) (for N-terminal domain of ParE) 2 .
Publication Year: 2010
Solution structures of DNA-bound gyrase.
(2011) Nucleic Acids Res 39
PubMed: 20870749 | PubMedCentral: PMC3025574 | DOI: 10.1093/nar/gkq799
The structures of the E. coli GyrB ATPase domain ( 12 ) (PDB ID 1EI1) (yellow) and the E. coli GyrA 33 kDa CTD ( 13 ) (PDB ID 1ZIO) (cyan) were used to model the protruding domains.
Publication Year: 2011
Novel phytochemical-antibiotic conjugates as multitarget inhibitors of Pseudomononas aeruginosa GyrB/ParE and DHFR.
(2013) Drug Des Devel Ther 7
PubMed: 23818757 | PubMedCentral: PMC3692347 | DOI: 10.2147/DDDT.S43964
Based on the template selection analysis, E. coli GyrB (PDB code: 1EI1, 2.3 Å), E. coli ParE (PDB code: 1S16, 2.1 Å) and E. coli DHFR (PDB code: 1RX3, 2.2 Å) were selected as s... itable templates with sequence identity of 74%, 75%, and 45%, respectively.
( A ) DNA Gyrase subunit B (GyrB) with template (PDB: 1EI1).
3 The RMSD values were obtained by structural superimposition of all the GyrB/ParE and DHFR homology models from both SWISS-MODEL and MODELLER with their respective E. coli templates (1EI1, 1S16, and 1RX3) using SUPERPOSE 4 web server ( http://wishart.biology.ualberta.ca/SuperPose/ ).
( A ) GyrB model (blue) and template structure E. coli (1EI1, red) bound with ADPNP (yellow stick model).
Publication Year: 2013
Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase.
(2013) Nucleic Acids Res 41
PubMed: 23804759 | PubMedCentral: PMC3763546 | DOI: 10.1093/nar/gkt560
The crystal structures of the ATPase (PDB:1EI1) and DNA binding–cleavage domain in presence of ciprofloxacin (PDB:2XCT) were fitted in the core enzyme map.
The crystal structures of the ATPase domain (PDB:1EI1) and DNA binding–cleavage domain (PDB: 3NUH) deleted from the E. coli GyrB specific insertion domain [560–735] were fitted in the cryo-EM map (gray surface).
Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.
PubMed: 23965305 | PubMedCentral: PMC3834822 | DOI: 10.1093/nar/gkt749
Structure determination Structures were solved by molecular replacement in Phaser ( 35 , 37 ) using as search models our ParC55/ParE30/18mer DNA+levofloxacin structure (PDB ID: 3RAE) as a starting mod... l and a ParE ATP domain homology modelled in 3D-JigSaw ( 38 ) on the basis of the structure of the ATPase domain of the E. coli gyrase (PDB ID: 1EI1) ( 39 ).
Next, the T-segment approaches (perhaps pre-coordinated by the ‘Towers’ and the long α-helices of the ATPase domains) and undergoes transient capture by upward ∼90° rotation of t he ATPase domains around the pivoting points, which shifts them closer by a few Ångstroms [in accordance with conformation of the ADPNP-stabilized GyrB NTD dimer from E. coli gyrase, PDB code: 1EI1, which was used to model the closed ATPase domains with ATP bound ( 39 )] (stage 4).
Structure of the N-terminal Gyrase B fragment in complex with ADP?Pi reveals rigid-body motion induced by ATP hydrolysis.
(2014) PLoS One 9
PubMed: 25202966 | PubMedCentral: PMC4159350 | DOI: 10.1371/journal.pone.0107289
Movie S1 Morphing between the GyrB43⋅AMPPNP complex (PDB entry 1EI1  ) and the post-hydrolysis complex GyrB43⋅ADP⋅P i , shown in cartoon representation with semi-transparen... molecular surface overlaid with the same colors as in Fig. 2 (AMPPNP state in yellow and ADP⋅P i state in magenta).
GyrB43 structures were solved by molecular replacement using the previously published structure of the 43-kDa N-terminal fragment of GyrB (PDB entry 1EI1  ) as search model using Phaser  .
g006 Figure 6 Structures of the GyrB43 nucleotide binding site as determined for (a) the substrate analog complex GyrB43⋅AMPPNP (PDB entry 1EI1  ) and (b) the post-hydrolysis complex GyrB43⋅ADP⋅P i with Fo-Fc omit map shown at a contour level of 3.0 σ.
The structure was solved by molecular replacement using the structure of GyrB43 ( E. coli ) in complex with AMPPNP that had been determined in a different space-group previously (PDB entry 1EI1  , Fig. 2a ), as search model.
(a) AMPPNP complex (PDB entry 1EI1  ), (b) ADP⋅P i complex, (c) ADP⋅BeF 3 complex and (d) ADP complex.
(PDB code: 1EI1)  in yellow.
Both structures ( Figs. 2c, d ) were solved by molecular replacement using the same search model (PDB entry 1EI1) as for the aforementioned structure of the GyrB43⋅ADP⋅P i complex.
(b) Superimposition of M. tuberculosis GyrB⋅AMPPNP in blue-green onto our reference structure E. coli GyrB43⋅AMPPNP (PDB code: 1EI1)  in yellow.
(PDB code: 1EI1)  contains a mutation (Y5S) in the N-terminal arm.
Furthermore, inter-species comparison between GyrB from E. coli (PDB code: 1EI1)  and Mycobacterium tuberculosis (PDB code: 3ZKB)  reveals a very well conserved ligand-protein interaction network ( Fig.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
One monomer (together with its associated ADPNP and magnesium ion) was taken from the deposited structure of E. coli GyrB43 (PDB entry 1ei1 ; Brino et al. , 2000 ▶ ) and used as the search tem... late in MOLREP (Vagin & Teplyakov, 2010 ▶ ), which correctly placed one copy of this in the asymmetric unit to give a recognisable GyrB43 homodimer after application of the appropriate twofold crystallographic symmetry operator.
Table 3 Summary of selected homologous PDB entries described in this study Protein Source PDB code Resolution () Aligned residues † R.m.s. deviation † () Identity † (%) Site 1 occupancy Reference GyrB43 E. coli 4pu9 2.40 353 0.69 99.7 Water Stanger et al. (2014 ▶ ) GyrB43 E. coli 1ei1 2.30 383 0.52 99.5 Water Brino et al. (2000 ▶ ) ParE E. coli 1s16 2.10 354 1.37 36.2 Mg 2+ ‡ Bellon et al. (2004 ▶ ) Topo II S. cerevisiae 1pvg 1.80 302 2.04 24.8 N of Lys Classen et al. (2003 ▶ ) Topo II H. sapiens 1zxn 2.51 281 1.97 22.1 N of Lys Wei et al. (2005 ▶ ) MutL E. coli 1nhi 2.00 270 3.18 15.9 K + Hu et al. (2003 ▶ ) Topo VIB S. shibatae 1mx0 2.30 235 2.28 15.7 N of Lys Corbett Berger (2003 ▶ ) BCK R. norvegicus 1gkz 2.20 107 1.95 21.5 K + Machius et al. (2001 ▶ ) † Values determined using the Secondary Structure Matching ( SSM ) algorithm within Coot (Emsley Cowtan, 2004 ▶ ) to superpose structures on the K-only GyrB43 model.
In the structure determined by Brino and coworkers (PDB entry 1ei1 ; Brino et al. , 2000 ▶ ), the equivalent site is occupied by a sulfate ion.
Publication Year: 2015
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