Primary Citation PubMed: 9278055
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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  ,  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  –  on the base of the known structure of E. coli GyrA (1AB4).
(C) Structure of the N-terminal fragment (GyrA59) of E. coli GyrA  (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  implemented in CCP4  using the breakage-reunion domain of the DNA gyrase from E. col...  (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 ).
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 ).
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.
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.
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 ( http://www.expasy.org/spdbv/ ).
Publication Year: 2014
PubMed ID is not available.
Published in 2015
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
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