1
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Davletgildeeva AT, Tyugashev TE, Zhao M, Kuznetsov NA, Ishchenko AA, Saparbaev M, Kuznetsova AA. Individual Contributions of Amido Acid Residues Tyr122, Ile168, and Asp173 to the Activity and Substrate Specificity of Human DNA Dioxygenase ABH2. Cells 2023; 12:1839. [PMID: 37508504 PMCID: PMC10377887 DOI: 10.3390/cells12141839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Human Fe(II)/α-ketoglutarate-dependent dioxygenase ABH2 plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases, e.g., N1-methyladenine (m1A), N3-methylcytosine (m3C), and some etheno derivatives. Moreover, ABH2 is capable of a less efficient oxidation of an epigenetic DNA mark called 5-methylcytosine (m5C), which typically is a specific target of DNA dioxygenases from the TET family. In this study, to elucidate the mechanism of the substrate specificity of ABH2, we investigated the role of several active-site amino acid residues. Functional mapping of the lesion-binding pocket was performed through the analysis of the functions of Tyr122, Ile168, and Asp173 in the damaged base recognition mechanism. Interactions of wild-type ABH2, or its mutants Y122A, I168A, or D173A, with damaged DNA containing the methylated base m1A or m3C or the epigenetic marker m5C were analyzed by molecular dynamics simulations and kinetic assays. Comparative analysis of the enzymes revealed an effect of the substitutions on DNA binding and on catalytic activity. Obtained data clearly demonstrate the effect of the tested amino acid residues on the catalytic activity of the enzymes rather than the DNA-binding ability. Taken together, these data shed light on the molecular and kinetic consequences of the substitution of active-site residues for the mechanism of the substrate recognition.
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Affiliation(s)
- Anastasiia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Mingxing Zhao
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander A Ishchenko
- Groupe Mechanisms of DNA Repair and Carcinogenesis, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, CEDEX, F-94805 Villejuif, France
| | - Murat Saparbaev
- Groupe Mechanisms of DNA Repair and Carcinogenesis, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, CEDEX, F-94805 Villejuif, France
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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2
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Bakman AS, Boichenko SS, Kuznetsova AA, Ishchenko AA, Saparbaev M, Kuznetsov NA. The Impact of Human DNA Glycosylases on the Activity of DNA Polymerase β toward Various Base Excision Repair Intermediates. Int J Mol Sci 2023; 24:ijms24119594. [PMID: 37298543 DOI: 10.3390/ijms24119594] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Base excision repair (BER) is one of the important systems for the maintenance of genome stability via repair of DNA lesions. BER is a multistep process involving a number of enzymes, including damage-specific DNA glycosylases, apurinic/apyrimidinic (AP) endonuclease 1, DNA polymerase β, and DNA ligase. Coordination of BER is implemented by multiple protein-protein interactions between BER participants. Nonetheless, mechanisms of these interactions and their roles in the BER coordination are poorly understood. Here, we report a study on Polβ's nucleotidyl transferase activity toward different DNA substrates (that mimic DNA intermediates arising during BER) in the presence of various DNA glycosylases (AAG, OGG1, NTHL1, MBD4, UNG, or SMUG1) using rapid-quench-flow and stopped-flow fluorescence approaches. It was shown that Polβ efficiently adds a single nucleotide into different types of single-strand breaks either with or without a 5'-dRP-mimicking group. The obtained data indicate that DNA glycosylases AAG, OGG1, NTHL1, MBD4, UNG, and SMUG1, but not NEIL1, enhance Polβ's activity toward the model DNA intermediates.
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Affiliation(s)
- Artemiy S Bakman
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Stanislav S Boichenko
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Group «Mechanisms of DNA Repair and Carcinogenesis», Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805 Villejuif, France
| | - Murat Saparbaev
- Group «Mechanisms of DNA Repair and Carcinogenesis», Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805 Villejuif, France
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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3
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Zakharova MY, Kuznetsova AA, Uvarova VI, Fomina AD, Kozlovskaya LI, Kaliberda EN, Kurbatskaia IN, Smirnov IV, Bulygin AA, Knorre VD, Fedorova OS, Varnek A, Osolodkin DI, Ishmukhametov AA, Egorov AM, Gabibov AG, Kuznetsov NA. Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Front Pharmacol 2021; 12:773198. [PMID: 34938188 PMCID: PMC8686763 DOI: 10.3389/fphar.2021.773198] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/29/2021] [Indexed: 02/05/2023] Open
Abstract
The design of effective target-specific drugs for COVID-19 treatment has become an intriguing challenge for modern science. The SARS-CoV-2 main protease, Mpro, responsible for the processing of SARS-CoV-2 polyproteins and production of individual components of viral replication machinery, is an attractive candidate target for drug discovery. Specific Mpro inhibitors have turned out to be promising anticoronaviral agents. Thus, an effective platform for quantitative screening of Mpro-targeting molecules is urgently needed. Here, we propose a pre-steady-state kinetic analysis of the interaction of Mpro with inhibitors as a basis for such a platform. We examined the kinetic mechanism of peptide substrate binding and cleavage by wild-type Mpro and by its catalytically inactive mutant C145A. The enzyme induces conformational changes of the peptide during the reaction. The inhibition of Mpro by boceprevir, telaprevir, GC-376, PF-00835231, or thimerosal was investigated. Detailed pre-steady-state kinetics of the interaction of the wild-type enzyme with the most potent inhibitor, PF-00835231, revealed a two-step binding mechanism, followed by covalent complex formation. The C145A Mpro mutant interacts with PF-00835231 approximately 100-fold less effectively. Nevertheless, the binding constant of PF-00835231 toward C145A Mpro is still good enough to inhibit the enzyme. Therefore, our results suggest that even noncovalent inhibitor binding due to a fine conformational fit into the active site is sufficient for efficient inhibition. A structure-based virtual screening and a subsequent detailed assessment of inhibition efficacy allowed us to select two compounds as promising noncovalent inhibitor leads of SARS-CoV-2 Mpro.
