A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp

Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12664-9. doi: 10.1073/pnas.0903460106. Epub 2009 Jul 16.


The actions of Escherichia coli DNA Polymerase IV (Pol IV) in mutagenesis are managed by its interaction with the beta sliding clamp. In the structure reported by Bunting et al. [EMBO J (2003) 22:5883-5892], the C-tail of Pol IV contacts a hydrophobic cleft on the clamp, while residues V303-P305 reach over the dimer interface to contact the rim of the adjacent clamp protomer. Using mutant forms of these proteins impaired for either the rim or the cleft contacts, we determined that the rim contact was dispensable for Pol IV replication in vitro, while the cleft contact was absolutely required. Using an in vitro assay to monitor Pol III*-Pol IV switching, we determined that a single cleft on the clamp was sufficient to support the switch, and that both the rim and cleft contacts were required. Results from genetic experiments support a role for the cleft and rim contacts in Pol IV function in vivo. Taken together, our findings challenge the toolbelt model and suggest instead that Pol IV contacts the rim of the clamp adjacent to the cleft that is bound by Pol III* before gaining control of the same cleft that is bound by Pol III*.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 4-Nitroquinoline-1-oxide / pharmacology
  • DNA Polymerase III / chemistry*
  • DNA Polymerase III / physiology
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / physiology
  • DNA Replication
  • Dimerization
  • Escherichia coli / drug effects
  • Escherichia coli / enzymology*
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Nitrofurazone / pharmacology
  • SOS Response, Genetics


  • 4-Nitroquinoline-1-oxide
  • beta subunit, DNA polymerase III
  • DNA Polymerase III
  • DNA Polymerase beta
  • Nitrofurazone