Nucleic Acids Research, Vol 25, Issue 17 3408-3414, Copyright © 1997 by Oxford University Press
SS Sturrock and DTF Dryden
The S subunits of type I DNA restriction/modification enzymes are
responsible for recognising the DNA target sequence for the enzyme. They
contain two domains of approximately 150 amino acids, each of which is
responsible for recognising one half of the bipartite asymmetric target. In
the absence of any known tertiary structure for type I enzymes or
recognisable DNA recognition motifs in the highly variable amino acid
sequences of the S subunits, it has previously not been possible to predict
which amino acids are responsible for sequence recognition. Using a
combination of sequence alignment and secondary structure prediction
methods to analyse the sequences of S subunits, we predict that all of the
51 known target recognition domains (TRDs) have the same tertiary
structure. Furthermore, this structure is similar to the structure of the
TRD of the C5-cytosine methyltransferase, Hha I, which recognises its DNA
target via interactions with two short polypeptide loops and a beta strand.
Our results predict the location of these sequence recognition structures
within the TRDs of all type I S subunits.
ARTICLES
A prediction of the amino acids and structures involved in DNA recognition by type I DNA restriction and modification enzymes
Institute of Cell and Molecular Biology, The King's Buildings, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK.
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