The interaction between coumarin drugs and DNA gyrase

The coumarin group of antibiotics have as their target the bacterial enzyme DNA gyrase. The drugs bind to the B subunit of gyrase and inhibit DNA supercoiling by blocking the ATPase activity. Recent data show that the binding site for the drugs lies within the N-terminal part of the B protein, and individual amino acids involved in coumarin interaction are being identified. The mode of inhibition of the gyrase ATPase reaction by coumarins is unlikely to be simple competitive inhibition, and the drugs may act by stabilizing a conformation of the enzyme with low affinity for ATP.     

Probing the binding of the coumarin drugs using peptide fragments of DNA gyrase B protein.

Bacterial DNA gyrase, has been identified as the target of several antibacterial agents, including the coumarin drugs. The coumarins inhibit the gyrase action by competitive binding to the ATP-binding site of DNA gyrase B (GyrB) protein. The high in vitro inhibitory potency of coumarins against DNA gyrase reactions has raised interest in studies on coumarin-gyrase interactions. In this context, a series of low-molecular weight peptides, including the coumarin resistance-determining region of subunit B of Escherichia coli gyrase, has been designed and synthesized. The first peptide model was built using the natural fragment 131-146 of GyrB and was able to bind to novobiocin (K(a) = 1.8 +/- 0.2 x 10(5)/m) and ATP (K(a) = 1.9 +/- 0.4 x 10(3)/m). To build the other sequences, changes in the Arg(136) residue were introduced so that the binding to the drug was progressively reduced with the hydrophobicity of this residue (K(a) = 1.3 +/- 0.1 x 10(5)/m and 1.0 +/- 0.2 x 10(5)/m for Ser and His, respectively). No binding was observed for the change Arg(136) to Leu. In contrast, the binding to ATP was not altered, independently of the changes promoted. On the contrary, for peptide-coumarin and peptide-ATP complexes, Mg(2+) appears to modulate the binding process. Our results demonstrate the crucial role of Arg(136) residue for the stability of coumarin-gyrase complex as well as suggest a different binding site for ATP and in both cases the interactions are mediated by magnesium ions.     

Structure of the progesterone receptor of chick oviduct. The 110 kDa B protein which binds the hormone has affinity for DNA

Purified "B" protein (MW approximately 110 kDa) that binds progesterone, and more than 90% of the activated receptor labelled with tritiated hormone in the oviduct cytosol of chicks pretreated with estrogen have the same chromatography behavior on DNA-cellulose. Conversely, neither the nonactivated "8S" receptor, that includes the heat-shock protein hsp90, nor the later bind to DNA. With other biochemical and immunological arguments, these results indicate that the hormone binding B unit of the progesterone receptor binds DNA as do all steroid hormone receptors.     

Temperature-sensitive suppressor mutations of the Escherichia coli DNA gyrase B protein

Escherichia coli strain LE316 contains a mutation in gyrB that results in the substitution of Val164 to Gly and confers both chlorobiocin resistance and temperature sensitivity. Selection for suppressors of the ts phenotype yielded second-site mutations in GyrB at His38 and Thr157. The properties of proteins bearing these mutations have been characterized, and a mechanism of suppression is proposed based upon structural considerations.     

The effects of metal ions on the structure and stability of the DNA gyrase B protein

The effects of mono- and divalent metal ions on the DNA gyrase B subunit, on its 43 kDa and 47 kDa domains, and on two mutants in the Toprim domain (D498A and D500C) were investigated by means of circular dichroism and protein melting experiments. Both types of metal ion, with the notable exception of Mn2+, did not affect the conformational properties of the enzyme subunit at room temperature, but were able to produce selective and differential effects on protein stability. In particular, monovalent (K+) ions increased the stability of the gyrase B structure, whereas destabilising effects were most prominent using Mn2+ as the metal ion. Ca2+ and Mg2+ produced comparable changes in the gyrase B melting profile. Additionally, we found that monovalent (K+) ions were more effective in the 43 kDa N-terminal domain where ATP binding occurs, whereas divalent ions caused large modifications in the conformational stability of the 47 kDa C-terminal domain. Our results on gyrase B mutants indicate that D498 interacts with Mn2+, whereas it has little effect on the binding of the other ions tested. A D500C mutation, in contrast, effectively impairs Mg2+ affinity, suggesting effective contacts between this ion and D500 in the wild-type enzyme. Hence, the sites of metal ion complexation within the Toprim domain are modulated by the nature of the ion species. These results suggest a double role played by metal ions in the catalytic steps involving DNA gyrase B. One has to do with direct involvement of cations complexed to the Toprim domain in the DNA cutting-rejoining process, the other, until now overlooked, is connected to the dramatic changes in protein flexibility produced by ion binding, which reduces the energy required for the huge conformational changes essential for the catalytic cycle to occur.     

