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A more recent version of this article appeared on May 5, 2006
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M513844200v1
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Papers In Press, published online ahead of print March 3, 2006
J. Biol. Chem, 10.1074/jbc.M513844200
Submitted on December 28, 2005
Revised on February 27, 2006
Accepted on March 3, 2006

The N-terminal php domain of the alpha subunit of the E. coli replicase binds the epsilon proofreading subunit

Anna Wieczorek and Charles S. McHenry

Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, CO 80262

Corresponding Author: diane.hager{at}uchsc.edu

The alpha 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, EV. (1998) Nucleic Acids Res. 26, 3746-52). Deletion of 60 residues from the N-terminus of the alpha php domain destroys epsilon binding. The minimal 255-residue php domain, estimated by sequence alignment with homolog YcdX, is insufficient for epsilon binding. However, a 320-residue segment including sequences that immediately precede the polymerase domain binds epsilon with the same affinity as the 1160-residue full-length alpha subunit. A subset of mutations of a conserved acidic residue (D43 in E. coli alpha ) present in the php domain of all bacterial replicases resulted in defects in epsilon 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 epsilon -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.


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