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Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase

Urulangodi, Madhusoodanan, Dhanaraju, Rajkumar, Gupta, Kanchan, Roy, Rajendra P., Bujnicki, Janusz M., Rao, Desirazu N.
Biochimie 2016 v.128-129 pp. 70-82
DNA methylation, adenine, dimerization, magnesium, methyltransferases, restriction endonucleases, single-stranded DNA
EcoP15I DNA methyltransferase (M.EcoP15I) recognizes short asymmetric sequence, 5′-CAGCAG-3′, and methylates the second adenine only on one strand of the double-stranded DNA (dsDNA). In vivo, this methylation is sufficient to protect the host DNA from cleavage by the cognate restriction endonuclease, R.EcoP15I, because of the stringent cleavage specificity requirements. Biochemical and structural characterization support the notion that purified M.EcoP15I exists and functions as dimer. However, the exact role of dimerization in M.EcoP15I reaction mechanism remains elusive. Here we engineered M.EcoP15I to a stable monomeric form and studied the role of dimerization in enzyme catalyzed methylation reaction. While the monomeric form binds single-stranded DNA (ssDNA) containing the recognition sequence it is unable to methylate it. Further we show that, while the monomeric form has AdoMet binding and Mg2+ binding motifs intact, optimal dsDNA binding required for methylation is dependent on dimerization. Together, our biochemical data supports a unique subunit organization for M.EcoP15I to catalyze the methylation reaction.