Primary Citation PubMed: 20596531
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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
Atomic coordinates and structure factors have been deposited in the Protein Data Bank under accession numbers 3LTN (complex with PD 0305970), 3K9F (complex with levofloxacin), 3KSA (drug-free cleaved ... omplex) and 3KSB (drug-free resealed complex).
Publication Year: 2010
Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase.
PubMed: 20805881 | PubMedCentral: PMC2923608 | DOI: 10.1371/journal.pone.0012245
The two disordered regions of the TopBK structure were modeled using the Toprim domain of 3K9F as a template.
The first picture of the enzyme-quinolone interactions was given by the low resolution structures of Streptococcus pneumoniae ParC breakage-reunion and ParE Toprim domain in complex with DNA and quinolones (PDB codes 3FOF and 3K9F,  ).
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
The latter was generated by fitting the E. coli TOPRIM sequence (GyrB residues 406–453, 622–638 and 728–799; i.e. removing the insertion region) onto the equivalent portion of ... treptococcus pneumoniae DNA topisomerase IV [( 5 ); PDB accession 3K9F chain C] using Swiss-PdbViewer ( 45 ) and SwissModel [( 46 ); http://swissmodel.expasy.org/ ].
Publication Year: 2011
New insights into fluoroquinolone resistance in Mycobacterium tuberculosis: functional genetic analysis of gyrA and gyrB mutations.
(2012) PLoS One 7
PubMed: 22761889 | PubMedCentral: PMC3386181 | DOI: 10.1371/journal.pone.0039754
The model was built based on the crystal structure of the complex of Streptococcus pneumoniae (PDB ID: 3K9F) as described in Materials and Methods.
Structural Modeling of the M. tuberculosis Gyrase-DNA-quinolone Complex Crystal structures of the N-terminal domain of M. tuberculosis GyrA (PDB ID: 3IFZ)  and the C-terminal domain of M. tuberculosis GyrB (PDB ID: 3M4I)  were superimposed onto the respective highly homologous regions in the crystal structure of the complex of Streptococcus pneumoniae gyrase with a DNA substrate and levofloxacin (PDB ID: 3K9F)  by using the SSM superposition tool in Coot  .
Publication Year: 2012
PubMed ID is not available.
Published in 2015
However, Mg 2+ ion was not observed in topo IV of Streptococcus pneumoniae [PDB: 3K9F] where the carboxylate group of levofloxacin was within hydrogen bonded distance with Ser residue.
Similarly corresponding Ser residue of topo IV has been seen to lie in close vicinity to carboxylate moiety of levofloxacin and moxifloxacin as observed in Streptococcus pneumoniae and Acinetobacter baumannii [PDB: 3K9F & 2XKK].
The co-ordinates of ciprofloxacin (PDB: 2XCT), levofloxacin (PDB: 3K9F), dextrofloxacin (PDB: 2BML) and moxifloxacin (PDB: 3FOF) were obtained from the crystal structures of their respective complexes.
Furthermore, the available crystal structures of quinolones complexed with DNA Gyrase from S. aureus (PDB: 2XCT) and topo IV (PDB: 3K9F, 3RAD, 3RAE & 2XKK) were also examined for the hydrogen bonded interaction pattern between Ser and quinolones.
Publication Year: 2015
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