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Affiliation(s)
- Maria Yu Zakharova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Victoria I Uvarova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
| | - Anastasiia D Fomina
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Liubov I Kozlovskaya
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Elena N Kaliberda
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Inna N Kurbatskaia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Ivan V Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Anatoly A Bulygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Vera D Knorre
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Alexandre Varnek
- Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, Strasbourg, France
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Alexander G Gabibov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia.,Department of Biology and Biotechnology, Higher School of Economics, Moscow, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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4
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Kladova OA, Alekseeva IV, Saparbaev M, Fedorova OS, Kuznetsov NA. Modulation of the Apurinic/Apyrimidinic Endonuclease Activity of Human APE1 and of Its Natural Polymorphic Variants by Base Excision Repair Proteins. Int J Mol Sci 2020; 21:ijms21197147. [PMID: 32998246 PMCID: PMC7583023 DOI: 10.3390/ijms21197147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/25/2022] Open
Abstract
Human apurinic/apyrimidinic endonuclease 1 (APE1) is known to be a critical player of the base excision repair (BER) pathway. In general, BER involves consecutive actions of DNA glycosylases, AP endonucleases, DNA polymerases, and DNA ligases. It is known that these proteins interact with APE1 either at upstream or downstream steps of BER. Therefore, we may propose that even a minor disturbance of protein–protein interactions on the DNA template reduces coordination and repair efficiency. Here, the ability of various human DNA repair enzymes (such as DNA glycosylases OGG1, UNG2, and AAG; DNA polymerase Polβ; or accessory proteins XRCC1 and PCNA) to influence the activity of wild-type (WT) APE1 and its seven natural polymorphic variants (R221C, N222H, R237A, G241R, M270T, R274Q, and P311S) was tested. Förster resonance energy transfer–based kinetic analysis of abasic site cleavage in a model DNA substrate was conducted to detect the effects of interacting proteins on the activity of WT APE1 and its single-nucleotide polymorphism (SNP) variants. The results revealed that WT APE1 activity was stimulated by almost all tested DNA repair proteins. For the SNP variants, the matters were more complicated. Analysis of two SNP variants, R237A and G241R, suggested that a positive charge in this area of the APE1 surface impairs the protein–protein interactions. In contrast, variant R221C (where the affected residue is located near the DNA-binding site) showed permanently lower activation relative to WT APE1, whereas neighboring SNP N222H did not cause a noticeable difference as compared to WT APE1. Buried substitution P311S had an inconsistent effect, whereas each substitution at the DNA-binding site, M270T and R274Q, resulted in the lowest stimulation by BER proteins. Protein–protein molecular docking was performed between repair proteins to identify amino acid residues involved in their interactions. The data uncovered differences in the effects of BER proteins on APE1, indicating an important role of protein–protein interactions in the coordination of the repair pathway.
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Affiliation(s)
- Olga A. Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
| | - Irina V. Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
| | - Murat Saparbaev
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, CEDEX, F-94805 Villejuif, France;
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
- Correspondence: (O.S.F.); (N.A.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
- Correspondence: (O.S.F.); (N.A.K.)
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5
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Kladova OA, Kuznetsova AA, Barthes NPF, Michel BY, Burger A, Fedorova OS, Kuznetsov NA. New Fluorescent Analogs of Nucleotides Based on 3-Hydroxychromone for Recording Conformational Changes of DNA. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Iakovlev DA, Alekseeva IV, Vorobjev YN, Kuznetsov NA, Fedorova OS. The Role of Active-Site Residues Phe98, His239, and Arg243 in DNA Binding and in the Catalysis of Human Uracil-DNA Glycosylase SMUG1. Molecules 2019; 24:molecules24173133. [PMID: 31466351 PMCID: PMC6749576 DOI: 10.3390/molecules24173133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 11/16/2022] Open
Abstract
Human SMUG1 (hSMUG1) hydrolyzes the N-glycosidic bond of uracil and some uracil lesions formed in the course of epigenetic regulation. Despite the functional importance of hSMUG1 in the DNA repair pathway, the damage recognition mechanism has been elusive to date. In the present study, our objective was to build a model structure of the enzyme-DNA complex of wild-type hSMUG1 and several hSMUG1 mutants containing substitution F98W, H239A, or R243A. Enzymatic activity of these mutant enzymes was examined by polyacrylamide gel electrophoresis analysis of the reaction product formation and pre-steady-state analysis of DNA conformational changes during enzyme-DNA complex formation. It was shown that substitutions F98W and H239A disrupt specific contacts generated by the respective wild-type residues, namely stacking with a flipped out Ura base in the damaged base-binding pocket or electrostatic interactions with DNA in cases of Phe98 and His239, respectively. A loss of the Arg side chain in the case of R243A reduced the rate of DNA bending and increased the enzyme turnover rate, indicating facilitation of the product release step.
