Mechanistic Insights into Cytosine-N3 Methylation by DNA Methyltransferase DNMT3A |
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| Affiliation: | 1. Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany;2. MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK;3. Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK;1. Center for Systems Biology, Soochow University, Suzhou 215006, China;2. Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China;3. University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China;1. Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany;2. Institute of Biochemistry, Leipzig University,Brüderstrasse 34, 04103 Leipzig, Germany;3. Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany;4. Institute of Pharmaceutical Sciences, University of Freiburg, Stefan-Meier-Str.19, 79104 Freiburg, Germany;5. Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany |
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| Abstract: | Recently, it has been discovered that different DNA-(cytosine C5)-methyltransferases including DNMT3A generate low levels of 3mC [Rosic et al. (2018), Nat. Genet., 50, 452–459]. This reaction resulted in the co-evolution of DNMTs and ALKB2 DNA repair enzymes, but its mechanism remained elusive. Here, we investigated the catalytic mechanism of DNMT3A for cytosine N3 methylation. We generated several DNMT3A variants with mutated catalytic residues and measured their activities in 5mC and 3mC generation by liquid chromatography linked to tandem mass spectrometry. Our data suggest that the methylation of N3 instead of C5 is caused by an inverted binding of the flipped cytosine target base into the active-site pocket of the DNA methyltransferase, which is partially compatible with the arrangement of catalytic amino acid residues. Given that all DNA-(cytosine C5)-methyltransferases have a common catalytic mechanism, it is likely that other enzymes of this class generate 3mC following the same mechanism. |
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