The Interaction of Drugs with DNA Gyrase: A Model for the Molecular Basis of Quinolone Action

Heddle, Jonathan G.; Barnard, Faye M.; Wentzell, Lois M.; Maxwell, Anthony

doi:10.1080/15257770008033048

Cited by 81 publications

(67 citation statements)

References 62 publications

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“…This corresponds to the head dimer interface as shown by crystallization of the 59-kDa N-terminal domain of E. coli GyrA (30). The proposed region of interaction between MfpA Mt , QnrB4, and gyrase should thus include the QRDR domain of GyrA, in which residues S83 and D87 are strongly involved in the quinolone-gyrase interaction (4,16,48). We performed experiments with GyrA subunits modified at these two positions and found that the effect of MfpA Mt on gyrase catalysis was nearly abolished when the residue at position 87 in GyrA was changed, but not with substitutions at position 83.…”

Section: Discussionmentioning

confidence: 99%

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The Pentapeptide Repeat Proteins MfpA _Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

et al. 2009

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MfpA Mt and QnrB4 are two newly characterized pentapeptide repeat proteins (PRPs) that interact with DNA gyrase. The mfpA Mt gene is chromosome borne in Mycobacterium tuberculosis, while qnrB4 is plasmid borne in enterobacteria. We expressed and purified the two PRPs and compared their effects on DNA gyrase, taking into account host specificity, i.e., the effect of MfpA Mt on M. tuberculosis gyrase and the effect of QnrB4 on Escherichia coli gyrase. Whereas QnrB4 inhibited E. coli gyrase activity only at concentrations higher than 30 M, MfpA Mt inhibited all catalytic reactions of the M. tuberculosis gyrase described for this enzyme (supercoiling, cleavage, relaxation, and decatenation) with a 50% inhibitory concentration of 2 M. We showed that the D87 residue in GyrA has a major role in the MfpA Mt 6), which results in a right-handed ␤-helical structure (8, 17). The functions of the majority of the members of this large and heterogeneous family remain unknown, but three PRPs, McbG (from Escherichia coli), MfpA Mt (from Mycobacterium tuberculosis), and Qnr (from Klebsiella pneumoniae and other enterobacteria) were reported to interact with DNA gyrase, at least with the E. coli enzyme (17,33,35,44). McbG was shown to protect E. coli DNA gyrase from the toxic action of microcin B17 (33). Qnr and MfpA Mt were involved in resistance to fluoroquinolones, which are synthetic antibacterial agents prescribed worldwide for the treatment of various infectious diseases, including tuberculosis (7).DNA gyrase is an essential ATP-dependent enzyme that transiently cleaves a segment of double-stranded DNA, passes another piece of DNA through the break, and reseals it (12). DNA gyrase is unique in catalyzing the negative supercoiling of DNA in order to facilitate the progression of RNA polymerase. Most eubacteria, such as E. coli, have two type II DNA topoisomerases, i.e., DNA gyrase and topoisomerase IV, but a few, such as M. tuberculosis, harbor only DNA gyrase (11).Quinolones target type II topoisomerases, and their activity is measured by the inhibition of supercoiling by gyrase or decatenation by topoisomerase IV and stabilization of complexes composed of topoisomerase covalently linked to cleaved DNA (16). The DNA gyrase active enzyme is a GyrA 2 GyrB 2 heterotetramer. The quinolone-gyrase interaction site in gyrase is thought to be located at the so-called quinolone resistance-determining regions (QRDR) in the A subunit (amino acids 57 to 196 in GyrA) and the B subunit (amino acids 426 to 466 in GyrB), which contain the majority of mutations conferring quinolone resistance (19). The GyrB QRDR is thought to interact with the GyrA QRDR to form a drug-binding pocket (18). Resistance to quinolones is usually due to chromosomal mutations either in the structural genes encoding type II topoisomerases (QRDR) (19,22) or in regulatory genes producing decreased cell wall permeability or enhancement of efflux pumps (36). The recent emergence of plasmid-borne resistance genes, such as qnr (9,13,31,38,46), aac(6Ј)- 39) and qepA (34...

