Metal activation of synthetic and degradative activities of .vphi.29 DNA polymerase, a model enzyme for protein-primed DNA replication

Abstract

Analysis of metal activation on the synthetic and degradative activities of 429 DNA polymerase was carried out in comparison with T4 DNA polymerase and Escherichia coli DNA polymerase I (Klenow fragment). In the three DNA polymerases studied, both the polymerization and the 3'+5' exonuclease activity had clear differences in their metal ion requirements. The results obtained support the existence of independent metal binding sites for the synthetic and degradative activities of 429 DNA polymerase, according with the distant location of catalytic domains (N-terminal for the 3'- 5' exonuclease and C-terminal for DNA polymerization) proposed for both Klenow fragment and 429 DNA polymerase. Furthermore, DNA competition experiments using 429 DNA polymerase suggested that the main differences observed in the metal usage to activate polymerization may be the consequence of metal-induced changes in the enzymeDNA interactions, whose strength distinguishes processive and nonprocessive DNA polymerases, Interestingly, the initiation of DNA polymerization using a protein as a primer, a special synthetic activity carried out by 429 DNA polymerase, exhibited a strong preference for Mn2+ as metal activator. The molecular basis for this preference is mainly the result of a large increase in the affinity for dATP.