Structural studies of EcoRII methylase: exploring similarities among methylases

EcoRII methyltransferase (M.EcoRII) is a cytosine-C5 DNA methylatingenzyme. A model of its three-dimensional structure is proposed on the basisof homology modeling. Crystal structures of two members of the same familyof enzymes, HaeIII and HhaI methyltransferases (M.HaeIII and M.HhaIrespectively), were used as template molecules. Molecular dynamics was usedto ensure sampling of conformationally stable structures. The final modelhas good geometry. The DNA and cofactor binding residues are in expectedpositions and form proper interactions. M.EcoRII is 147 amino acids longerthan the template molecules, and hence the model contains several loopsthat are significantly longer than those in M.HaeIII and M.HhaI. The modelprovides a framework for interpretation and designing site-directed mutantsthat have a potential to improve crystallization experiments of thisenzyme, and possibly other similar enzymes.