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J. Biol. Chem., Vol. 281, Issue 18, 12561-12567, May 5, 2006

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The NH₂-terminal php Domain of the Subunit of the Escherichia coli Replicase Binds the Proofreading Subunit^*

From the Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, Colorado 80262

The subunit of the replicase of all bacteria contains a php domain, initially identified by its similarity to histidinol phosphatase but of otherwise unknown function (Aravind, L., and Koonin, E. V. (1998) Nucleic Acids Res. 26, 3746-3752). Deletion of 60 residues from the NH₂ terminus of the php domain destroys binding. The minimal 255-residue php domain, estimated by sequence alignment with homolog YcdX, is insufficient for binding. However, a 320-residue segment including sequences that immediately precede the polymerase domain binds with the same affinity as the 1160-residue full-length subunit. A subset of mutations of a conserved acidic residue (Asp⁴³ in Escherichia coli ) present in the php domain of all bacterial replicases resulted in defects in binding. Using sequence alignments, we show that the prototypical Gram(+) Pol C, which contains the polymerase and proofreading activities within the same polypeptide chain, has an -like sequence inserted in a surface loop near the center of the homologous YcdX protein. These findings suggest that the php domain serves as a platform to enable coordination of proofreading and polymerase activities during chromosomal replication.

Received for publication, December 28, 2005 , and in revised form, February 27, 2006.

^* This work was supported by Research Grant GM060273 from the National Institutes of Health. 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.

¹ To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, 4200 East Ninth Ave., B-121, Denver, CO 80262. E-mail: Charles.McHenry{at}uchsc.edu.

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