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The  Eco RV DNA methyltransferase (M· Eco RV) is an α-adenine methyltransferase. We have used two different programs to predict the secondary structure of M· Eco RV. The resulting consensus prediction was tested by a mutant profiling analysis. 29 neutral mutations of M· Eco RV were generated by five cycles of random mutagenesis and selection for active variants to increase the reliability of the prediction and to get a secondary structure prediction for some ambiguously predicted regions. The predicted consensus secondary structure elements could be aligned to the common topology of the structures of the catalytic domains of M· Hha I and M· Taq I. In a complementary approach we have isolated nine catalytically inactive single mutants. Five of these mutants contain an amino acid exchange within the catalytic domain of M· Eco RV (Val20-Ala, Lys81Arg, Cys192Arg, Asp193Gly, Trp231Arg). The Trp231Arg mutant binds DNA similarly to wild-type M· Eco RV, but is catalytically inactive. Hence this mutant behaves like a  bona fide  active site mutant. According to the structure prediction, Trp231 is located in a loop at the putative active site of M· Eco RV. The other inactive mutants were insoluble. They contain amino acid exchanges within the conserved amino acid motifs X, III or IV in M· Eco RV confirming the importance of these regions.

protein engineering, design and selection

Structure prediction of the  Eco RV DNA methyltransferase based on mutant profiling, secondary structure analysis, comparison with known structures of methyltransferases and isolation of catalytically inactive single mutants