1AB4

59KDA FRAGMENT OF GYRASE A FROM E. COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.226 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1AB4

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

    Organizational Affiliation

    Department of Biochemistry, University of Leicester, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GYRASE AA493Escherichia coliMutation(s): 0 
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P0AES4 (Escherichia coli (strain K12))
Explore P0AES4 
Go to UniProtKB:  P0AES4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.63α = 90
b = 119.63β = 90
c = 94.98γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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