The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient

Abstract

Approximately 30% of human tumors characterized to date express DNA polymerase beta (pol β) variant proteins. Two of the polymerase beta cancer-associated variants are sequence-specific mutators, and one of them binds to DNA but has no polymerase activity. The Leu22Pro (L22P) DNA polymerase beta variant was identified in a gastric carcinoma. Leu22 resides within the 8 kDa amino terminal domain of DNA polymerase beta, which exhibits dRP lyase activity. This domain catalyzes the removal of deoxyribose phosphate during short patch base excision repair. We show that this cancer-associated variant has very little dRP lyase activity but retains its polymerase activity. Although residue 22 has no direct contact with the DNA, we report here that the L22P variant has reduced DNA-binding affinity. The L22P variant protein is deficient in base excision repair. Molecular dynamics calculations suggest that alteration of Leu22 to Pro changes the local packing, the loop connecting helices 1 and 2 and the overall juxtaposition of the helices within the N-terminal domain. This in turn affects the shape of the binding pocket that is required for efficient dRP lyase catalysis.

Association of a Newly Identified Variant of DNA Polymerase Beta (polβΔ63-123, 208-304) with the Risk Factor of Ovarian Carcinoma in India

“…Leu22Pro tumor-associated variant of polβ is dRP lyase deficient (Dalal et al, 2008). It is being reported that the E295K mutation in polβ which is a gastric cancer-associated variant interferes with base excision repair and induces cellular transformation (Lang et al, 2007).…”

“…Pol β variants, K289M and I260M have functional phenotypes that could be related to the etiology of human cancer (Lang et al, 2003;Dalal et al, 2005). The Val246 variant was shown to mis-incorporate nucleotides through altered DNA positioning in the active site (Dalal et al, 2008). It was evidenced that expression of the E295K gastric carcinoma-associated pol beta variant (Lang et al, 2007) in mouse cells interferes with BER and induces sister chromatid exchanges and cellular transformation (Lang et al, 2007).…”

Association of Two Polymorphisms of DNA Polymerase Beta in Exon-9 and Exon-11 with Ovarian Carcinoma in India

“…Another Leu22Pro tumor-associated variant of polβ is dRP lyase deficient (Dalal et al, 2008). Therefore, any kind of point mutation can change the conformation during the polymerase opening and thereby altering the DNA positioning in the active site (Yang et al, 2004).…”

Y265C DNA polymerase beta knockin mice survive past birth and accumulate base excision repair intermediate substrates

“…The 5′-dRP-containing DNA substrate was prepared just before use, as describe previously (28,29); and the assay was set up according to Prakash et al (30) with minor modifications (SI Text).…”