Conformational Dynamics of DNA Repair by Escherichia Coli Endonuclease III

Overview

Journal J Biol Chem

Specialty Biochemistry

Date 2015 Apr 15

PMID 25869130

Citations 18

Authors

Nikita A Kuznetsov

Olga A Kladova

Alexandra A Kuznetsova

Alexander A Ishchenko

Murat K Saparbaev

Dmitry O Zharkov

Olga S Fedorova

Affiliations

Soon will be listed here.

Abstract

Escherichia coli endonuclease III (Endo III or Nth) is a DNA glycosylase with a broad substrate specificity for oxidized or reduced pyrimidine bases. Endo III possesses two types of activities: N-glycosylase (hydrolysis of the N-glycosidic bond) and AP lyase (elimination of the 3'-phosphate of the AP-site). We report a pre-steady-state kinetic analysis of structural rearrangements of the DNA substrates and uncleavable ligands during their interaction with Endo III. Oligonucleotide duplexes containing 5,6-dihydrouracil, a natural abasic site, its tetrahydrofuran analog, and undamaged duplexes carried fluorescent DNA base analogs 2-aminopurine and 1,3-diaza-2-oxophenoxazine as environment-sensitive reporter groups. The results suggest that Endo III induces several fast sequential conformational changes in DNA during binding, lesion recognition, and adjustment to a catalytically competent conformation. A comparison of two fluorophores allowed us to distinguish between the events occurring in the damaged and undamaged DNA strand. Combining our data with the available structures of Endo III, we conclude that this glycosylase uses a multistep mechanism of damage recognition, which likely involves Gln(41) and Leu(81) as DNA lesion sensors.

Citing Articles

An Insight into the Mechanism of DNA Cleavage by DNA Endonuclease from the Hyperthermophilic Archaeon .

Davletgildeeva A, Kuznetsova A, Ishchenko A, Saparbaev M, Kuznetsov N Int J Mol Sci. 2024; 25(16).

PMID: 39201583 PMC: 11354406. DOI: 10.3390/ijms25168897.

Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides.

Yudkina A, Kim D, Zharkov T, Zharkov D, Endutkin A Int J Mol Sci. 2024; 25(11).

PMID: 38892193 PMC: 11172447. DOI: 10.3390/ijms25116006.

Recognition of a Clickable Abasic Site Analog by DNA Polymerases and DNA Repair Enzymes.

Endutkin A, Yudkina A, Zharkov T, Kim D, Zharkov D Int J Mol Sci. 2022; 23(21).

PMID: 36362137 PMC: 9655677. DOI: 10.3390/ijms232113353.

Biochemical and functional characterization of an endonuclease III from Thermococcus barophilus Ch5.

Tang C, Jiang D, Zhang L World J Microbiol Biotechnol. 2022; 38(8):145.

PMID: 35750964 DOI: 10.1007/s11274-022-03328-y.

A Low-Activity Polymorphic Variant of Human NEIL2 DNA Glycosylase.

Kakhkharova Z, Zharkov D, Grin I Int J Mol Sci. 2022; 23(4).

PMID: 35216329 PMC: 8879280. DOI: 10.3390/ijms23042212.

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