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

Proteins. 1997 May;28(1):41-52.


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-beta, gamma-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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / physiology
  • Coumarins / antagonists & inhibitors*
  • Coumarins / chemistry
  • Coumarins / metabolism
  • Crystallography, X-Ray
  • DNA Gyrase
  • DNA Topoisomerases, Type II / chemistry*
  • DNA Topoisomerases, Type II / metabolism*
  • Escherichia coli / chemistry*
  • Escherichia coli / enzymology*
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Weight
  • Novobiocin / analogs & derivatives*
  • Novobiocin / metabolism
  • Protein Binding
  • Protein Conformation
  • Solutions
  • Structure-Activity Relationship
  • Thermodynamics


  • Coumarins
  • Solutions
  • Novobiocin
  • clorobiocin
  • coumarin
  • DNA Gyrase
  • DNA Topoisomerases, Type II