TY - JOUR

T1 - SNP-Associated Substitutions of Amino Acid Residues in the dNTP Selection Subdomain Decrease Polβ Polymerase Activity

AU - Kladova, Olga A.

AU - Tyugashev, Timofey E.

AU - Miroshnikov, Aleksandr A.

AU - Novopashina, Daria S.

AU - Kuznetsov, Nikita A.

AU - Kuznetsova, Aleksandra A.

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

PY - 2024/5

Y1 - 2024/5

N2 - In the cell, DNA polymerase β (Polβ) is involved in many processes aimed at maintaining genome stability and is considered the main repair DNA polymerase participating in base excision repair (BER). Polβ can fill DNA gaps formed by other DNA repair enzymes. Single-nucleotide polymorphisms (SNPs) in the POLB gene can affect the enzymatic properties of the resulting protein, owing to possible amino acid substitutions. For many SNP-associated Polβ variants, an association with cancer, owing to changes in polymerase activity and fidelity, has been shown. In this work, kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring polymorphic variants G274R, G290C, and R333W. Previously, the amino acid substitutions at these positions have been found in various types of tumors, implying a specific role of Gly-274, Gly-290, and Arg-333 in Polβ functioning. All three polymorphic variants had reduced polymerase activity. Two substitutions—G274R and R333W—led to the almost complete disappearance of gap-filling and primer elongation activities, a decrease in the deoxynucleotide triphosphate–binding ability, and a lower polymerization constant, due to alterations of local contacts near the replaced amino acid residues. Thus, variants G274R, G290C, and R333W may be implicated in an elevated level of unrepaired DNA damage.

AB - In the cell, DNA polymerase β (Polβ) is involved in many processes aimed at maintaining genome stability and is considered the main repair DNA polymerase participating in base excision repair (BER). Polβ can fill DNA gaps formed by other DNA repair enzymes. Single-nucleotide polymorphisms (SNPs) in the POLB gene can affect the enzymatic properties of the resulting protein, owing to possible amino acid substitutions. For many SNP-associated Polβ variants, an association with cancer, owing to changes in polymerase activity and fidelity, has been shown. In this work, kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring polymorphic variants G274R, G290C, and R333W. Previously, the amino acid substitutions at these positions have been found in various types of tumors, implying a specific role of Gly-274, Gly-290, and Arg-333 in Polβ functioning. All three polymorphic variants had reduced polymerase activity. Two substitutions—G274R and R333W—led to the almost complete disappearance of gap-filling and primer elongation activities, a decrease in the deoxynucleotide triphosphate–binding ability, and a lower polymerization constant, due to alterations of local contacts near the replaced amino acid residues. Thus, variants G274R, G290C, and R333W may be implicated in an elevated level of unrepaired DNA damage.

KW - DNA polymerase beta

KW - DNA repair

KW - enzymatic activity

KW - single-nucleotide polymorphism

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85194127428&origin=inward&txGid=1aed9f78d82b55115060ab177efc26ad

UR - https://www.mendeley.com/catalogue/33bdd14d-c658-382f-b61e-658c5295a804/

U2 - 10.3390/biom14050547

DO - 10.3390/biom14050547

M3 - Article

C2 - 38785954

VL - 14

JO - Biomolecules

JF - Biomolecules

SN - 2218-273X

IS - 5

M1 - 547

ER -