The impact of single-nucleotide polymorphisms of human apurinic/apyrimidinic endonuclease 1 on specific DNA binding and catalysis

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The impact of single-nucleotide polymorphisms of human apurinic/apyrimidinic endonuclease 1 on specific DNA binding and catalysis. / Alekseeva, Irina V.; Davletgildeeva, Anastasiia T.; Arkova, Olga V. et al.

In: Biochimie, Vol. 163, 01.08.2019, p. 73-83.

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

BibTeX

@article{bd296a2b700748529652216ea4bc421a,

title = "The impact of single-nucleotide polymorphisms of human apurinic/apyrimidinic endonuclease 1 on specific DNA binding and catalysis",

abstract = "Human apurinic/apyrimidinic (AP) endonuclease APE1 is a crucial enzyme of the base excision repair (BER) pathway, which is in charge of recognition and initiation of removal of AP-sites in DNA. It is known that some single-nucleotide polymorphism (SNP) variants of APE1 have a reduced activity as compared to wild-type APE1. It has been hypothesized that genetic variation in APE1 might be responsible for an increased risk of some types of cancer. In the present work, analysis of SNPs of the APE1 gene was performed to select the set of variants having substitutions of amino acid residues on the surface of the enzyme globule and in the DNA-binding site, thereby affecting protein–protein interactions or the catalytic reaction, respectively. For seven APE1 variants (R221C, N222H, R237A, G241R, M270T, R274Q, and P311S), conformational dynamics and catalytic activities were examined. The conformational changes in the molecules of APE1 variants and in a DNA substrate were recorded as fluorescence changes of Trp and 2-aminopurine residues, respectively, using the stopped-flow technique. The results made it possible to determine the kinetic mechanism underlying the interactions of the APE1 variants with DNA substrates, to calculate the rate constants of the elementary stages, and to identify the stages of the process affected by mutation.",

keywords = "Abasic site, DNA repair, Fluorescence, Human apurinic/apyrimidinic endonuclease, Stopped-flow enzyme kinetics, RECOGNITION, ACTIVE-SITE, BIOLOGICAL CONSEQUENCES, Human apurinic/apyrimidinic endonudease, CONFORMATIONAL DYNAMICS, 2-AMINOPURINE, DAMAGE, BASE EXCISION-REPAIR, FLUORESCENCE, DIVALENT METAL-IONS, HUMAN AP ENDONUCLEASE, DNA/metabolism, Humans, Substrate Specificity, DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry, Models, Molecular, DNA Repair, Protein Conformation, Polymorphism, Single Nucleotide, DNA Damage, Kinetics, Mutation",

author = "Alekseeva, {Irina V.} and Davletgildeeva, {Anastasiia T.} and Arkova, {Olga V.} and Kuznetsov, {Nikita A.} and Fedorova, {Olga S.}",

year = "2019",

month = aug,

day = "1",

doi = "10.1016/j.biochi.2019.05.015",

language = "English",

volume = "163",

pages = "73--83",

journal = "Biochimie",

issn = "0300-9084",

publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - The impact of single-nucleotide polymorphisms of human apurinic/apyrimidinic endonuclease 1 on specific DNA binding and catalysis

AU - Alekseeva, Irina V.

AU - Davletgildeeva, Anastasiia T.

AU - Arkova, Olga V.

AU - Kuznetsov, Nikita A.

AU - Fedorova, Olga S.

PY - 2019/8/1

Y1 - 2019/8/1

N2 - Human apurinic/apyrimidinic (AP) endonuclease APE1 is a crucial enzyme of the base excision repair (BER) pathway, which is in charge of recognition and initiation of removal of AP-sites in DNA. It is known that some single-nucleotide polymorphism (SNP) variants of APE1 have a reduced activity as compared to wild-type APE1. It has been hypothesized that genetic variation in APE1 might be responsible for an increased risk of some types of cancer. In the present work, analysis of SNPs of the APE1 gene was performed to select the set of variants having substitutions of amino acid residues on the surface of the enzyme globule and in the DNA-binding site, thereby affecting protein–protein interactions or the catalytic reaction, respectively. For seven APE1 variants (R221C, N222H, R237A, G241R, M270T, R274Q, and P311S), conformational dynamics and catalytic activities were examined. The conformational changes in the molecules of APE1 variants and in a DNA substrate were recorded as fluorescence changes of Trp and 2-aminopurine residues, respectively, using the stopped-flow technique. The results made it possible to determine the kinetic mechanism underlying the interactions of the APE1 variants with DNA substrates, to calculate the rate constants of the elementary stages, and to identify the stages of the process affected by mutation.

AB - Human apurinic/apyrimidinic (AP) endonuclease APE1 is a crucial enzyme of the base excision repair (BER) pathway, which is in charge of recognition and initiation of removal of AP-sites in DNA. It is known that some single-nucleotide polymorphism (SNP) variants of APE1 have a reduced activity as compared to wild-type APE1. It has been hypothesized that genetic variation in APE1 might be responsible for an increased risk of some types of cancer. In the present work, analysis of SNPs of the APE1 gene was performed to select the set of variants having substitutions of amino acid residues on the surface of the enzyme globule and in the DNA-binding site, thereby affecting protein–protein interactions or the catalytic reaction, respectively. For seven APE1 variants (R221C, N222H, R237A, G241R, M270T, R274Q, and P311S), conformational dynamics and catalytic activities were examined. The conformational changes in the molecules of APE1 variants and in a DNA substrate were recorded as fluorescence changes of Trp and 2-aminopurine residues, respectively, using the stopped-flow technique. The results made it possible to determine the kinetic mechanism underlying the interactions of the APE1 variants with DNA substrates, to calculate the rate constants of the elementary stages, and to identify the stages of the process affected by mutation.

KW - Abasic site

KW - DNA repair

KW - Fluorescence

KW - Human apurinic/apyrimidinic endonuclease

KW - Stopped-flow enzyme kinetics

KW - RECOGNITION

KW - ACTIVE-SITE

KW - BIOLOGICAL CONSEQUENCES

KW - Human apurinic/apyrimidinic endonudease

KW - CONFORMATIONAL DYNAMICS

KW - 2-AMINOPURINE

KW - DAMAGE

KW - BASE EXCISION-REPAIR

KW - FLUORESCENCE

KW - DIVALENT METAL-IONS

KW - HUMAN AP ENDONUCLEASE

KW - DNA/metabolism

KW - Humans

KW - Substrate Specificity

KW - DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry

KW - Models, Molecular

KW - DNA Repair

KW - Protein Conformation

KW - Polymorphism, Single Nucleotide

KW - DNA Damage

KW - Kinetics

KW - Mutation

UR - http://www.scopus.com/inward/record.url?scp=85066463017&partnerID=8YFLogxK

U2 - 10.1016/j.biochi.2019.05.015

DO - 10.1016/j.biochi.2019.05.015

M3 - Article

C2 - 31150756

AN - SCOPUS:85066463017

VL - 163

SP - 73

EP - 83

JO - Biochimie

JF - Biochimie

SN - 0300-9084

ER -

ID: 20343766