Structure of the productive DNMT1-DNA complex. The DNA is beige with cytosines from the parental and target strands in blue and purple, respectively. Purple spheres are zinc ions. Figure courtesy of Jikui Song.
DNA methylation is a stable epigenetic modification essential for processes such as gene silencing, genome imprinting and X-chromosome inactivation. The methyltransferase DNMT1 maintains this modification during DNA replication by recognizing methylated CpG dinucleotide steps on the parental strand and transferring a methyl group from an S-adenosylmethionine (AdoMet) cofactor to the correct cytosine on the target strand. DNMT1 is a large modular protein that uses a cysteine-rich CXXC (Cys-X-X-Cys) domain to couple recognition of unmodified DNA to placement of an autoinhibitory loop in the methyltransferase active site. Substrate selectivity requires a conformational transition upon recognition of modified DNA.
Patel and colleagues have solved the structure of a productive complex of mouse DNMT1 (mDNMT1) with modified DNA at 2.6-Å resolution (PDB 4DA4). To form the complex, the authors cross-linked hemimethylated DNA to a truncated version of mDNMT1 in which the CXXC domain and the autoinhibitory loop were removed. The DNA is inserted into the catalytic cleft and undergoes a significant helical distortion during interrogation of the methylation status of the CpG step. Recognition of both the parental and target strands is achieved by an extensive array of base-specific and water-mediated DNA backbone interactions. The methylated cytosine on the parental strand remains stacked within the helix and is recognized by a shallow concave hydrophobic surface on the target recognition domain (TRD). Compared to the previously determined structure of an autoinhibited mDNMT1-DNA complex, the largest conformational change in mDNMT1 was observed for the active site catalytic loop, which is buttressed by an α-helix and inspects the minor groove in the productive complex. The target cytosine is looped out of the helix and into the active site, where it is methylated due to proximity to AdoMet (present in the crystal structure as the reaction by-product, S-adenosylhomocysteine (AdoHcy)). The orphan guanine is translated by one step along the helix and results in a non-canonical base pair with a guanine in the target strand. This base pair and the adjacent methylated Watson-Crick pair are stabilized by specific hydrogen-bond interactions with TRD residues. Residues from the bromo-adjacent homology 2 (BAH2) domain become ordered and engage in further interactions with the DNA phosphate backbone of the target strand.
Combined with mutational analysis, the structure of the productive mDNMT1-DNA complex reveals how mutually supportive autoinhibitory and active mechanisms ensure maintenance of methylation patterns during replication.