title: Effect of DNA polymerase beta loop variants on discrimination of O6-methyldeoxyguanosine modification present in the nucleotide versus template substrate.
abstract: We have examined the mechanism of DNA polymerase beta (pol beta) lesion discrimination using alkylated dNTP versus alkylated DNA template substrates and the pol beta variants R253M and E249K. Both of these amino acid variants are located in the loop region of the palm domain and are known to play a role in pol beta fidelity and discrimination of 3'-azido-3'-deoxythymidine triphosphate substrates. We observed that these variants affect O(6)-methyldeoxyguanosine- (m6G-) modified dNTP discrimination without affecting m6G template translesion synthesis. Under steady-state conditions, the ratio of inherent reactivity values for the m6dGTP substrate relative to the dGTP substrate was greater for both variant polymerases than for wild-type (WT) pol beta. Biochemical assays of translesion synthesis using m6G lesion-containing templates demonstrated no significant differences between the variants and WT. Using N-methyl-N-nitrosourea- (MNU-) modified DNA templates in the HSV-tk in vitro assay, no difference among the enzymes in the frequency of alkylation-induced G to A transition mutations was observed. However, differences among the polymerases in the frequency of alkylation-induced C to A transversions were observed, consistent with a mutator tendency for E249K and an antimutator tendency for R253M. We conclude that a specific interaction at the loop of the palm domain is involved in pol beta discrimination of the m6G lesion when present on the incoming dNTP substrate but not when present in the DNA template. Our data support a role for the flexible loop in pol beta error discrimination.
authors.affiliation: Department of Biochemistry and Molecular Biology, The Gittlen Cancer Research Institute, and MD-PhD Program, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, Pennsylvania 17033, USA.
authors.forename: Subarna
authors.initials: S
authors.lastname: Hamid
authors.forename: Kristin A
authors.initials: KA
authors.lastname: Eckert
mesh_terms: D000477:Alkylating Agents / Q000737:chemistry; D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D001120:Arginine / Q000235:genetics; D001483:Base Sequence; D004249:DNA Damage; D019951:DNA Polymerase beta / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics; D017931:DNA Primers / Q000737:chemistry*; D003845:Deoxycytosine Nucleotides / Q000737:chemistry; D003849:Deoxyguanosine / Q000031:analogs & derivatives* / Q000737:chemistry; D018698:Glutamic Acid / Q000235:genetics; D008239:Lysine / Q000235:genetics; D008715:Methionine / Q000235:genetics; D008770:Methylnitrosourea / Q000737:chemistry; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary / Q000235:genetics; D051381:Rats; D013379:Substrate Specificity / Q000235:genetics; D013698:Templates, Genetic; D013942:Thymine Nucleotides / Q000737:chemistry
chemical_list: D000477:Alkylating Agents; D017931:DNA Primers; D003845:Deoxycytosine Nucleotides; D013942:Thymine Nucleotides; C024107:2'-deoxycytidine 5'-triphosphate; D018698:Glutamic Acid; D008770:Methylnitrosourea; D001120:Arginine; C015558:O(6)-methyl-2'-deoxyguanosine; D008715:Methionine; D019951:DNA Polymerase beta; D003849:Deoxyguanosine; D008239:Lysine; C024157:thymidine 5'-triphosphate