Autoinhibitory Structure

DNMT-1 Autoinhibitory Structure

Although the methyl transferase domain has substrate preference, however, an autoinbitory mechanism has been discovered that DNMT1 use  to ensure only the hemi-methylated CpG dinucleotide can enter the active site.
CXXC domain

Different fromthe DNMT-1 inhibitory structure, the recognition of hemi-methylcytosine is carried out by CXXC (zinc finger recognition domain in the N terminus) in autoinhibitory domain.

The CXXC domain targets both the major and minor grooves of the DNA over a CpG-containing 4-bp footprint. A loop segment (Arg684-Ser685-Lys686-Gln687) from the CXXC domain penetrates into the major groove and forms base-specific and phosphodiester intermolecular interactions.The guanine bases in the CpG dinucleotide are recognized by side-chain interactions involving Lys686 and Gln687 of the CXXC domain, whereas the cytosine bases in the CpG dinucleotide are recognized by backbone interactions involving Ser685 and Lys686 of the CXXC domain.DNA recognition is further anchored by salt bridges between arginine side chains of the CXXC domain and the phosphodiester backbone of the DNA.

Pymol derived interaction between the loop segment(Arg684-Ser685-Lys686-Gln687) of CXXC domain(red) with bounded Zn2+ ion and major groove of DNA

Methyltransferase domain

The methyltransferase domain of mDNMT1 folds into two subdomains:catalytic core and the TRD(target recognition domain)

catalytic core(in cyan) of C terminal methyltransferase with bounded AdoHcy with filled in sphere

The catalytic core of DNMT1 consists of seven-stranded β-sheet that is flanked by three α-helices on either side.

At one end, this central β-sheet is further joined by a two-stranded anti-parallel β-sheet from the BAH1 domain.

The TRD subdomain is inserted between the central β-sheet and the last three a-helices of the catalytic core. The majority of the TRD folds into an independent structural unit and is stabilized in part by a Cys3Hiscoordinated Zn2+ ion

electrostatic interaction between Zn2+ and TRD fold

In addition, a hairpin-like fold at the start of the TRD forms hydrophobic contacts with the catalytic core and the BAH1 domain

The exclusion of the unmethylated DNA from the active site is the result of an autoinhibitory CXXC-BAH1 linker, which contains a highly acidic segment spanning residues D703 to D711 and is positioned directly between the DNA and the active site.

The largest difference between the productive and the autoinhibitory structure is in the conformational change of the catalytic loop.
-productive structure: catalytic loop followed by a straight alpha helix which can penetrates the minor loop
-autoinhibitory structure: catalytic loop followed by an alpha helix having a kink at the N terminus, which excludes catalytic loop from accessing the DNA minor groove.