1AB4

59KDA FRAGMENT OF GYRASE A FROM E. COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the breakage-reunion domain of DNA gyrase.

Cabral, J.H.Jackson, A.P.Smith, C.V.Shikotra, N.Maxwell, A.Liddington, R.C.

(1997) Nature 388: 903-906

  • DOI: 10.1038/42294

  • PubMed Abstract: 
  • DNA gyrase is a type II DNA topoisomerase from bacteria that introduces supercoils into DNA. It catalyses the breakage of a DNA duplex (the G segment), the passage of another segment (the T segment) through the break, and then the reunification of th ...

    DNA gyrase is a type II DNA topoisomerase from bacteria that introduces supercoils into DNA. It catalyses the breakage of a DNA duplex (the G segment), the passage of another segment (the T segment) through the break, and then the reunification of the break. This activity involves the opening and dosing of a series of molecular 'gates' which is coupled to ATP hydrolysis. Here we present the crystal structure of the 'breakage-reunion' domain of the gyrase at 2.8 A resolution. Comparison of the structure of this 59K (relative molecular mass, 59,000) domain with that of a 92K fragment of yeast topoisomerase II reveals a very different quaternary organization, and we propose that the two structures represent two principal conformations that participate in the enzymatic pathway. The gyrase structure reveals a new dimer contact with a grooved concave surface for binding the G segment and a cluster of conserved charged residues surrounding the active-site tyrosines. It also shows how breakage of the G segment can occur and, together with the topoisomerase II structure, suggests a pathway by which the T segment can be released through the second gate of the enzyme. Mutations that confer resistance to the quinolone antibacterial agents cluster at the new dimer interface, indicating how these drugs might interact with the gyrase-DNA complex.


    Related Citations: 
    • Structure and Mechanism of DNA Topoisomerase II
      Berger, J.M.,Gamblin, S.J.,Harrison, S.C.,Wang, J.C.
      (1996) Nature 379: 225
    • DNA Gyrase: Structure and Function
      Reece, R.J.,Maxwell, A.
      (1991) Crit.Rev.Biochem.Mol.Biol. 26: 335
    • Erratum. Structure and Mechanism of DNA Topoisomerase II
      Berger, J.M.,Gamblin, S.J.,Harrison, S.C.,Wang, J.C.
      (1996) Nature 380: 179


    Organizational Affiliation

    Department of Biochemistry, University of Leicester, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GYRASE A
A
493Escherichia coli (strain K12)Gene Names: gyrA (hisW, nalA, parD)
EC: 5.99.1.3
Find proteins for P0AES4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AES4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.226 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 119.630α = 90.00
b = 119.630β = 90.00
c = 94.980γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance