Fidelity Mechanisms of DNA Polymerase β

DNA polymerase β (Pol β) is one of the best characterized eukaryotic DNA polymerases. Pol β is a member of the X family of DNA polymerases. The Pol β protein has two catalytic activities: DNA polymerase activity and dRP lyase activity. Pol β has no known proofreading activity, so its accuracy in vitro results exclusively from the nucleotide selectivity of this enzyme. Presteady-state kinetic analysis has shown that Pol β functions in nucleotide selectivity predominantly during phosphodiester bond formation, although this enzyme also possesses some ability to discriminate the correct from the incorrect deoxynucleoside triphosphate (dNTP) substrate during ground state binding. Recent results strongly suggest that Pol β does not employ an induced fit mechanism of nucleotide discrimination. The fidelity of Pol β appears to be determined through steric exclusion against the incorrect substrate and by the precise positioning of the catalytic residues, DNA, and substrate within the active site of the enzyme. Imprecise positioning of active site residues or DNA can result in the incorporation of the incorrect substrate into DNA. Amino acid residues both distant and near to the active site of Pol β influence its geometry, suggesting that the movements and positioning of subdomains of Pol β have a significant impact upon its fidelity.