Site-directed deletion mutagenesis within the T4 endonuclease V gene: dispensable sequences within putative loop regions

Endonuclease V from bacteriophage T4 may be one of the first DNA-repair enzymes to have its three-dimensional structure determined by X-ray crystallography (Morikawa et al., 1988). However, since this structure is not yet available, analyses of the sequence of the protein were performed in order to guide site-directed mutational studies of enzyme structure-function relationships. The enzyme is predominantly α-helical, so that an algorithm which finds the locations of turns or loops in the structure would be expected to approximately locate the helices along the sequence. Two loop sites were identified which might be adjacent in the tertiary structure according to a model developed from the loop predictions and the derived secondary structure. Deletion of three residues at each loop site produced protein molecules which retained considerable in vitro enzyme activity and in vivo repair function. However, the mutant proteins did not accumulate as well within the cell as the wild-type enzyme, suggesting that the nascent molecules folded inefficiently. Combination of the two deletions yielded a molecule with activity enhanced over one of the individual mutants, a result which can be interpreted as a classic second-site mutational reversion. This result supports the hypothesis that these regions are adjacent in the enzyme tertiary structure.