Fig. 2: Cryo-EM structure of hmDNA-bound MTA1cMTA9.
From: Mechanism for the substrate recognition by a eukaryotic DNA N6-adenine methyltransferase complex
a Cryo-EM map of the MTA1cMTA9–hmDNA–SAM complex. Two strands of hmDNA are colored wheat and gray, respectively. b Cryo-EM density of hmDNA in the MTA1cMTA9–hmDNA–SAM complex is shown in transparent surface. The structure of hmDNA is shown in cartoon and a stick. The flipped residues dA0 and dT0’ are labeled. c Overall structure of MTA1c MTA9 in complex with hmDNA and SAM. d The substrate-binding loop and gate loop 1 of MTA1 contact and distort the hmDNA duplex. Their structures and densities, as well as those of hmDNA, are shown. e dA0 binds to the catalytic site in MTA1. The target dA0 is shown in wheat stick. The residues involved in interacting with dA0 are highlighted in yellow stick representation. f His291 in the interface loop of MTA1 and Gln380 in MTA9 insert into the hmDNA duplex. g Arg221 in the gate loop1 of MTA1 inserts into hmDNA and contacts mdA-1’ (6mA). h Phe293 in the substrate-binding loop of MTA1 and His379 in MTA9 contact hmDNA. i MTA1cMTA9–hmDNA interface. Residues in MTA1 and MTA9 involved in hmDNA binding are highlighted in yellow stick representation. j Relative MTase activity of MTA1c mutants on hmDNA and umDNA. For umDNA, the assay was performed in the presence of 1 μM MTA1cMTA9-B or its mutants for 2 h at 30 °C. For hmDNA, the assay was performed in the presence of 0.25 μM MTA1cMTA9-B or its mutants for 0.5 h at 30 °C. Data are represented as mean ± SD from independent measurements (n = 3). The numbering of corresponding residues in MTA9 is indicated in parentheses. Source data are provided as a Source Data file.
