Computer-assisted primary and secondary structure analyses of DNA polymerases of herpes simplex, Epstein-Barr and varicella zoster viruses reveal conserved domains with some homology to DNA-binding domain in E. coli DNA pol I.

The primary and secondary structure of herpes simplex virus type 1 (HSV-1), varicella-zoster (VZV) and Epstein-Barr virus (EBV) DNA polymerases was calculated by means of computer programs. The comparison of HSV-1 polymerase (pol) sequence to the known primary and tertiary structure of E. coli DNA pol I revealed five short homologous sequences, one of which coincided with the alpha-helical structure of the DNA-binding domain of E. coli DNA pol. Comparison by primary and secondary structure computer programs of the three DNA polymerases coded by herpesviruses HSV-1, VZV and EBV led to the identification of polypeptide sequences shared by the three DNA pols. In a similar way, the secondary structure of the DNA pol polypeptide in the vicinity of the mutation leading to PAA resistance in HSV-1 DNA pol helped to identify the role of this sequence in the binding of phosphate donated by the nucleoside triphosphate molecule which binds to the DNA pol. Although the computer secondary structure programs are about 60% accurate, it was possible to obtain new information on the properties of certain domains in the DNA polymerases of HSV-1, VZV and EBV.