Published online 27 July 2004
Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved
Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases
Institute of Molecular Biology, State Research Center of Virology and Biotechnology ‘Vector’, Novosibirsk 630559, Russia and 1 Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA
* To whom correspondence should be addressed. Tel: +1 585 275 8046; Fax: +1 585 275 2070; Email: modDNA{at}mail.rochester.edu
Received June 3, 2004; Revised and Accepted July 1, 2004
The phage T4Dam and EcoDam DNA-[adenine-N6] methyltransferases (MTases) methylate GATC palindromic sequences, while the BamHI DNA-[cytosine-N4] MTase methylates the GGATCC palindrome (which contains GATC) at the internal cytosine residue. We compared the ability of these enzymes to interact productively with defective duplexes in which individual elements were deleted on one chain. A sharp decrease in kcat was observed for all three enzymes if a particular element of structural symmetry was disrupted. For the BamHI MTase, integrity of the ATCC was critical, while an intact GAT sequence was necessary for the activity of T4Dam, and an intact GA was necessary for EcoDam. Theoretical alignment of the region of best contacts between the protein and DNA showed that in the case of a palindromic interaction site, a zone covering the 5'-symmetric residues is located in the major groove versus a zone of contact covering the 3'-symmetric residues in the minor groove. Our data fit a simple rule of thumb that the most important contacts are aligned around the methylation target base: if the target base is in the 5' half of the palindrome, the interaction between the enzyme and the DNA occurs mainly in the major groove; if it is in the 3' half, the interaction occurs mainly in the minor groove.