The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors,clorobiocin

Coumarin antibiotics, such as clorobiocin, novobiocin, and coumermycin A1, inhibit the supercoiling activity of gyrase by binding to the gyrase B (GyrB) subunit. Previous crystallographic studies of a 24-kDa N-terminal domain of GyrB from E. coli complexed with novobiocin and a cyclothialidine analogue have shown that both ligands act by binding at the ATP-binding site. Clorobiocin is a natural antibiotic isolated from several Streptomyces strains and differs from novobiocin in that the methyl group at the 8 position in the coumarin ring of novobiocin is replaced by a chlorine atom, and the carbamoyl at the 3′ position of the noviose sugar is substituted by a 5-methyl-2-pyrrolylcarbonyl group. To understand the difference in affinity, in order that this information might be exploited in rational drug design, the crystal structure of the 24-kDa GyrB fragment in complex with clorobiocin was determined to high resolution. This structure was determined independently in two laboratories, which allowed the validation of equivalent interpretations. The clorobiocin complex structure is compared with the crystal structures of gyrase complexes with novobiocin and 5′-adenylyl-β,γ-imidodiphosphate, and with information on the bound conformation of novobiocin in the p24-novobiocin complex obtained by heteronuclear isotope-filtered NMR experiments in solution. Moreover, to understand the differences in energetics of binding of clorobiocin and novobiocin to the protein, the results from isothermal titration calorimetry are also presented. © 1997 Wiley-Liss Inc.     

Preliminary crystallographic analysis of the ATP-hydrolysing domain of the Escherichia coli DNA gyrase B protein.

The 43 kDa N-terminal ATPase domain of the Escherichia coli DNA gyrase B protein has been purified from an over-expressing strain. This protein has been crystallized in two crystal forms, both in the presence of the non-hydrolysable ATP analogue 5'-adenylyl-beta,gamma-imidodiphosphate. The first crystal form is monoclinic P2(1), with cell dimensions a = 76 A, b = 88 A, c = 82 A, beta = 105.5 degrees, and diffracts to at least 2.7 A resolution using synchrotron radiation. Crystal density measurements suggest that there are two molecules in the asymmetric unit (Vm = 3.08 A3/Da). The second crystal form is orthorhombic C222(1), with cell dimensions a = 89.2 A, b = 143.1 A and c = 79.8 A. The crystals diffract to beyond 3 A and are stable for at least 100 hours when exposed to X-rays from a rotating anode source. The asymmetric unit of this crystal form appears to contain one molecule (Vm = 2.96 A3/Da). Data have already been collected to 5 A resolution from native crystals of this second form, and to 6 A resolution from three heavy-atom derivatives. Electron density maps calculated using phases obtained from these derivatives show features consistent with secondary structural elements, and have allowed the molecular boundary to be determined. Higher resolution native and derivative data are being collected.     

The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding

DNA gyrase is the only enzyme known to negatively supercoil DNA. The enzyme is a heterotetramer of A(2)B(2) subunit composition. Alignment of the primary sequence of gyrase B (GyrB) from various species shows that they can be grouped into two classes. The GyrB of Gram-negative eubacteria has a stretch of about 165 amino acids in the C-terminal half, which is lacking in other GyrB subunits and type II topoisomerases. In Escherichia coli, no function has so far been attributed to this stretch. In this study, we have tried to assess the function of this region both in vivo and in vitro. A deletant (GyrBDelta160) lacking this region is non-functional in vivo. The holoenzyme reconstituted from gyrase A (GyrA) and GyrBDelta160 shows reduced but detectable supercoiling and quinolone-induced cleavage activity in vitro. GyrBDelta160 retains its ability to bind to GyrA and novobiocin. However, when reconstituted with GyrA, the deletant shows greatly impaired DNA binding. The intrinsic ATPase activity of the GyrBDelta160 is comparable to that of wild type GyrB, but this activity is not stimulated by DNA. These studies indicate that the additional stretch present in GyrB is essential for the DNA binding ability of E. coli gyrase.     

