Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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 ( ).

( 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).

Publication Year: 2013

Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.

(2013) Nucleic Acids Res 41

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).

Publication Year: 2013

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 [13] ) 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 [13] ) as search model using Phaser [17] .

g006 Figure 6 Structures of the GyrB43 nucleotide binding site as determined for (a) the substrate analog complex GyrB43⋅AMPPNP (PDB entry 1EI1 [13] ) 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 [13] , Fig. 2a ), as search model.

(a) AMPPNP complex (PDB entry 1EI1 [13] ), (b) ADP⋅P i complex, (c) ADP⋅BeF 3 complex and (d) ADP complex.

(PDB code: 1EI1) [13] 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) [13] in yellow.

(PDB code: 1EI1) [13] contains a mutation (Y5S) in the N-terminal arm.

Furthermore, inter-species comparison between GyrB from E. coli (PDB code: 1EI1) [13] and Mycobacterium tuberculosis (PDB code: 3ZKB) [25] reveals a very well conserved ligand-protein interaction network ( Fig.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4388272

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