M. Hhal is a type of m5C-MTase, which catalyzes the transfer of a methyl group from AdoMet to 5C of cytosine. This enzyme recognizes a specific 5’-GCGC-3’ sequence and methylate the first cytosine residue. The crystal structure of M.Hhal reveals six most highly conserved motifs which is not involved in DNA binding.
Picture of M.Hhal (above) and mDNMT1 only showing CXXC, auto-inhibitory linker and Catalytic domain (below)
A structural overlay of M.Hhal and mDNMT1 shows a superposition of their catalytic core.
All six highly conserved domains in mDNMT1 except domain IV adopt a very similar structure to those in M.Hhal.
Structural superposition of six conserved sequence motifs between mDNMT1(650-1602)-DNA 19-mer and M.HhaI-DNA complexes. A, Motif I. B, motif IV. C, motif VI. D, motif VIII. E, motif IX. F motif X. Picture taken from Jikui Song, et al. Science 331, 1036 (2011)
Although there is a superposition of catalytic core of mDNMT1 and M.Hhal, the un-methylated DNA in mDNMT1-DNA complex is displaced laterally by the width of a DNA duplex. In M.Hhal-DNA complex, the DNA has direct contact with catalytic domain and the cytosine is inserted into the active site. In contrast, the un-methylated DNA in mDNMT1-DNA complex is anchored by CXXC domain, which is excluded from the active site by the auto-inhibitory CXXC-BAH1 linker. The auto-inhibitory linker contains a highly acidic segment residue, which can interact with negatively charged DNA backbone in a favorable manner.
picture showing the surface of the auto-inhibitory linker separating DNA and the catalytic core
Although both mDNMT1 and M.Hhal catalyze methylation to CpG dinucleotides, their TRD show a little sequence similarity and exhibit the greatest structural divergence.
Structure-based sequence alignment between catalytic methyltransferase domains
of mDNMT1, mouse DNMT3A (mDNMT3A) and M.HhaI. Identical or similar residues
are colored in green. Completely conserved residues are colored in red and
highlighted in yellow. Taken from Jikui Song, et al. Science 331, 1036 (2011)
of mDNMT1, mouse DNMT3A (mDNMT3A) and M.HhaI. Identical or similar residues
are colored in green. Completely conserved residues are colored in red and
highlighted in yellow. Taken from Jikui Song, et al. Science 331, 1036 (2011)
