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Papers In Press, published online ahead of print January 24, 2002
J. Biol. Chem, 10.1074/jbc.M108708200
Submitted on September 10, 2001
Revised on January 22, 2002
Accepted on January 24, 2002
Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, CO 80262
Corresponding Author: charles.mchenry{at}uchsc.edu
Using Psi-BLAST, we have developed a method for identifying the poorly conserved delta subunit of the DNA polymerase III holoenzyme from all sequenced bacteria. This approach, starting with E. coli delta, leads to not only the identification of delta, but the DnaX and delta’ subunits of the DnaX complex and other AAA+-class ATPases. This suggests that, although not an ATPase, delta is related structurally to the other subunits of the DnaX complex that loads the beta sliding clamp processivity factor onto DNA. To test this prediction, we aligned delta sequences with those of delta’, and, using the start of delta’ domain III established from its X-ray crystal structure, predicted the juncture between domain II and III of delta. This putative delta Domain III could be expressed to high levels, consistent with the prediction that it folds independently. Delta Domain III, like domain III of DnaX and delta’, assembles by itself into a complex with the other DnaX complex components. Cross-linking studies indicated a contact of delta with the DnaX subunits. These observations are consistent with a model where two tau subunits, and one each of the gamma, delta’ and delta subunits mutually interact to form a pentameric functional core for the DnaX complex.
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