Mapping the tRNA Binding Site on the Surface of Human DNMT2 Methyltransferase

Jurkowski, Tomasz P.; Shanmugam, Raghuvaran; Helm, Mark; Jeltsch, Albert

doi:10.1021/bi3002659

Cited by 18 publications

(17 citation statements)

References 27 publications

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“…However, the binding of the two different substrates was similar in both cases, indicating that ground-state tRNA binding does not contribute to specificity of tRNA methylation by Dnmt2. A similar observation has been made previously in a study aiming to identify amino acid residues involved in tRNA binding and recognition of human DNMT2 (23). We conclude that GsDnmt2 shows a striking change in substrate specificity when compared with other Dnmt2 enzymes, which is not based on tRNA-binding preferences.…”

Section: Resultssupporting

confidence: 83%

“…What could be the molecular basis of the unexpected loss of Geobacter tRNA Asp methylation by GsDnmt2 and the corresponding gain of methylation of tRNA Glu ? So far, various amino acids involved in tRNA recognition of the human enzyme could be mapped (23), but the sequence elements needed on the tRNA side were largely unknown. Initially, the G34 base at the wobble position of the anticodon, which is modified to mannosylqueuosine in eukaryotic cells, was associated with Dnmt2 activity (6).…”

Section: Discussionmentioning

confidence: 99%

“…The molecular basis for the specific interaction of Dnmt2 with its tRNA substrates is not yet known. Previously, we have mapped the binding of tRNA Asp to human DNMT2 by mutating several conserved lysine and arginine residues in human DNMT2 and concluded that the anticodon stem/loop of tRNA Asp is a main region of contact for human DNMT2 for the methyl transfer reaction by human DNMT2 (23). Supporting this notion, Muller et al.…”

Section: Introductionmentioning

confidence: 99%

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The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu

Shanmugam

Aklujkar

Schäfer

et al. 2014

Nucleic Acids Research

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Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.

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Section: Resultssupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu

Shanmugam

Aklujkar

Schäfer

et al. 2014

Nucleic Acids Research

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“…We assess the conservation of key residues involved in the substrate interaction according to the experimental data [43]. The residues that interfere strongly in the catalytic action of human DNMT2 are present in DNMT2 of drosophilids with synonymous mutations of physicochemical properties in two sites: R275>K and K367>R (Fig 2).…”

Section: Resultsmentioning

confidence: 99%

Linking epigenetic function to electrostatics: The DNMT2 structural model example

Vieira¹,

Vieira²,

Sinigaglia³

et al. 2017

PLoS ONE

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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 Drosophila melanogaster 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.

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“…The crystal structure of several Dnmt2 homologs has been determined, but unfortunately only without the tRNA substrate [35,36,37]. However, in one study, information on the effect of point mutations in Dnmt2 on tRNA binding and enzymatic activity was used to model tRNA Asp binding on the Dnmt2 structure [38]. This suggests that Dnmt2 mainly contacts the anticodon loop and the stem of the tRNA in order to place the target cytosine near the active site of the enzyme.…”

Section: Molecular Consequences Of Queuosine Modification and Dnmtmentioning

confidence: 99%

Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

Ehrenhofer‐Murray

2017

Biomolecules

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Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5’-triphosphate (GTP) by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed.

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Mapping the tRNA Binding Site on the Surface of Human DNMT2 Methyltransferase

Cited by 18 publications

References 27 publications

The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu

The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu

Linking epigenetic function to electrostatics: The DNMT2 structural model example

Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

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