Crystal structure of an N-terminal fragment of the DNA gyrase B protein

  title={Crystal structure of an N-terminal fragment of the DNA gyrase B protein},
  author={Dale B. Wigley and Gideon J. Davies and Eleanor J. Dodson and Anthony Maxwell and Guy G. Dodson},
The crystal structure of an N-terminal fragment of the Escherichia coli DNA gyrase B protein, com-plexed with a nonhn/drolysable ATP analogue, has been solved at 2.5 Å resolution. It consists of two domains, both containing novel protein folds. The protein fragment forms a dimer, whose N-terminal domains are responsible for ATP binding and hydrolysis. The C-terminal domains form the sides of a 20 Å hole through the protein dimer which may play a role in DNA strand passage during the… 
The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs.
It is shown that a gene encoding a 43-kDa protein corresponding to the N-terminal fragment of the DNA gyrase B subunit hydrolyzes ATP and binds coumarin drugs, consistent with a scheme in which the active form of the protein is a dimer.
Crystal engineering: a case study using the 24 kDa fragment of the DNA gyrase B subunit from Escherichia coli.
It was found that single amino-acid changes on the surface could have a dramatic effect on the crystallization properties of the protein and generally resulted in an improved in the number of crystal-screen hits as well as an improvement in crystal quality.
Structure of the N-Terminal Gyrase B Fragment in Complex with ADP⋅Pi Reveals Rigid-Body Motion Induced by ATP Hydrolysis
The remaining conformational states of the enzyme along the ATP hydrolysis reaction path are determined by solving crystal structures of GyrB43 in complex with ADP⋅BeF3, ADP ⋅Pi, and ADP.
Structure and mechanism of DNA topoisomerase II
The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an
An Escherichia coli DNA topoisomerase I mutant has a compensatory mutation that alters two residues between functional domains of the DNA gyrase A protein
Nucleotide sequence analysis revealed that the compensatory gyrA mutation in Escherichia coli DM750 affects DNA supercoiling by interchanging the identities of Ala-569 and Thr-586 in the DNA gyrase A
Solution structures of DNA-bound gyrase
The proposed gyrase model, with the DNA binding along the sides of the molecule and wrapping around the CTDs located near the exit gate of the protein, adds new information on the mechanism of DNA negative supercoiling.
Dimerization of Escherichia coli DNA-gyrase B Provides a Structural Mechanism for Activating the ATPase Catalytic Center*
A channel formed at the dimer interface is described that provides a structural mechanism to allow reactive water molecules to access the γ-phosphate group of the bound ATP molecule and demonstrates that dimerization strongly contributes to the folding and stability of the catalytic site for ATP hydrolysis.
Crystal engineering: deletion mutagenesis of the 24 kDa fragment of the DNA gyrase B subunit from Staphylococcus aureus.
The 24 kDa fragment of DNA gyrase B from Staphylococcus aureus was expressed in Escherichia coli and purified for crystallization and the most stable mutants produced crystals.
The C-terminal domain of DNA gyrase A adopts a DNA-bending β-pinwheel fold
A physical explanation for the ability of DNA gyrase to constrain a positive superhelical DNA wrap is provided and the particular substrate preferences of topoisomerase IV might be dictated in part by the function of this domain.
Backbone assignment of the N-terminal 24-kDa fragment of Escherichia coli topoisomerase IV ParE subunit
The backbone assignment for the N-terminal domain of E. coli ParE is reported and the secondary structural information and the assignment will aid in structure—based antibacterial agents development targeting eParE.


The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein.
It is shown that the 33 kDa protein can bind to DNA on its own in a manner which induces positive supercoiling of the DNA and is proposed to represent a domain of the gyrase A subunit which is involved in the wrapping of DNA around DNA gyrases.
DNA gyrase: purification and catalytic properties of a fragment of gyrase B protein.
A protein isolated from Escherichia coli complements the DNA gyrase A (NalA) protein to generate an activity that relaxes supercoiled DNA, which lacks both the DNA-supercoiling and DNA-dependent ATPase activities of DNA Gyrase.
Tryptic fragments of the Escherichia coli DNA gyrase A protein.
DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy.
We have determined the sequence of the E. coli gyrB gene, using a new sequencing approach in which transposition from a mini-Mu plasmid into the DNA provides random start points for dideoxynucleotide
Energy coupling in DNA gyrase and the mechanism of action of novobiocin.
It is postulate that ATP and App[NH]p are allosteric effectors of a conformational change of gyrase that leads to one round of supercoiling and that cyclic conformational changes accompanying alteration in nucleotide affinity also seem to be a common feature of energy transduction in other diverse processes including muscle contraction, protein synthesis, and oxidative phosphorylation.
A topoisomerase from Escherichia coli related to DNA gyrase.
Topoisomerase II' resembles gyrase in its sensitivity to oxolinic acid, the wrapping of DNA in an apparent positive supercoil around the enzyme, and the introduction in an aborted reaction of site-specific double-strand breaks in the DNA with concomitant covalent attachment of protein to both newly created 5' ends.