Department of Biochemistry and Molecular Pharmacology
Amino Acid Sequence; Binding Sites; Catalytic Domain; Crystallography, X-Ray; DNA Polymerase III; Escherichia coli; Escherichia coli Proteins; Metals; Molecular Sequence Data; Mutation; Protein Stability; Protein Structure, Tertiary; Sequence Alignment
Bacteriology | Structural Biology
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 A 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.
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Citation: BMC Struct Biol. 2013 May 14;13:8. doi: 10.1186/1472-6807-13-8. Link to article on publisher's site
DOI of Published Version
BMC structural biology
Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O'Donnell, Mike; Kuriyan, John; and Lamers, Meindert H., "A structural role for the PHP domain in E. coli DNA polymerase III" (2013). Open Access Articles. 2411.