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Nucleic Acids Res. 2008 Feb;36(2):411-22. Epub 2007 Nov 26.

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

Author information

1
Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

Abstract

Approximately 30% of human tumors characterized to date express DNA polymerase beta (pol beta) 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.

PMID:
18039710
PMCID:
PMC2241857
DOI:
10.1093/nar/gkm1053
[Indexed for MEDLINE]
Free PMC Article

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