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Open Access Highly Accessed Research article

A structural role for the PHP domain in E. coli DNA polymerase III

Tiago Barros1, Joel Guenther1, Brian Kelch1, Jordan Anaya1, Arjun Prabhakar1, Mike O’Donnell2, John Kuriyan13* and Meindert H Lamers14*

Author Affiliations

1 Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, CA 94720, USA

2 Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA

3 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

4 Present address: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK

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BMC Structural Biology 2013, 13:8  doi:10.1186/1472-6807-13-8

Published: 14 May 2013

Abstract

Background

In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive.

Results

Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity.

Conclusions

While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.

Keywords:
DNA polymerase III; DNA replication; PHP domain; Proofreading exonuclease