Revealing an Internal Stabilization Deficiency in the DNA Polymerase β K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography

Batra, V.K.; Alnajjar, Khadijeh S.; Sweasy, Joann B.; McKenna, Charles E.; Goodman, Myron F.; Wilson, Samuel H.

doi:10.1021/acs.biochem.9b01072

Cited by 1 publication

(1 citation statement)

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“…At the same time, dissociation constants K d , polymerase reaction rate constant k obs , and rate of product release k ss are similar between the Polβ variant and wild type (WT) Polβ. The Lys289Met variant more frequently attaches dCTP opposite cytidine in DNA, thereby showing poor discrimination of dNTPs during the transferase reaction [25,26]. It has been demonstrated that the rate constant of dNTP incorporation into 1-nt gap-containing DNA in this variant is considerably lower than that of WT Polβ.…”

Section: Introductionmentioning

confidence: 99%

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

Kladova,

Tyugashev,

Miroshnikov

et al. 2024

Biomolecules

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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.

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Section: Introductionmentioning

confidence: 99%