Fig. 2: H4K20me3 binding allosterically stimulates DNMT1 activity.

a Ribbon and surface diagram of the structure of hDNMT1_351–1600 (PDB 4WXX [10.2210/pdb4WXX/pdb]), with individual segments color coded. The RFTS–CXXC linker helix is denoted as Helix^RC. The detailed interactions between the autoinhibitory linker and the BAH1 domain are shown in the expanded view. The hydrogen bonds are shown as dashed lines. b Close-up view of the structural overlay between hDNMT1_351–1600 (PDB 4WXX [10.2210/pdb4WXX/pdb]) and the bDNMT1_BAH1–H4K20me3 complex, with the autoinhibitory linker and the H4K20me3 peptide colored in slate and yellow, respectively, and the corresponding binding site in hDNMT1_351–1600 shown as electrostatic surface. The bDNMT1_BAH1 domain was removed for clarity. c ITC binding analysis of the interaction between hDNMT1_BAH1, either WT, W796A, or Mut^YW, and the autoinhibitory linker peptide, in the absence of presence of the H4_14–25K20me3 peptide. d DNA methylation activity of hDNMT1_351-1600, WT, W796A, Mut^YW, or Mut^linker. Data are mean ± s.d. (n = 3 biological replicates). Statistical analysis for WT vs. mutants used two-tailed Student’s t test. ***p < 0.001. e H4K20me3-dependent DNA methylation activity of hDNTM1_351–1600, either WT or W796A. The total concentration of H4_14–25K20me0 and H4_14–25K20me3 peptides were maintained at 100 μM to eliminate the substrate-competing effects of the H4 peptides. Data are mean ± s.d. (n = 3 biological replicates). f The RMSD values obtained for the autoinhibitory linker in the structural models of WT (PDB 4WXX [10.2210/pdb4WXX/pdb]) or W796A hDNMT1_351–1600 and the hDNMT1_351–1600-H4K20me3 complex (complex 1 and complex 2) during 100 ns MD simulations. g Sausage view of the RMSF values of the autoinhibitory linker in peptide-free and H4K20me3-bound hDNMT1_351–1600 (complex 2), colored in blue and red, respectively. Source data are provided as a Source Data file.