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. Author manuscript; available in PMC: 2014 Apr 23.
Published in final edited form as: Biochemistry. 2013 Apr 12;52(16):2828–2838. doi: 10.1021/bi400163k

Figure 2.

Figure 2

(A) Mechanism for the methyl transfer reaction catalyzed by M.HhaI involving concerted methyl transfer and covalent bonding of Cys81–S− with C6 of cytosine. Key structures of the obtained mechanism with bond distances are shown. Blue dashed lines indicate hydrogen bonds. Red dashed lines denote key distances. (B) Free energy profile. The potential energy profile and bond length analyses are shown in Figure S2 of Supporting Information. (C) Distance between cytosine N3 and HOε2 of Glu119 (black) and the distance between cytosine N3 and Oε2 of Glu119 (red) in the QM/MM-MD simulation; there are two configurations at the transition state 1 (TS1) with Glu119 hydrogen oscillating between being covalently linked to cytosine N3 and Glu119. These are circled in 2A. See Movie S1 of Supporting Information.