Linking epigenetic function to electrostatics: The DNMT2 structural model example

<div><p>The amino acid sequence of DNMT2 is very similar to the catalytic domains of bacterial and eukaryotic proteins. However, there is great variability in the region of recognition of the target sequence. While bacterial DNMT2 acts as a DNA methyltransferase, previous studies have indicated low DNA methylation activity in eukaryotic DNMT2, with preference by tRNA methylation. Drosophilids are known as DNMT2-only species and the DNA methylation phenomenon is a not elucidated case yet, as well as the ontogenetic and physiologic importance of DNMT2 for this species group. In addition, more recently study showed that methylation in the genome in <i>Drosophila melanogaster</i> is independent in relation to DNMT2. Despite these findings, Drosophilidae family has more than 4,200 species with great ecological diversity and historical evolution, thus we, therefore, aimed to examine the drosophilids DNMT2 in order to verify its conservation at the physicochemical and structural levels in a functional context. We examined the twenty-six DNMT2 models generated by molecular modelling and five crystallographic structures deposited in the Protein Data Bank (PDB) using different approaches. Our results showed that despite sequence and structural similarity between species close related, we found outstanding differences when they are analyzed in the context of surface distribution of electrostatic properties. The differences found in the electrostatic potentials may be linked with different affinities and processivity of DNMT2 for its different substrates (DNA, RNA or tRNA) and even for interactions with other proteins involved in the epigenetic mechanisms.</p></div

Linking epigenetic function to electrostatics: The DNMT2 structural model example - Fig 6

<p><b>(A)</b> Correlation between experimental ln K_cat/K_m values and the electrostatic potential differences. <b>(B)</b> Predicted K_cat/K_m from methyltransferase 2 structures. The experimental values from HhaI and HaeIII are highlighted in red. <b>(C)</b> Clusters from correlation ln K_cat/K_m and electrostatic potential differences setting drosophilids correlations with all others. The values were transformed to the same quadrant. <b>(D)</b> Correlation between ln (K_cat/K_m) for <i>D</i>. <i>melanogaster</i> DNMT2 and electrostatic potential differences for each DNMT2 protein pair. <b>(E)</b> Correlation between ln (K_cat/K_m) for <i>D</i>. <i>willistoni</i> DNMT2 and electrostatic potential differences for each DNMT2 protein pair. <b>(F)</b> Correlation between ln (K_cat/K_m) for <i>D</i>. <i>rhopaloa</i> DNMT2 and electrostatic potential differences for each DNMT2 protein pair.</p

Kinetic constants for DNA methyltransferase from HaeIII and HhaI.

<p>Kinetic constants for DNA methyltransferase from HaeIII and HhaI.</p

Sequence of HaeIII mutants from Cohen et al. 2004.

<p>Sequence of HaeIII mutants from Cohen et al. 2004.</p

Superposition of drosophilids and human DNMT2 surface representations showing the conservation of residues that have a strong influence in the binding site, according to Jurkowski et al. 2012 where residues that strongly interfere with catalysis activity (> 4-fold) are colored red, 2-4-fold orange and catalytic residues colored purple.

<p>The residues K367 and R275 from human DNMT2 correspond to arginine (R) and lysine (K) in drosophilids, respectively. The <i>G</i>. <i>sulfurreducens</i> and <i>E</i>. <i>histolytica</i> DNMT2 surfaces are presented separately.</p

Multiple structural alignments of all DNMT2 by STAMP in VMD-multiseq.

<p>The structures are colored by sequence identity, similarity, RMSD and Qres values (where 1 indicates that the structures are identical and 0 more dissimilar). <b>(A)</b> Overriding DNMT2 of HhaI (PDB 1MHT) and HaeIII (PDB 1DCT) structures. <b>(B)</b> Superposition of remaining DNA/tRNA MTase2 structures, including <i>Gs</i>DNMT2.</p

Sequence of human DNMT2 mutants from Jurkowski et al. 2012.

<p>Sequence of human DNMT2 mutants from Jurkowski et al. 2012.</p

Cupin: A candidate molecular structure for the Nep1-like protein family-4

Sition of some of the conserved residues in the -structure (right side). The sphere in the middle of the structure represents the putative metal ion.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p

Cupin: A candidate molecular structure for the Nep1-like protein family-1

Sition of some of the conserved residues in the -structure (right side). The sphere in the middle of the structure represents the putative metal ion.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p

Cupin: A candidate molecular structure for the Nep1-like protein family-2

Ion for type I NLP consensus sequence (a), type II NLP consensus sequence (b) and cupin (c). The solid line (shaded gray) represents the confidence level for the , and the dashed line for the . SP = signal peptide. IMR = Inter Motif Region. represents the GHRHDWE motif in type I and II NLP consensus sequences and ihrhscee in , respectively.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p