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The conserved aspartate in motif III of β family AdoMet-dependent DNA methyltransferase is important for methylation

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Abstract

S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases) are involved in diverse cellular functions. These enzymes show little sequence conservation but have a conserved structural fold. The DNA MTases have characteristic motifs that are involved in AdoMet binding, DNA target recognition and catalysis. Motif III of these MTases have a highly conserved acidic residue, often an aspartate, whose functional significance is not clear. Here, we report a mutational study of the residue in the β family MTase of the Type III restriction-modification enzyme EcoP15I. Replacement of this residue by alanine affects its methylation activity. We propose that this residue contributes to the affinity of the enzyme for AdoMet. Analysis of the structures of DNA, RNA and protein MTases reveal that the acidic residue is conserved in all of them, and interacts with N6 of the adenine moiety of AdoMet. Interestingly, in the SET-domain protein lysine MTases, which have a fold different from other AdoMet-dependent MTases, N6 of the adenine moiety is hydrogen bonded to the main chain carbonyl group of the histidine residue of the highly conserved motif III. Our study reveals the evolutionary conservation of a carbonyl group in DNA, RNA and protein AdoMet-dependent MTases for specific interaction by hydrogen bond with AdoMet, despite the lack of overall sequence conservation.

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Acknowledgements

This work was supported by the Science and Engineering Research Board, Department of Science and Technology (DST), India (EMR/2016/000872 to KS). AG thanks DST India for an INSPIRE Scholarship. IA thanks University Grants Commission, India, for a Senior Research Fellowship. OPC thanks the Department of Biotechnology, India, for Research Associate Fellowship.

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  1. These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Biology, Indian Institute of Science Education and Research, Pune, 411 008, India

    Aathira Gopinath, Manasi Kulkarni, Ishtiyaq Ahmed, Om Prakash Chouhan & Kayarat Saikrishnan

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  1. Aathira Gopinath
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  2. Manasi Kulkarni
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  3. Ishtiyaq Ahmed
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  4. Om Prakash Chouhan
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  5. Kayarat Saikrishnan
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Correspondence to Kayarat Saikrishnan.

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This article is part of the Topical Collection: Chromatin Biology and Epigenetics.

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Gopinath, A., Kulkarni, M., Ahmed, I. et al. The conserved aspartate in motif III of β family AdoMet-dependent DNA methyltransferase is important for methylation. J Biosci 45, 10 (2020). https://doi.org/10.1007/s12038-019-9983-2

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  • DOI: https://doi.org/10.1007/s12038-019-9983-2

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