The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.

Human Rad51 protein (HsRad51) is a homolog of Escherichia coli RecA protein, and functions in DNA repair and recombination. In higher eukaryotes, Rad51 protein is essential for cell viability. The N-terminal region of HsRad51 is highly conserved among eukaryotic Rad51 proteins but is absent from RecA, suggesting a Rad51-specific function for this region. Here, we have determined the structure of the N-terminal part of HsRad51 by NMR spectroscopy. The N-terminal region forms a compact domain consisting of five short helices, which shares structural similarity with a domain of endonuclease III, a DNA repair enzyme of E. coli. NMR experiments did not support the involvement of the N-terminal domain in HsRad51-HsBrca2 interaction or the self-association of HsRad51 as proposed by previous studies. However, NMR tiration experiments demonstrated a physical interaction of the domain with DNA, and allowed mapping of the DNA binding surface. Mutation analysis showed that the DNA binding surface is essential for double-stranded and single-stranded DNA binding of HsRad51. Our results suggest the presence of a DNA binding site on the outside surface of the HsRad51 filament and provide a possible explanation for the regulation of DNA binding by phosphorylation within the N-terminal domain.     

DNA gyrase can cleave short DNA fragments in the presence of quinolone drugs.

We have analysed the DNA cleavage reaction of DNA gyrase using oligonucleotides annealed to a single-stranded M13 derivative containing a preferred gyrase cleavage site. We find that gyrase can cleave duplexes down to approximately 20 bp in size in the presence of the quinolone drugs ciprofloxacin and oxolinic acid. Ciprofloxacin shows a variation in its site specificity with an apparent preference for G bases adjacent to the cleavage sites, whereas oxolinic acid stimulates cleavage predominantly at the previously determined site. With either drug, cleavage will not occur within 6 bases from the end of a DNA duplex or a nick. We suggest that cleavage site specificity with short DNA duplexes is determined by drug-DNA interactions whereas with longer fragments the positioning effect of the DNA wrap around gyrase prescribes the site of cleavage.     

Structure-activity relationship in two series of aminoalkyl substituted coumarin inhibitors of gyrase B.

Two series of aminosubstituted coumarins were synthesised and evaluated in vitro as inhibitors of DNA gyrase and as potential antibacterials. Novel novobiocin-like coumarins, 4-(dialkylamino)methylcoumarins and 4-((2-alkylamino)ethoxy)coumarins, were discovered as gyrase B inhibitors with promising antibacterial activity in vitro.     

Tryptic fragments of the Escherichia coli DNA gyrase A protein

Treatment of the Escherichia coli DNA gyrase A protein with trypsin generates two large fragments which are stable to further digestion. The molecular masses of these fragments are 64 and 33 kDa, and they are shown to be derived from the N terminus and the C terminus of the A protein, respectively. These fragments could represent structural and/or functional domains within the A subunit of DNA gyrase. The trypsin-cleaved A protein (A'), in combination with the B subunit of gyrase, can support ATP-dependent supercoiling of relaxed DNA and other reactions of DNA gyrase. The isolated 64-kDa fragment will also catalyse DNA supercoiling in the presence of the B protein, but the 33-kDa fragment shows no enzymic activities. We conclude that the N-terminal 64-kDa fragment represents the DNA breakage/reunion domain of the A protein, while the 33-kDa fragment may contribute to the stability of the gyrase-DNA complex.     

