TY - JOUR

T1 - Catalytic efficiency of predicted deleterious missense variants of human DNA dioxygenase ABH2

AU - Sagalakova, Viktoriia V.

AU - Davletgildeeva, Anastasiia T.

AU - Kolesnikova, Viktoriia A.

AU - Kuznetsov, Nikita A.

PY - 2026

Y1 - 2026

N2 - Human DNA dioxygenase ABH2 is a key Fe(II)/α-ketoglutarate-dependent enzyme that removes a broad range of cytotoxic alkylated lesions, including N ¹ -methyladenine (m¹A) and N ³ -methylcytosine (m³C), from double-stranded DNA, thereby supporting genome stability. Naturally occurring missense single nucleotide variants (SNVs) in the ABH2 gene can modulate its catalytic properties and, consequently, the efficiency of direct DNA repair. In this study, we functionally characterized eight ABH2 variants featuring SNVs-associated substitutions G103R, S125L, S188F, F195S, M226T, R248Q, R248W, or T252I, that had been previously (Davletgildeeva et al., 2025) classified as potentially deleterious by multiple prediction algorithms. We quantified kinetic parameters of the corresponding ABH2 variants toward double-stranded DNA substrates containing either m¹A or m³C and compared their catalytic efficiency to that of the wild-type enzyme. For most of the variants, the negative prognosis was justified, as the introduced substitutions, while maintaining the general architecture of the protein globule and having insignificant differences in thermal stability, led to a decrease (G103R, S188F, T252I, and, to a lesser extent, S125L) or even complete loss (R248Q and R248W) of the catalytic activity of the ABH2 enzyme toward both tested damaged nucleobases. At the same time, M226T and F195S variants demonstrated an increase in activity of the enzyme toward m3C, thus contradicting the obtained negative prognosis. Our findings show that naturally occurring ABH2 missense variants can differentially alter the repair efficiency of m1A and m3C lesions in double-stranded DNA, ranging from partial to complete loss or lesion-selective enhancement of catalytic activity. Structural analysis suggests that these functional effects arise from disruption of local interactions and/or changes in conformational flexibility required to form a catalytically competent enzyme–DNA complex. Overall, these results delineate a diverse functional landscape of naturally occurring ABH2 missense variants and provide a quantitative framework for understanding how sequence variation shapes the enzyme’s DNA repair capacity.

AB - Human DNA dioxygenase ABH2 is a key Fe(II)/α-ketoglutarate-dependent enzyme that removes a broad range of cytotoxic alkylated lesions, including N ¹ -methyladenine (m¹A) and N ³ -methylcytosine (m³C), from double-stranded DNA, thereby supporting genome stability. Naturally occurring missense single nucleotide variants (SNVs) in the ABH2 gene can modulate its catalytic properties and, consequently, the efficiency of direct DNA repair. In this study, we functionally characterized eight ABH2 variants featuring SNVs-associated substitutions G103R, S125L, S188F, F195S, M226T, R248Q, R248W, or T252I, that had been previously (Davletgildeeva et al., 2025) classified as potentially deleterious by multiple prediction algorithms. We quantified kinetic parameters of the corresponding ABH2 variants toward double-stranded DNA substrates containing either m¹A or m³C and compared their catalytic efficiency to that of the wild-type enzyme. For most of the variants, the negative prognosis was justified, as the introduced substitutions, while maintaining the general architecture of the protein globule and having insignificant differences in thermal stability, led to a decrease (G103R, S188F, T252I, and, to a lesser extent, S125L) or even complete loss (R248Q and R248W) of the catalytic activity of the ABH2 enzyme toward both tested damaged nucleobases. At the same time, M226T and F195S variants demonstrated an increase in activity of the enzyme toward m3C, thus contradicting the obtained negative prognosis. Our findings show that naturally occurring ABH2 missense variants can differentially alter the repair efficiency of m1A and m3C lesions in double-stranded DNA, ranging from partial to complete loss or lesion-selective enhancement of catalytic activity. Structural analysis suggests that these functional effects arise from disruption of local interactions and/or changes in conformational flexibility required to form a catalytically competent enzyme–DNA complex. Overall, these results delineate a diverse functional landscape of naturally occurring ABH2 missense variants and provide a quantitative framework for understanding how sequence variation shapes the enzyme’s DNA repair capacity.

KW - DNA demethylation

KW - DNA dioxygenase ABH2

KW - DNA repair

KW - Functional role of amino acid residues

KW - Single nucleotide variant

UR - https://www.scopus.com/pages/publications/105054796835

UR - https://www.mendeley.com/catalogue/8431ddb5-a0d3-350f-ba4b-0477a6f16eed/

U2 - 10.1016/j.dnarep.2026.103977

DO - 10.1016/j.dnarep.2026.103977

M3 - Article

VL - 167

JO - DNA Repair

JF - DNA Repair

SN - 1568-7864

ER -