Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, epsilon, θ and β reveals a highly flexible arrangement of the proofreading domain

Nucleic Acids Res. 2013 May 1;41(10):5354-67. doi: 10.1093/nar/gkt162. Epub 2013 Apr 10.

Abstract

A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ:β2 complexes. Nuclear magnetic resonance experiments with reconstituted αεθ:β2 demonstrate retention of high mobility of a segment of 22 residues in the linker that connects the exonuclease domain of ε with its α-binding segment. In spite of this, small-angle X-ray scattering data show that the isolated complex with strengthened CBMs has a compact, but still flexible, structure. Photo-crosslinking with p-benzoyl-L-phenylalanine incorporated at different sites in the α-PHP domain confirm the conformational variability of the tether. Structural models of the αεθ:β2 replicase complex with primer-template DNA combine all available structural data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • DNA Polymerase III / chemistry*
  • DNA Polymerase III / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Exodeoxyribonucleases / chemistry*
  • Exodeoxyribonucleases / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Peptides / chemistry
  • Protein Folding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Tertiary

Substances

  • Escherichia coli Proteins
  • Peptides
  • DNA polymerase III, alpha subunit
  • beta subunit, DNA polymerase III
  • holE protein, E coli
  • DNA Polymerase III
  • dnaQ protein, E coli
  • Exodeoxyribonucleases

Associated data

  • PDB/4GX8
  • PDB/4GX9