TY - JOUR

T1 - Molecular dynamic analysis of the functional role of amino acid residues V99, F124 and S125 of human DNA dioxygenase ABH2

AU - Zhao, M.

AU - Tyugashev, T. E.

AU - Davletgildeeva, A. T.

AU - Kuznetsov, N. A.

N1 - Zhao M., Tyugashev T.E., Davletgildeeva A.T., Kuznetsov N.A. Molecular dynamic analysis of the functional role of amino acid residues V99, F124 and S125 of human DNA dioxygenase ABH2. Vavilovskii Zhurnal Genetiki i Selektsii=Vavilov J Genet Breed. 2025;29(7):1062-1072. doi 10.18699/vjgb-25-111 The work was carried out within the framework of state assignment No. 121031300041-4.

PY - 2025

Y1 - 2025

N2 - The ABH2 enzyme belongs to the AlkB-like family of Fe(II)/α-ketoglutarate-dependent dioxygenases. Various non-heme dioxygenases act on a wide range of substrates and have a complex catalytic mechanism involvingα-ketoglutarate and an Fe(II) ion as a cofactor. Representatives of the AlkB family catalyze the direct oxidation of alkyl substituents in the nitrogenous bases of DNA and RNA, providing protection against the mutagenic effects of endogenous and exogenous alkylating agents, and also participate in the regulation of the methylation level of some RNAs. DNA dioxygenase ABH2, localized predominantly in the cell nucleus, is specific for double-stranded DNA substrates and, unlike most other human AlkB-like enzymes, has a fairly broad spectrum of substrate specificity, oxidizing alkyl groups of such modified nitrogenous bases as, for example, N1-methyladenosine, N3-methylcytidine, 1,N6-ethenoadenosine and 3,N4-ethenocytidine. To analyze the mechanism underlying the enzyme’s substrate specificity and to clarify the functional role of key active-site amino acid residues, we performed molecular dynamics simulations of complexes of the wild-type ABH2 enzyme and its mutant forms containing amino acid substitutions V99A, F124A and S125A with two types of DNA substrates carrying methylated bases N1- ethyladenine and N3-methylcytosine, respectively. It was found that the V99A substitution leads to an increase in the mobility of protein loops L1 and L2 involved in binding the DNA substrate and changes the distribution of π-π contacts between the side chain of residue F102 and nitrogenous bases located near the damaged nucleotide. The F124A substitution leads to the loss of π-π stacking with the damaged base, which in turn destabilizes the architecture of the active site, disrupts the interaction with the iron ion and prevents optimal catalytic positioning of α-ketoglutarate in the active site. The S125A substitution leads to the loss of direct interaction of the L2 loop with the 5’-phosphate group of the damaged nucleotide, weakening the binding of the enzyme to the DNA substrate. Thus, the obtained data revealed the functional role of three amino acid residues of the active site and contributed to the understanding of the structural-functional relationships in the recognition of a damaged nucleotide and the formation of a catalytic complex by the human ABH2 enzyme.

AB - The ABH2 enzyme belongs to the AlkB-like family of Fe(II)/α-ketoglutarate-dependent dioxygenases. Various non-heme dioxygenases act on a wide range of substrates and have a complex catalytic mechanism involvingα-ketoglutarate and an Fe(II) ion as a cofactor. Representatives of the AlkB family catalyze the direct oxidation of alkyl substituents in the nitrogenous bases of DNA and RNA, providing protection against the mutagenic effects of endogenous and exogenous alkylating agents, and also participate in the regulation of the methylation level of some RNAs. DNA dioxygenase ABH2, localized predominantly in the cell nucleus, is specific for double-stranded DNA substrates and, unlike most other human AlkB-like enzymes, has a fairly broad spectrum of substrate specificity, oxidizing alkyl groups of such modified nitrogenous bases as, for example, N1-methyladenosine, N3-methylcytidine, 1,N6-ethenoadenosine and 3,N4-ethenocytidine. To analyze the mechanism underlying the enzyme’s substrate specificity and to clarify the functional role of key active-site amino acid residues, we performed molecular dynamics simulations of complexes of the wild-type ABH2 enzyme and its mutant forms containing amino acid substitutions V99A, F124A and S125A with two types of DNA substrates carrying methylated bases N1- ethyladenine and N3-methylcytosine, respectively. It was found that the V99A substitution leads to an increase in the mobility of protein loops L1 and L2 involved in binding the DNA substrate and changes the distribution of π-π contacts between the side chain of residue F102 and nitrogenous bases located near the damaged nucleotide. The F124A substitution leads to the loss of π-π stacking with the damaged base, which in turn destabilizes the architecture of the active site, disrupts the interaction with the iron ion and prevents optimal catalytic positioning of α-ketoglutarate in the active site. The S125A substitution leads to the loss of direct interaction of the L2 loop with the 5’-phosphate group of the damaged nucleotide, weakening the binding of the enzyme to the DNA substrate. Thus, the obtained data revealed the functional role of three amino acid residues of the active site and contributed to the understanding of the structural-functional relationships in the recognition of a damaged nucleotide and the formation of a catalytic complex by the human ABH2 enzyme.

KW - DNA repair

KW - base methylation

KW - human DNA dioxygenase ABH2

KW - MD modeling

KW - functional role of amino acid residues

UR - https://www.scopus.com/pages/publications/105024815721

U2 - 10.18699/vjgb-25-111

DO - 10.18699/vjgb-25-111

M3 - Article

VL - 29

SP - 1062

EP - 1072

JO - Vavilov Journal of Genetics and Breeding

JF - Vavilov Journal of Genetics and Breeding

SN - 2500-3259

IS - 7

ER -