Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs

The Escherichia coli K-12 restriction enzyme Mrr recognizes and cleaves N6- methyladenine- and 5-methylcytosine-containing DNA. Its amino acid sequence has been subjected to structure prediction and comparison with other seque nces from publicly available sources. The results obtained suggest that Mrr and related putative endonucleases possess a cleavage domain typical for a ll the so far structurally characterized type II restriction enzymes, howev er with an unusual glutamine residue at the central position of the (D/E)-( D/E)XK hallmark of the active site. The 'missing' acidic side chain was ins tead found anchored in a different, unusual position, suggesting that Mrr r epresents a third topological variant of the endonuclease active site in ad dition to the two alternatives determined previously (Skirgaila et al., 199 8. J. Mel. Biol. 279, 473-481). One of the newly identified putative endonu cleases from the Mn family is composed of two diverged cleavage domains, wh ich possess both the 'typical' D-EXK and the 'Mrr-like' D-QXK variants of t he active site. Among the Mn homologs there are also proteins from yeast, i n which restriction phenotype has not been observed, suggesting that the fr ee-standing Eukaryotic PD-(D/E)XK superfamily members might be implicated i n other cellular processes involving enzymatic DNA cleavage. (C) 2001 Elsev ier Science B.V. All rights reserved.