Fig. 5: Conformational transition of the catalytic helix of murine DNMT1.
Close-up views of the conformation of the catalytic helix in the GCG (PDB 4DA4) (a), ACG (b), and CCG (c) complexes. The side chains of the DNA-interacting residues R1241 and Y1243 are shown in stick representation in the GCG complex (a). These two residues are either completely (in the ACG complex) or partially (CCG complex) non-traceable in the other two complexes. The hydrogen-bonding interaction is shown as dashed line in red. The minor groove width at the +2 flank sites (C4′/A4′) is indicated by dashed lines in black. The disordered segments in (b) and (c) are shown by dashed lines in slate and cyan, respectively. Close-up view of the catalytic helix overlaid between a DNMT1 structure with no DNA bound to the catalytic domain (PDB 3PT9) and the CCG complex (d) or the ACG complex (e). Fo-Fc omit map of residues 1242–1249 of mDNMT1731–1602 in the GCG DNA complex (PDB 4DA4). The straight conformation and associated map (2.0 σ level) are colored in silver and magenta, respectively. The kinked conformation and associated map (1.9 σ level) are colored in aquamarine and green, respectively. Enlargement of the AdoMet-binding pockets in the GCG (g), CCG (h) and ACG (i) complexes. The distances between the N7 atom of AdoHcy (SAH) and the side chain or the backbone of residue K1247 are indicated by dashed lines. Note that the side chain of K1247 is non-traceable in (h–i) due to missing electron density.