The N-terminal A domain of Staphylococcus aureus fibronectin-binding protein A binds to tropoelastin

Staphylococcus aureus is an important human pathogen. Its virulence factors include a variety of MSCRAMMs (microbial surface component recognizing adhesive matrix molecules), each capable of binding specifically to the host extracellular matrix. The fibronectin-binding protein, FnBPA, has been shown previously to bind immobilized fibronectin, fibrinogen, and alpha-elastin peptides. Here we show that region A of FnBPA (rAFnBPA) binds to recombinant human tropoelastin. Binding occurs to three separate truncates of tropoelastin, encompassing domains 2-18, 17-27, and 27-36, signifying that the interaction occurs at multiple sites. The greatest affinity was for the N-terminal truncate. We observed a pH dependency for the rAFnBPA-tropoelastin interaction with strong, nonsaturable binding at low pH. The interaction ceased at higher pH. These data support a model of surface-surface interactions between the negative charges present on rAFnBPA and the positive lysines of tropoelastin. A protein lacking the negatively charged C-terminal fibronectin-binding motif of the A domain of FnBPA and another construct lacking subdomain N1 were both capable of binding immobilized tropoelastin with a lower affinity. The binding properties of five site-directed mutants of rAFnBPA were compared with wild-type rAFnBPA. There was no decreased affinity for immobilized tropoelastin, in contrast to the defective binding of these mutants to alpha-elastin and fibrinogen. The data indicate novel interactions between tropoelastin and FnBPA that include the use of surface charges. These results demonstrate that FnBPA is capable of directly binding tropoelastin prior to its incorporation into elastin.     

Synthesis and in vitro evaluation of novel highly potent coumarin inhibitors of gyrase B.

The design, synthesis, and in vitro biological activity of a series of novel coumarin inhibitors of gyrase B is presented. Replacement of the 3-acylamino residue (3-NHCOR) of coumarin drugs with reversed isosteres C(=O)R, C(=N-OR)R', COOR, CONHR and CONHOR leads to highly potent analogues which displayed excellent inhibition of the negative supercoiling of the relaxed DNA and antibacterial activity.     

The DNA dependence of the ATPase activity of DNA gyrase

We have studied the ATPase activity of DNA gyrase both in the absence and presence of DNA. In the absence of DNA we show that the gyrase B protein alone has a very low level of ATPase activity which can be increased many-fold by pretreatment of the B protein with heat or urea. When both the gyrase A protein and linear DNA are also present, the ATPase activity of the untreated B protein is greatly stimulated. We find that the extent of stimulation is dependent upon the length of the DNA but largely independent of DNA sequence. DNA molecules greater than 100 base pairs in length are much more effective in stimulating the gyrase ATPase than those of 70 base pairs or less, although short DNA molecules will stimulate the ATPase at high concentrations. The behavior of long and short DNA molecules with respect to ATPase stimulation is also reflected in their abilities to bind DNA gyrase. To account for these data we propose a model for the interaction of gyrase with ATP and DNA in which ATP hydrolysis requires the binding of DNA to two sites on the enzyme.     

The action of the bacterial toxin, microcin B17, on DNA gyrase

Microcin B17 (MccB17) is a peptide-based bacterial toxin that targets DNA gyrase, the bacterial enzyme that introduces supercoils into DNA. The site and mode of action of MccB17 on gyrase are unclear. We review what is currently known about MccB17-gyrase interactions and summarise approaches to understanding its mode of action that involve modification of the toxin. We describe experiments in which treatment of the toxin at high pH leads to the deamidation of two asparagine residues to aspartates. The modified toxin was found to be inactive in vivo and in vitro, suggesting that the Asn residues are essential for activity. Following on from these studies we have used molecular modelling to suggest a 3D structure for microcin B17. We discuss the implications of this model for MccB17 action and investigate the possibility that it binds metal ions.     

Analysis of the DNA gyrase genes ofAcholeplasma laidlawii PG-8B

A 5-kb region of theAcholeplasma laidlawii PG-8B genome was sequenced. The region contained the genes for RecF, DNA gyrase subunits A and B (GyrA and GyrB), and a fragment of the ATP-binding subunit of the hypothetical ABC transporter. In phylogenetic analysis,A. laidlawii GyrA and GyrB formed statistically significant, stable clusters with the corresponding proteins ofClostridium acetobutylicum, Staphylococcus aureus, Bacillus subtilis, andStreptococcus pneumoniae. A laidlawii PG-8B clones resistant to fluoroquinolone (FQ) antibiotic ciprofloxacin (Cff) were obtained on a selective medium. The clones carried mutations in the quinolone resistance-determining region (QRDR) ofgyrA, which resulted in substitutions Ser83→Ala, Ser83→Phe, or Asp91→Asn. No mutations were found ingyrB QRDR of the resistant clones.