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J. Biol. Chem., Vol. 279, Issue 32, 33047-33050, August 6, 2004

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Increased dNTP Binding Affinity Reveals a Nonprocessive Role for Escherichia coli Clamp with DNA Polymerase IV^*

Jeffrey G. Bertram, Linda B. Bloom, Mike O'Donnell¶, and Myron F. Goodman||

From the Departments of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, University Park, Los Angeles, California 90089-1340, the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610-0245, and the ^¶Rockefeller University and Howard Hughes Medical Institute, New York, New York, 10021

Replication forks often stall at undamaged or damaged template sites in Escherichia coli. Subsequent resumption of DNA synthesis occurs by replacing DNA polymerase III, which is bound to DNA by the -sliding clamp, with one of three damage-induced DNA polymerases II, IV, or V. The principal role of the clamp is to tether the normally weakly bound polmerases to DNA thereby increasing their processivities. DNA polymerase IV binds dNTP substrates with about 10-fold lower affinity compared with the other E. coli polymerases, which if left unchecked could hinder its ability to synthesize DNA in vivo. Here we report a new property for the clamp, which when bound to DNA polymerase IV results in a large increase in dNTP binding affinity that concomitantly increases the efficiency of nucleotide incorporation at normal and transiently slipped mispaired primer/template ends. Primer-template DNA slippage resulting in single nucleotide deletions is a biological hallmark of DNA polymerase IV infidelity responsible for enhancing cell fitness in response to stress. We show that the increased DNA polymerase IV-dNTP binding affinity is an intrinsic property of the DNA polymerase IV- clamp interaction and not an indirect consequence of an increased binding of DNA polymerase IV to DNA.

Received for publication, June 8, 2004

^* This work was supported by National Institutes of Health Grants GM21422 and ES012259 (to M. F. G.), GM55596 (to L. B. B.), and GM38839 (to M. O'D.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

^|| To whom correspondence should be addressed: University of Southern California, Dept. of Biological Sciences, SHS172, University Park, Los Angeles, CA 90089-1340. Tel.: 213-740-5190; Fax: 213-740-8631; E-mail: mgoodman{at}usc.edu.

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