A PREDICTION OF THE AMINO-ACIDS AND STRUCTURES INVOLVED IN DNA RECOGNITION BY TYPE-I DNA RESTRICTION AND MODIFICATION ENZYMES

The S subunits of type I DNA restriction/modification enzymes are resp onsible for recognising the DNA target sequence for the enzyme. They c ontain two domains of approximately 150 amino acids, each of which is responsible for recognising one half of the bipartite asymmetric targe t. In the absence of any known tertiary structure for type I enzymes o r recognisable DNA recognition motifs in the highly variable amino aci d sequences of the S subunits, it has previously not been possible to predict which amino acids are responsible for sequence recognition, Us ing a combination of sequence alignment the same tertiary structure. F urthermore, this structure is similar to the structure of the TRD of t he C5-cytosine methyltransferase, Hhal, which recognises its DNA targe t via interactions with two short polypeptide loops and a beta strand, Our results predict the location of these sequence recognition struct ures within the TRDs of all type IS subunits.