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Kinetic Milestones of Damage Recognition by DNA Glycosylases of the Helix-Hairpin-Helix Structural Superfamily

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Mechanisms of Genome Protection and Repair

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1241))

Abstract

X-ray data show that DNA glycosylases, which initiate the pathway of base excision repair in DNA, belong to six structural superfamilies. Here, we provide an overview of the latest results of kinetic studies on the mechanisms of specific recognition of a damaged nucleotide at the early steps of DNA repair by human (OGG1 and MBD4) or Escherichia coli (Nth and MutY) N-DNA-glycosylases belonging to superfamily Helix-hairpin-Helix (HhH). A comparison of real-time conformational transformations of DNA glycosylases and DNA with the structural data obtained for free enzymes and their complexes with substrates and intermediates have made it possible to build molecular-kinetic models of the enzymatic processes. These models have allowed researchers to associate the conformational transitions of the interacting molecules with elementary steps of an enzymatic process. Additionally, these models have revealed the stages that make the largest contribution to the specificity of the enzyme for DNA substrates. These data provide an opportunity to gain further insight into the structural and dynamic principles underlying the enzymatic processes that ensure highly efficient functioning of the repair-protective system of all living organisms and that maintain DNA integrity.

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Acknowledgements

This work was supported by a Russian-Government-funded project (No. АААА-А17-117020210022-4) and grant of Ministry of Science and Higher Education No MD-3775.2019.4. The part of the work including analysis of experimental data for MBD4 was supported by the Russian Scientific Foundation project No. 16-14-10038.

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  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia

    Nikita A. Kuznetsov & Olga S. Fedorova

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  1. Nikita A. Kuznetsov
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  2. Olga S. Fedorova
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Correspondence to Olga S. Fedorova .

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  1. Novosibirsk State University, Novosibirsk, Russia

    Dmitry O. Zharkov

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Kuznetsov, N.A., Fedorova, O.S. (2020). Kinetic Milestones of Damage Recognition by DNA Glycosylases of the Helix-Hairpin-Helix Structural Superfamily. In: Zharkov, D. (eds) Mechanisms of Genome Protection and Repair. Advances in Experimental Medicine and Biology, vol 1241. Springer, Cham. https://doi.org/10.1007/978-3-030-41283-8_1

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