Structural and Biochemical Analysis of Sliding Clamp/Ligand Interactions Suggest a Competition Between Replicative and Translesion DNA Polymerases

Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the β sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16). The seven C-terminal residues bind to a pocket located at the surface of one β monomer. This region was previously identified as the binding site of another β clamp binding protein, the δ subunit of the γ complex. We show that peptide P16 competitively prevents β-clamp-mediated stimulation of both Pol IV and α subunit DNA polymerase activities, suggesting that the site of interaction of the α subunit with β is identical with, or overlaps that of Pol IV. This common binding site for δ, Pol IV and α subunit is shown to be formed by residues that are highly conserved among many bacterial β homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design.