Fig. 7: Structural comparison of DIM2 and DNMT1.
From: Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation
a Structural overlay between the apo forms of DIM2 and DNMT1 (residues 351-1600) (PDB 4WXX). The RFTS domains of DIM2 and DNMT1 are colored in cyan and yellow, respectively. The rest of DIM2 and DNMT1 are colored in slate and wheat, respectively. Positioning of the DIM2 (b) or DNMT1 (c) RFTS domain (ribbon representation) on top of the MTase domain (electrostatic surface representation). The DNA-binding site of the MTase domain of each protein is marked by a dotted circle. Close-up view of the RFTS-MTase interactions within DIM2 (d) or DNMT1 (e). The hydrogen bonds are depicted as red dashed lines. f Atomic model of DNMT1 (yellow)-DNA (salmon) complex (PDB 4DA4), with the residues surrounding the 5-methylcytosine (mC+1′) on the template strand shown in the expanded view. The 5-methyl group of mC+1′, zinc ions and SAH molecule are shown in sphere representation. Hydrogen bond is depicted as a dashed line. g Atomic model of DIM2 (cyan)-DNA (salmon) complex, with the residues surrounding the +1-flanking nucleotide (G+1′) on the complimentary strand shown in the expanded view. Close-up view of the DNA interactions by DNMT1 (h) or DIM2 (i) MTase domains, centered on at the target site, as well as the −1 to +2-flanking nucleotides. The black arrows indicate the positional shift of Orphan G0′ from an ideal B-form DNA. The hydrogen bonding interactions are shown as dashed lines.
