CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage

Elife. 2018 Nov 20:7:e41215. doi: 10.7554/eLife.41215.

Abstract

Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.

Keywords: B. subtilis; T-segment; cryoEM; gyrase; molecular biophysics; structural biology; structure; topoisomerases.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry*
  • Adenosine Triphosphate / metabolism
  • Binding Sites
  • Cloning, Molecular
  • Cryoelectron Microscopy
  • DNA Cleavage
  • DNA Gyrase / chemistry*
  • DNA Gyrase / metabolism
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Gene Expression
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • Isoenzymes / chemistry
  • Isoenzymes / metabolism
  • Models, Molecular
  • Oligonucleotides / chemistry
  • Oligonucleotides / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Protein Multimerization
  • Protein Subunits / chemistry*
  • Protein Subunits / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Streptococcus pneumoniae / genetics*
  • Streptococcus pneumoniae / metabolism

Substances

  • DNA, Bacterial
  • Isoenzymes
  • Oligonucleotides
  • Protein Subunits
  • Recombinant Proteins
  • Adenosine Triphosphate
  • DNA Gyrase