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Affiliation(s)
- Danila A Iakovlev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia
| | - Irina V Alekseeva
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia
| | - Yury N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University (NSU), 2 Pirogova St., Novosibirsk 630090, Russia.
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University (NSU), 2 Pirogova St., Novosibirsk 630090, Russia.
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7
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Kuznetsova AA, Matveeva AG, Milov AD, Vorobjev YN, Dzuba SA, Fedorova OS, Kuznetsov NA. Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway. Nucleic Acids Res 2019; 46:11454-11465. [PMID: 30329131 PMCID: PMC6265485 DOI: 10.1093/nar/gky912] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Human apurinic/apyrimidinic (AP) endonuclease APE1 catalyses the hydrolysis of phosphodiester bonds on the 5′ side of an AP-site (in the base excision repair pathway) and of some damaged nucleotides (in the nucleotide incision repair pathway). The range of substrate specificity includes structurally unrelated damaged nucleotides. Here, to examine the mechanism of broad substrate specificity of APE1, we performed pulsed electron–electron double resonance (PELDOR) spectroscopy and pre-steady-state kinetic analysis with Förster resonance energy transfer (FRET) detection of DNA conformational changes during DNA binding and lesion recognition. Equilibrium PELDOR and kinetic FRET data revealed that DNA binding by APE1 leads to noticeable damage-dependent bending of a DNA duplex. Molecular dynamics simulations showed that the damaged nucleotide is everted from the DNA helix and placed into the enzyme’s binding pocket, which is formed by Asn-174, Asn-212, Asn-229, Ala-230, Phe-266 and Trp-280. Nevertheless, no damage-specific contacts were detected between these amino acid residues in the active site of the enzyme and model damaged substrates containing 1,N6-ethenoadenosine, α-adenosine, 5,6-dihydrouridine or F-site. These data suggest that the substrate specificity of APE1 is controlled by the ability of a damaged nucleotide to flip out from the DNA duplex in response to an enzyme-induced DNA distortion.
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Affiliation(s)
- Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna G Matveeva
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yuri N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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8
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Kuznetsova AA, Iakovlev DA, Misovets IV, Ishchenko AA, Saparbaev MK, Kuznetsov NA, Fedorova OS. Pre-steady-state kinetic analysis of damage recognition by human single-strand selective monofunctional uracil-DNA glycosylase SMUG1. MOLECULAR BIOSYSTEMS 2018; 13:2638-2649. [PMID: 29051947 DOI: 10.1039/c7mb00457e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In all organisms, DNA glycosylases initiate base excision repair pathways resulting in removal of aberrant bases from DNA. Human SMUG1 belongs to the superfamily of uracil-DNA glycosylases catalyzing the hydrolysis of the N-glycosidic bond of uridine and uridine lesions bearing oxidized groups at C5: 5-hydroxymethyluridine (5hmU), 5-formyluridine (5fU), and 5-hydroxyuridine (5hoU). An apurinic/apyrimidinic (AP) site formed as the product of an N-glycosylase reaction is tightly bound to hSMUG1, thus inhibiting the downstream action of AP-endonuclease APE1. The steady-state kinetic parameters (kcat and KM; obtained from the literature) correspond to the enzyme turnover process limited by the release of hSMUG1 from the complex with the AP-site. In the present study, our objective was to carry out a stopped-flow fluorescence analysis of the interaction of hSMUG1 with a DNA substrate containing a dU:dG base pair to follow the pre-steady-state kinetics of conformational changes in both molecules. A comparison of kinetic data obtained by means of Trp and 2-aminopurine fluorescence and Förster resonance energy transfer (FRET) detection allowed us to elucidate the stages of specific and nonspecific DNA binding, to propose the mechanism of damaged base recognition by hSMUG1, and to determine the true rate of the catalytic step. Our results shed light on the kinetic mechanism underlying the initiation of base excision repair by hSMUG1 using the "wedge" strategy for DNA lesion search.
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Affiliation(s)
- Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia.
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9
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Mutational and Kinetic Analysis of Lesion Recognition by Escherichia coli Endonuclease VIII. Genes (Basel) 2017; 8:genes8050140. [PMID: 28505099 PMCID: PMC5448014 DOI: 10.3390/genes8050140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 12/14/2022] Open
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.
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