Conformational Dynamics of Dioxygenase AlkB and DNA in the Course of Catalytically Active Enzyme–Substrate Complex Formation
- Authors: Kanazhevskaya L.Y.1, Smyshlyaev D.A.2, Alekseeva I.V.1, Fedorova O.S.1,2
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Affiliations:
- Institute of Chemical Biology and Fundamental Medicine
- Department of Natural Sciences, Novosibirsk State University
- Issue: Vol 45, No 6 (2019)
- Pages: 630-640
- Section: Article
- URL: https://journals.rcsi.science/1068-1620/article/view/229276
- DOI: https://doi.org/10.1134/S1068162019060190
- ID: 229276
Cite item
Abstract
Fe2+/2-ketoglutarate-dependent DNA-dioxygenase AlkB from Escherichia coli is able to restore the native structure of alkylated DNA bases. The enzymatic process utilizes the molecular oxygen, and proceeds through a mechanism of oxidative dealkylation. Here, the kinetics of conformational changes of AlkB and DNA substrates in the course of binding steps were studied. Nickel and cobalt divalent ions were used instead of Fe2+ as metal cofactors in order to inhibit the catalytic activity of AlkB and to study certain stages leading to the formation of a catalytically active enzyme–substrate complex.
About the authors
L. Y. Kanazhevskaya
Institute of Chemical Biology and Fundamental Medicine
Author for correspondence.
Email: Lyubov.Kanazhevskaya@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090
D. A. Smyshlyaev
Department of Natural Sciences, Novosibirsk State University
Email: Lyubov.Kanazhevskaya@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090
I. V. Alekseeva
Institute of Chemical Biology and Fundamental Medicine
Email: Lyubov.Kanazhevskaya@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090
O. S. Fedorova
Institute of Chemical Biology and Fundamental Medicine; Department of Natural Sciences, Novosibirsk State University
Email: Lyubov.Kanazhevskaya@niboch.nsc.ru
Russian Federation, Novosibirsk, 630090; Novosibirsk, 630090