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Section: Discussionmentioning

confidence: 99%

“…Quinolones target type II topoisomerases, and their activity is measured by the inhibition of supercoiling by gyrase or decatenation by topoisomerase IV and stabilization of complexes composed of topoisomerase covalently linked to cleaved DNA (16). The DNA gyrase active enzyme is a GyrA 2 GyrB 2 heterotetramer.…”

Section: Stav][dn][lf][str][g]mentioning

confidence: 99%

The Pentapeptide Repeat Proteins MfpA _Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

et al. 2009

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“…Addition of the antibiotic norfloxacin induces lambdoid bacteriophages into the lytic life cycle (Matsushiro et al, 1999;Walterspiel et al, 1992) by activation of the RecAmediated SOS response (Heddle et al, 2000). RecA is then responsible for directing phage derepression via rapid autocleavage of the lambdoid repressor protein CI (Craig & Roberts, 1980).…”

Section: P C M Fogg and Othersmentioning

confidence: 99%

Cumulative effect of prophage burden on Shiga toxin production in Escherichia coli

et al. 2012

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“…Quinolone drugs bind to gyrase-DNA complexes, but only weakly to either gyrase or DNA (34,37,38,41,47). It is thought that quinolones bind to a pocket consisting of the QRDR of GyrA and the region of distorted DNA bound to it (17). In such a pocket, the quinolone would interact with elements of both the DNA and the enzyme.…”

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Quinolone-Binding Pocket of DNA Gyrase: Role of GyrB

Heddle

Maxwell

2002

Antimicrob Agents Chemother

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106

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DNA gyrase is a prokaryotic type II topoisomerase and a major target of quinolone antibacterials. The majority of mutations conferring resistance to quinolones arise within the quinolone resistance-determining region of GyrA close to the active site (Tyr 122 ) where DNA is bound and cleaved. However, some quinolone resistance mutations are known to exist in GyrB. Present structural data suggest that these residues lie a considerable distance from the quinolone resistance-determining region, and it is not obvious how they affect quinolone action. We have made and purified two such mutant proteins, GyrB(Asp 426 3Asn) and GyrB(Lys 447 3Glu), and characterized them in vitro. We found that the two proteins behave similarly to GyrA quinolone-resistant proteins. We showed that the mutations exert their effect by decreasing the amount of quinolone bound to a gyrase-DNA complex. We suggest that the GyrB residues form part of a quinolonebinding pocket that includes DNA and the quinolone resistance-determining region in GyrA and that large conformational changes during the catalytic cycle of the enzyme allow these regions to come into close proximity.Quinolone drugs are a large and widely used class of synthetic antibacterial compounds (10,11,19). First-generation (acidic) quinolones include nalidixic acid and oxolinic acid (OXO). Subsequent generations have been modified to increase spectrum and potency. The most significant modification has been the addition of a fluorine atom at position C-6 in drugs such as ciprofloxacin (CFX), which results in a considerable increase in activity (30). The newer drugs also commonly contain a secondary amine in addition to the carboxylic acid group common to most quinolones, making them amphoteric rather than acidic (Fig. 1A). More recent modifications that increase drug potency include the presence of a methoxy group at C-8 (48).In Escherichia coli the major target for the quinolones is DNA gyrase (14,35). DNA gyrase is a type II topoisomerase that is able to alter the topological state of DNA by cleaving both strands, passing a double strand of DNA through the gap and resealing the ends (6). In the presence of ATP, this results in negative supercoiling, a reaction unique to gyrase. The crystal structures of the 43-kDa N-terminal domain of GyrB (responsible for ATP hydrolysis and capturing a DNA strand) and a 59-kDa fragment of the 64-kDa N-terminal domain of GyrA (containing the residues for DNA binding and cleavage and the quinolone resistance-determining region [QRDR; residues 67 to 106]) have been determined (24, 39). The structure of the 47-kDa C-terminal domain of GyrB is not known but can be inferred from the analogous enzyme from Saccharomyces cerevisiae, topoisomerase II, for which the crystal structures of a 92-kDa region have been solved (5, 12).Resistance to quinolones commonly arises in DNA gyrase via mutations in the QRDR (44). Such mutations include GyrA(Ser 83 3Trp), which gives Ϸ20-fold resistance to a wide range of quinolones (9, 46). This region of GyrA is close to t...

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The Interaction of Drugs with DNA Gyrase: A Model for the Molecular Basis of Quinolone Action

Cited by 81 publications

References 62 publications

The Pentapeptide Repeat Proteins MfpA _Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

The Pentapeptide Repeat Proteins MfpA _Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

Cumulative effect of prophage burden on Shiga toxin production in Escherichia coli

Quinolone-Binding Pocket of DNA Gyrase: Role of GyrB

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The Interaction of Drugs with DNA Gyrase: A Model for the Molecular Basis of Quinolone Action

Cited by 81 publications

References 62 publications

The Pentapeptide Repeat Proteins MfpA Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

The Pentapeptide Repeat Proteins MfpA Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

Cumulative effect of prophage burden on Shiga toxin production in Escherichia coli

Quinolone-Binding Pocket of DNA Gyrase: Role of GyrB

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The Pentapeptide Repeat Proteins MfpA _Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex

The Pentapeptide Repeat Proteins MfpA _Mt and QnrB4 Exhibit Opposite Effects on DNA Gyrase Catalytic Reactions and on the Ternary Gyrase-DNA-Quinolone Complex