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Genes 2017, 8(5), 140; doi:10.3390/genes8050140

Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII

1
Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
2
Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
*
Authors to whom correspondence should be addressed.
Academic Editors: Linda Bloom and Jörg Bungert
Received: 27 February 2017 / Revised: 3 May 2017 / Accepted: 9 May 2017 / Published: 13 May 2017
(This article belongs to the Special Issue Protein-DNA Interactions)
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Abstract

Escherichia coli endonuclease VIII (Endo VIII) is a DNA glycosylase with substrate specificity for a wide range of oxidatively damaged pyrimidine bases. Endo VIII catalyzes hydrolysis of the N-glycosidic bond and β, δ-elimination of 3′- and 5′-phosphate groups of an apurinic/apyrimidinic site. Single mutants of Endo VIII L70S, L70W, Y71W, F121W, F230W, and P253W were analyzed here with the aim to elucidate the kinetic mechanism of protein conformational adjustment during damaged-nucleotide recognition and catalytic-complex formation. F121W substitution leads to a slight reduction of DNA binding and catalytic activity. F230W substitution slows the rate of the δ-elimination reaction indicating that interaction of Phe230 with a 5′-phosphate group proceeds in the latest catalytic step. P253W Endo VIII has the same activity as the wild type (WT) enzyme. Y71W substitution slightly reduces the catalytic activity due to the effect on the later steps of catalytic-complex formation. Both L70S and L70W substitutions significantly decrease the catalytic activity, indicating that Leu70 plays an important role in the course of enzyme-DNA catalytic complex formation. Our data suggest that Leu70 forms contacts with DNA earlier than Tyr71 does. Therefore, most likely, Leu70 plays the role of a DNA lesion “sensor”, which is used by Endo VIII for recognition of a DNA damage site. View Full-Text
Keywords: base excision repair; DNA glycosylase; conformational dynamics; stopped-flow enzyme kinetics; endonuclease VIII base excision repair; DNA glycosylase; conformational dynamics; stopped-flow enzyme kinetics; endonuclease VIII
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MDPI and ACS Style

Kladova, O.A.; Kuznetsova, A.A.; Fedorova, O.S.; Kuznetsov, N.A. Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII. Genes 2017, 8, 140.

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