Using ψ-BLAST, we have developed a method for identifying the poorly conserved δ subunit of the DNA polymerase III holoenzyme from all sequenced bacteria. This approach, starting withEscherichia coli δ, leads not only to the identification of δ but also to the DnaX and δ′ subunits of the DnaX complex and other AAA+-class ATPases. This suggests that, although not an ATPase, δ is related structurally to the other subunits of the DnaX complex that loads the β sliding clamp processivity factor onto DNA. To test this prediction, we aligned δ sequences with those of δ′ and, using the start of δ′ Domain III established from its x-ray crystal structure, predicted the juncture between Domains II and III of δ. This putative δ Domain III could be expressed to high levels, consistent with the prediction that it folds independently. δ Domain III, like Domain III of DnaX and δ′, assembles by itself into a complex with the other DnaX complex components. Cross-linking studies indicated a contact of δ with the DnaX subunits. These observations are consistent with a model where two τ subunits and one each of the γ, δ′, and δ subunits mutually interact to form a pentameric functional core for the DnaX complex.
Bullard, James M.; Pritchard, Arthur E.; Song, Min Sun; Glover, Bradley P.; Wieczorek, Anna; Chen, Joe; Janjic, Nebojsa; and McHenry, Charles S., "A Three-Domain Structure for the delta Subunit of the DNA Polymerase III Holoenzyme delta Domain III Binds delta' and Assembles Into the DnaX Complex" (2002). Chemistry Faculty Publications and Presentations. 23.
Journal of Biological Chemistry