Citations in PubMed

Primary Citation PubMed: 9278055 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target.

(2007) PLoS One 2

PubMed: 17375187 | PubMedCentral: PMC1810434 | DOI: 10.1371/journal.pone.0000301

GRASP2 [51] , [52] electrostatic surface potentials within the DNA-binding grooves calculated for DNA-binding domains of topoisomerases IIA from different organisms usi... g models generated by 3D-JIGSAW [41] – [43] on the base of the known structure of E. coli GyrA (1AB4).

(C) Structure of the N-terminal fragment (GyrA59) of E. coli GyrA [19] (1AB4).

Publication Year: 2007

Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62

PubMed: 17077506 | PubMedCentral: PMC2225206 | DOI: 10.1107/S1744309106044150

Preliminary attempts at molecular replacement into the pseudo-cell using AMoRe (Navaza, 1994 ▶ ) were performed using the complete model of the 59 kDa fragment of DNA gyrase from E. co... i (PDB code 1ab4 ; Morais Cabral et al. , 1997 ▶ ).

Topoisomerase IV has been shown to be the primary target for quinolones in Gram-positive species (Oliphant & Green, 2002 ▶ ), but currently structural information is only available for the DNA-cleavage domains of topoisomerases from eukaryotic (PDB code 1bgw ; Berger et al. , 1996 ▶ ) and Gram-negative bacterial species (PDB codes 1ab4 and 1zvu ; Morais-Cabral et al. , 1997 ▶ ; Corbett et al. , 2005 ▶ ).

Publication Year: 2006

Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase.

(2010) PLoS One 5

PubMed: 20805881 | PubMedCentral: PMC2923608 | DOI: 10.1371/journal.pone.0012245

The structure of GA57BK was determined by molecular replacement with AMoRe [46] implemented in CCP4 [47] using the breakage-reunion domain of the DNA gyrase from E. col... [36] (pdb accession code 1AB4) as a search model.

The sequence names are as follows: MtGyr (PDB code 3IFZ) (this work), M. tuberculosis DNA gyrase; EcGyr (PDB code 1AB4) (36), E. coli DNA gyrase; SaTopIV (PDB code 2INR) (34), S. aureus topoisomerase IV; SpTopIV (PDB code 2NOV) (33), S. pneumoniae topoisomerase IV; EcTopIV (PDB code 1ZVU), E. coli topoisomerase IV and ScTopII (PDB code 2RGR) (29), S. cerevisiae topoisomerase II.

The PDB codes for the five structures are given: 3IFZ (this work) and 3ILW (25) correspond to M. tuberculosis DNA gyrase, 1AB4 (36) to E. coli DNA gyrase, 2INR (34) to S. aureus topoisomerase IV, 2NOV (33) to S. pneumoniae topoisomerase IV.

M. tuberculosis DNA gyrase GA57BK (3IFZ) (this work) in light green, M. tuberculosis DNA gyrase MtGyrA59 (3ILW, 25) in pale green, E. coli DNA gyrase (1AB4) (36) in dark green, S. pneumoniae topoisomerase IV (2NOV) (33) in red, S. aureus topoisomerase IV (2INR) (34) in pale red, S. pneumoniae complexed with DNA (3FOF) (26) in dark red and E. coli topoisomerase IV (1ZVU) in firebrick.

Publication Year: 2010

A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function.

(2010) Nucleic Acids Res 38

PubMed: 20675723 | PubMedCentral: PMC2995079 | DOI: 10.1093/nar/gkq665

A MR solution was obtained using the structure of the E. coli GyrA N-terminal domain (PDBID 1AB4) as a search model ( 41 ).

Publication Year: 2010

Vibrio cholerae ParE2 poisons DNA gyrase via a mechanism distinct from other gyrase inhibitors.

(2010) J Biol Chem 285

PubMed: 20952390 | PubMedCentral: PMC3001019 | DOI: 10.1074/jbc.M110.138776

In B , the mutations listed in A were mapped onto the crystal structure of E. coli GyrA59 colored in green (PDB entry 1AB4 ( 52 ).

Publication Year: 2010

Structural insights into quinolone antibiotic resistance mediated by pentapeptide repeat proteins: conserved surface loops direct the activity of a Qnr protein from a gram-negative bacterium.

(2011) Nucleic Acids Res 39

PubMed: 21227918 | PubMedCentral: PMC3089455 | DOI: 10.1093/nar/gkq1296

Modelling of the AhQnr:DNA gyrase complex A partial model of E. coli DNA gyrase was constructed by combining the crystal structure of the E. coli GyrA 59 kDa fragment [PDB accession 1AB4; ( 44... )] and an homology model of the E. coli TOPRIM domain.

Publication Year: 2011

Guiding strand passage: DNA-induced movement of the gyrase C-terminal domains defines an early step in the supercoiling cycle.

(2011) Nucleic Acids Res 39

PubMed: 21880594 | PubMedCentral: PMC3239214 | DOI: 10.1093/nar/gkr680

The distance between the C-terminal residues of the GyrA body is >9 nm [PDB-ID 1AB4 ( 17 )], suggesting that FRET between dyes on different CTDs would be inefficient.

The models for GyrA alone and in the gyrase/DNA complex were obtained by manually placing the structure of the GyrA body [homology model for B. subtilis GyrA, created using SWISS-model ( 25 ) and the structure of E. coli GyrA ( 26 ), PDB-ID 1AB4, as a template] and the CTDs [homology model for B. subtilis GyrA, created using the structure of E. coli GyrA ( 10 ), PDB-ID 1ZI0, as a template], such that the experimentally determined inter-dye distances were fulfilled.

Publication Year: 2011

The structural modeling of the interaction between levofloxacin and the Mycobacterium tuberculosis gyrase catalytic site sheds light on the mechanisms of fluoroquinolones resistant tuberculosis in Colombian clinical isolates.

(2014) Biomed Res Int 2014

PubMed: 24877086 | PubMedCentral: PMC4022255 | DOI: 10.1155/2014/367268

A comparison was carried out using the E. coli DNA gyrase sequence (PDB access number 1AB4) and visualized with DeepView/Swiss-PdbViewer v3.7 ( ).

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4427296

The homologous structure of Escherichia coli GyrA (PDB: 1AB4) [ 35 ] with a sequence identity of 93% served as a suitable template for model generation.

Publication Year: 2015