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J. Biol. Chem., Vol. 277, Issue 15, 13246-13256, April 12, 2002

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A Three-domain Structure for the  Subunit of the DNA Polymerase III Holoenzyme  Domain III Binds ' and Assembles into the DnaX Complex^*

James M. Bullard, Arthur E. Pritchard^§, Min-Sun Song^§, Bradley P. Glover^§, Anna Wieczorek^§, Joe Chen^§, Nebojsa Janjic, and Charles S. McHenry^§¶

From  Replidyne, Inc., Denver, Colorado 80206 and the ^§ Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, Colorado 80262

Using -BLAST, we have developed a method for identifying the poorly conserved  subunit of the DNA polymerase III holoenzyme from all sequenced bacteria. This approach, starting with Escherichia coli , leads not only to the identification of  but also to the DnaX and ' subunits of the DnaX complex and other AAA⁺-class ATPases. This suggests that, although not an ATPase,  is related structurally to the other subunits of the DnaX complex that loads the  sliding clamp processivity factor onto DNA. To test this prediction, we aligned  sequences with those of ' and, using the start of ' Domain III established from its x-ray crystal structure, predicted the juncture between Domains II and III of . This putative  Domain III could be expressed to high levels, consistent with the prediction that it folds independently.  Domain III, like Domain III of DnaX and ', assembles by itself into a complex with the other DnaX complex components. Cross-linking studies indicated a contact of  with the DnaX subunits. These observations are consistent with a model where two  subunits and one each of the , ', and  subunits mutually interact to form a pentameric functional core for the DnaX complex.

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