TY - JOUR

T1 - The Impact of SNP-Induced Amino Acid Substitutions L19P and G66R in the dRP-Lyase Domain of Human DNA Polymerase β on Enzyme Activities

AU - Kladova, Olga A.

AU - Tyugashev, Timofey E.

AU - Yakimov, Denis V.

AU - Mikushina, Elena S.

AU - Novopashina, Daria S.

AU - Kuznetsov, Nikita A.

AU - Kuznetsova, Aleksandra A.

N1 - The part of this work involving mutagenesis, enzyme purification, and kinetic analysis was specifically funded by Russian Science Foundation grant no. 21-74-10103. Partial governmental support for equipment use was received from Russian Ministry of Science and Higher Education project no. 121031300041-4.

PY - 2024/4

Y1 - 2024/4

N2 - Base excision repair (BER), which involves the sequential activity of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases, is one of the enzymatic systems that preserve the integrity of the genome. Normal BER is effective, but due to single-nucleotide polymorphisms (SNPs), the enzymes themselves—whose main function is to identify and eliminate damaged bases—can undergo amino acid changes. One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA. SNPs can significantly affect the catalytic activity of an enzyme by causing an amino acid substitution. In this work, pre-steady-state kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring variants of Polβ that have the substitutions L19P and G66R in the dRP-lyase domain. Despite the substantial distance between the dRP-lyase domain and the nucleotidyltransferase active site, it was found that the capacity to form a complex with DNA and with an incoming dNTP is significantly altered by these substitutions. Therefore, the lower activity of the tested polymorphic variants may be associated with a greater number of unrepaired DNA lesions.

AB - Base excision repair (BER), which involves the sequential activity of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases, is one of the enzymatic systems that preserve the integrity of the genome. Normal BER is effective, but due to single-nucleotide polymorphisms (SNPs), the enzymes themselves—whose main function is to identify and eliminate damaged bases—can undergo amino acid changes. One of the enzymes in BER is DNA polymerase β (Polβ), whose function is to fill gaps in DNA. SNPs can significantly affect the catalytic activity of an enzyme by causing an amino acid substitution. In this work, pre-steady-state kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring variants of Polβ that have the substitutions L19P and G66R in the dRP-lyase domain. Despite the substantial distance between the dRP-lyase domain and the nucleotidyltransferase active site, it was found that the capacity to form a complex with DNA and with an incoming dNTP is significantly altered by these substitutions. Therefore, the lower activity of the tested polymorphic variants may be associated with a greater number of unrepaired DNA lesions.

KW - DNA polymerase beta

KW - DNA repair

KW - enzymatic activity

KW - single-nucleotide polymorphism

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85191382247&origin=inward&txGid=681cb653fa9eabb14a9dbe8f8a4416ab

UR - https://www.mendeley.com/catalogue/b6d5cabe-4445-3658-ae07-366a888171f4/

U2 - 10.3390/ijms25084182

DO - 10.3390/ijms25084182

M3 - Article

C2 - 38673769

VL - 25

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 8

M1 - 4182

ER -