Aphidicolin inhibits DNA polymerase II of Escherichia coli , an alpha-like DNA polymerase

The polB gene of E. coli encodes DNA polymerase II. We have reported the cloning (1,2) and sequencing of the polB gene (3) (GenBank Accession number M35371). DNA polymerase II appears to be a non-essential function since the polB gene is missing from some widely used strains (3). Several sub-families of DNA polymerases have been identified (4). In this communication, we demonstrate that DNA polymerase II of E. coli is an a-like DNA polymerase by amino acid sequence conservation and inhibition by aphidicolin. A search of the MBCRR Protein Pattern Library indicated significant similarity (6.3 standard deviations above the mean of comparisons with a negative control set) to only a single pattern (pattern 156) generated from a set of a-like polymerases (Fig. 1). DNA polymerase II has the highest overall similarity to human DNA polymerase a and phage T4 DNA polymerase. The entire length of DNA polymerase n is similar to a subregion of both polymerases and within this region the sequences are both approximately 22% identical. There are three sequence motifs characteristic of the a-like family (regions I, II, III) (4, 5). The H region shown in Figure 1 corresponds to region I characterized by the presence of 5 7 contiguous conserved amino acids (YGDTDS). The E region corresponds to region II. In addition to a central conserved sequence of 5-10 residues (DSLYPS), there are additional sequence identities on both sides of the conserved center. Regions F and G correspond to region HI with invariant residues at five positions. These three regions are in the same linear arrangement (11-111-1) as other DNA polymerases in this family and the relative distances between the regions are similar.