The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain
To maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes them...
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| Format: | Article |
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MDPI AG
2023-05-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/12/9/1300 |
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| author | Olga A. Kladova Timofey E. Tyugashev Elena S. Mikushina Nikita A. Kuznetsov Daria S. Novopashina Aleksandra A. Kuznetsova |
| author_facet | Olga A. Kladova Timofey E. Tyugashev Elena S. Mikushina Nikita A. Kuznetsov Daria S. Novopashina Aleksandra A. Kuznetsova |
| author_sort | Olga A. Kladova |
| collection | DOAJ |
| description | To maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes themselves (whose primary function is the recognition and removal of damaged bases) are subject to amino acid substitutions owing to natural single-nucleotide polymorphisms (SNPs). One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA with complementary dNMPs. It is known that many SNPs can cause an amino acid substitution in this enzyme and a significant decrease in the enzymatic activity. In this study, the activity of four natural variants of Polβ, containing substitution E154A, G189D, M236T, or R254I in the transferase domain, was analyzed using molecular dynamics simulations and pre-steady-state kinetic analyses. It was shown that all tested substitutions lead to a significant reduction in the ability to form a complex with DNA and with incoming dNTP. The G189D substitution also diminished Polβ catalytic activity. Thus, a decrease in the activity of studied mutant forms may be associated with an increased risk of damage to the genome. |
| first_indexed | 2024-03-11T04:22:14Z |
| format | Article |
| id | doaj.art-659fe33fca8149e3ad5ac4aa5f0c6fa6 |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-11T04:22:14Z |
| publishDate | 2023-05-01 |
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| record_format | Article |
| series | Cells |
| spelling | doaj.art-659fe33fca8149e3ad5ac4aa5f0c6fa62023-11-17T22:44:01ZengMDPI AGCells2073-44092023-05-01129130010.3390/cells12091300The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase DomainOlga A. Kladova0Timofey E. Tyugashev1Elena S. Mikushina2Nikita A. Kuznetsov3Daria S. Novopashina4Aleksandra A. Kuznetsova5Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, RussiaTo maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes themselves (whose primary function is the recognition and removal of damaged bases) are subject to amino acid substitutions owing to natural single-nucleotide polymorphisms (SNPs). One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA with complementary dNMPs. It is known that many SNPs can cause an amino acid substitution in this enzyme and a significant decrease in the enzymatic activity. In this study, the activity of four natural variants of Polβ, containing substitution E154A, G189D, M236T, or R254I in the transferase domain, was analyzed using molecular dynamics simulations and pre-steady-state kinetic analyses. It was shown that all tested substitutions lead to a significant reduction in the ability to form a complex with DNA and with incoming dNTP. The G189D substitution also diminished Polβ catalytic activity. Thus, a decrease in the activity of studied mutant forms may be associated with an increased risk of damage to the genome.https://www.mdpi.com/2073-4409/12/9/1300DNA repairDNA polymerase betasingle-nucleotide polymorphismenzymatic activity |
| spellingShingle | Olga A. Kladova Timofey E. Tyugashev Elena S. Mikushina Nikita A. Kuznetsov Daria S. Novopashina Aleksandra A. Kuznetsova The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain Cells DNA repair DNA polymerase beta single-nucleotide polymorphism enzymatic activity |
| title | The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain |
| title_full | The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain |
| title_fullStr | The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain |
| title_full_unstemmed | The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain |
| title_short | The Activity of Natural Polymorphic Variants of Human DNA Polymerase β Having an Amino Acid Substitution in the Transferase Domain |
| title_sort | activity of natural polymorphic variants of human dna polymerase β having an amino acid substitution in the transferase domain |
| topic | DNA repair DNA polymerase beta single-nucleotide polymorphism enzymatic activity |
| url | https://www.mdpi.com/2073-4409/12/9/1300 |
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