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Restriction–modification systems serve as primitive immune systems in bacteria. To perform this function, expression of the restriction endonuclease and the methyltransferase genes should be coordinated. In SsoII restriction–modification system, the methyltransferase (M.SsoII) itself acts as a transcription factor repressing its own gene and stimulating expression of the endonuclease gene. Thus, M.SsoII is a protein which recognizes 2 different sites in DNA. As a methyltransferase, it recognizes in double-stranded DNA the sequence 5'-CCNGG-3' (where N = A, C, G or T) and methylates the C5 atom of the internal cytosine residue. As a transcription factor, it recognizes the so-called regulatory site 5'-AGGACAAATTGTCCT-3', a 15-bp quasipalindromic sequence. M.SsoII has been shown to be a monomer in apo-form and to remain monomeric upon binding to DNA containing the methylation site. On the contrary, 2 specific complexes were detected in gel-shift experiments upon M.SsoII binding to DNA containing the regulatory site; they were shown to contain 1 or 2 subunits of M.SsoII per one DNA duplex, correspondingly. The possibility of the dimerization was further corroborated by the fact that M.SsoII could be photocrosslinked by 4-(N-maleimido)benzophenone only in the presence of the regulatory DNA. The dimerization process proved to be cooperative. The N-terminal 71 residues of M.SsoII had been found to be responsible for the regulatory function of M.SsoII. An assumption was made that it could be a structurally separated domain of M.SsoII containing a helix–turn–helix motif. We used a protein homologous to the N-terminal part of M.SsoII, Δ(72–379)M.Ecl18kI – a deletion mutant of SsoII-like DNA methyltransferase Ecl18kI. It was capable of binding DNA containing the regulatory site which indicated that the deletion mutant remained folded properly and thus could exist as a separated domain in the full-length protein. Circular dichroism spectroscopy showed that 32% of Δ(72–379)M.Ecl18kI belonged to α-helices, which agreed with the assumption about the helix–turn–helix motif presence.