Type I Restriction and Modification Systems

Structural Model of EcoR124I

We have recently published a structural model for the DNA methylase of the Type IC R-M enzyme EcoR124I. This work was based on two X-ray crystallographic structures for the HsdS subunit (Calisto et al., 2005; Kim et al., 2005) and a published pdb file for the structure of the HsdM subunit of EcoKI (Obarska et al., 2006), which allowed in silico modelling of the complete MTase based on the know EcoR124I DNA sequence. In addition, information from van Noort et al (2004), who had first visualised the EcoR124I endonuclease and MTase bound to DNA, was used to direct the inclusion of "bent" DNA, where the MTase was shown to introduce a bend of 49° in the DNA. This can be seen in the animated gif above. This model was then used to analyse a series of mutations that had been isolated within the hsdS gene and allowed some prediction of the "mechanism behind the phenotypes".

Structural Model of HsdR

A combination of biophysical analysis and in silico modelling has been applied to the HsdR subunits of Type I R-M systems (Obarska-Kosinska et al 2008), following an earlier analysis of the domain structure of the HsdR subunit of EcoKI (Dryden et al., 1995) using limited proteolysis. Small angle neutron scattering provided a "confining" space into which the modelled domains of HsdR were fitted.