Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase

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Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase. / Popov, A. V.; Yudkina, A. V.; Vorobjev, Yu N. et al.

In: Biochemistry (Moscow), Vol. 85, No. 2, 17.02.2020, p. 192-204.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{3c06086cb74d4ca593d487eba79cb51c,

title = "Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase",

abstract = "8-Oxoguanine-DNA N-glycosylase (OGG1) is a eukaryotic DNA repair enzyme responsible for the removal of 8-oxoguanine (oxoG), one of the most abundant oxidative DNA lesions. OGG1 catalyzes two successive reactions - N-gly-cosidic bond hydrolysis (glycosylase activity) and DNA strand cleavage on the 3{\textquoteright}-side of the lesion by {\ss}-elimination (lyase activity). The enzyme also exhibits lyase activity with substrates containing apurinic/apyrimidinic (AP) sites (deoxyribose moieties lacking the nucleobase). OGG1 is highly specific for the base opposite the lesion, efficiently excising oxoG and cleaving AP sites located opposite to C, but not opposite to A. The activity is also profoundly decreased by amino acid changes that sterically interfere with oxoG binding in the active site of the enzyme after the lesion is everted from the DNA duplex. Earlier, the molecular dynamics approach was used to study the conformational dynamics of such human OGG1 mutants in complexes with the oxoG:C-containing substrate DNA, and the population density of certain conformers of two OGG1 catalytic residues, Lys249 and Asp268, was suggested to determine the enzyme activity. Here, we report the study of molecular dynamics of human OGG1 bound to the oxoG:A-containing DNA and OGG1 mutants bound to the AP:C-con-taining DNA. We showed that the enzyme low activity is associated with a decrease in the populations of Lys249 and Asp268 properly configured for catalysis. The experimentally measured rate constants for the OGG1 mutants show a good agreement with the models. We conclude that the enzymatic activity of OGG1 is determined majorly by the population density of the catalytically competent conformations of the active site residues Lys249 and Asp268.",

keywords = "8-oxoguanine-DNA N-glycosylase, DNA damage, DNA repair, substrate specificity, DNA Glycosylases/chemistry, Catalytic Domain, Biocatalysis, DNA/chemistry, DNA Repair, Humans, Protein Conformation, Molecular Dynamics Simulation, MOLECULAR-DYNAMICS, FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE, REPAIR ENZYME, ESCHERICHIA-COLI, SUBSTRATE RECOGNITION, CLONING, EXCISION, IONIZING-RADIATION, FREE-ENERGY, OGG1 GENE",

author = "Popov, {A. V.} and Yudkina, {A. V.} and Vorobjev, {Yu N.} and Zharkov, {D. O.}",

year = "2020",

month = feb,

day = "17",

doi = "10.1134/S0006297920020066",

language = "English",

volume = "85",

pages = "192--204",

journal = "Biochemistry (Moscow)",

issn = "0006-2979",

publisher = "Maik Nauka-Interperiodica Publishing",

number = "2",

}

RIS

TY - JOUR

T1 - Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase

AU - Popov, A. V.

AU - Yudkina, A. V.

AU - Vorobjev, Yu N.

AU - Zharkov, D. O.

PY - 2020/2/17

Y1 - 2020/2/17

N2 - 8-Oxoguanine-DNA N-glycosylase (OGG1) is a eukaryotic DNA repair enzyme responsible for the removal of 8-oxoguanine (oxoG), one of the most abundant oxidative DNA lesions. OGG1 catalyzes two successive reactions - N-gly-cosidic bond hydrolysis (glycosylase activity) and DNA strand cleavage on the 3’-side of the lesion by ß-elimination (lyase activity). The enzyme also exhibits lyase activity with substrates containing apurinic/apyrimidinic (AP) sites (deoxyribose moieties lacking the nucleobase). OGG1 is highly specific for the base opposite the lesion, efficiently excising oxoG and cleaving AP sites located opposite to C, but not opposite to A. The activity is also profoundly decreased by amino acid changes that sterically interfere with oxoG binding in the active site of the enzyme after the lesion is everted from the DNA duplex. Earlier, the molecular dynamics approach was used to study the conformational dynamics of such human OGG1 mutants in complexes with the oxoG:C-containing substrate DNA, and the population density of certain conformers of two OGG1 catalytic residues, Lys249 and Asp268, was suggested to determine the enzyme activity. Here, we report the study of molecular dynamics of human OGG1 bound to the oxoG:A-containing DNA and OGG1 mutants bound to the AP:C-con-taining DNA. We showed that the enzyme low activity is associated with a decrease in the populations of Lys249 and Asp268 properly configured for catalysis. The experimentally measured rate constants for the OGG1 mutants show a good agreement with the models. We conclude that the enzymatic activity of OGG1 is determined majorly by the population density of the catalytically competent conformations of the active site residues Lys249 and Asp268.

AB - 8-Oxoguanine-DNA N-glycosylase (OGG1) is a eukaryotic DNA repair enzyme responsible for the removal of 8-oxoguanine (oxoG), one of the most abundant oxidative DNA lesions. OGG1 catalyzes two successive reactions - N-gly-cosidic bond hydrolysis (glycosylase activity) and DNA strand cleavage on the 3’-side of the lesion by ß-elimination (lyase activity). The enzyme also exhibits lyase activity with substrates containing apurinic/apyrimidinic (AP) sites (deoxyribose moieties lacking the nucleobase). OGG1 is highly specific for the base opposite the lesion, efficiently excising oxoG and cleaving AP sites located opposite to C, but not opposite to A. The activity is also profoundly decreased by amino acid changes that sterically interfere with oxoG binding in the active site of the enzyme after the lesion is everted from the DNA duplex. Earlier, the molecular dynamics approach was used to study the conformational dynamics of such human OGG1 mutants in complexes with the oxoG:C-containing substrate DNA, and the population density of certain conformers of two OGG1 catalytic residues, Lys249 and Asp268, was suggested to determine the enzyme activity. Here, we report the study of molecular dynamics of human OGG1 bound to the oxoG:A-containing DNA and OGG1 mutants bound to the AP:C-con-taining DNA. We showed that the enzyme low activity is associated with a decrease in the populations of Lys249 and Asp268 properly configured for catalysis. The experimentally measured rate constants for the OGG1 mutants show a good agreement with the models. We conclude that the enzymatic activity of OGG1 is determined majorly by the population density of the catalytically competent conformations of the active site residues Lys249 and Asp268.

KW - 8-oxoguanine-DNA N-glycosylase

KW - DNA damage

KW - DNA repair

KW - substrate specificity

KW - DNA Glycosylases/chemistry

KW - Catalytic Domain

KW - Biocatalysis

KW - DNA/chemistry

KW - DNA Repair

KW - Humans

KW - Protein Conformation

KW - Molecular Dynamics Simulation

KW - MOLECULAR-DYNAMICS

KW - FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE

KW - REPAIR ENZYME

KW - ESCHERICHIA-COLI

KW - SUBSTRATE RECOGNITION

KW - CLONING

KW - EXCISION

KW - IONIZING-RADIATION

KW - FREE-ENERGY

KW - OGG1 GENE

UR - http://www.scopus.com/inward/record.url?scp=85079700375&partnerID=8YFLogxK

U2 - 10.1134/S0006297920020066

DO - 10.1134/S0006297920020066

M3 - Article

C2 - 32093595

AN - SCOPUS:85079700375

VL - 85

SP - 192

EP - 204

JO - Biochemistry (Moscow)

JF - Biochemistry (Moscow)

SN - 0006-2979

IS - 2

ER -

ID: 23583216