The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

Uddhav K Shigdel,Martin Karplus,Victor Ovchinnikov,Kwangho Nam,Jenny A Shih,Gregory L Verdine,Seung-Joo Lee

doi:10.1038/s41467-020-18290-2

Abstract

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.

Highlights

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes
The G:C to T:A transversion mutation has been found in codon 12 of the highly oncogenic protein K-ras, which resulted in the formation of lung tumors in mice deficient in the oxidative DNA repair genes, myh and ogg[12]
To entrap the complex of hOGG1 with intrahelical G or oxoG, we identified several potential sites for DXL in the protein–DNA interface based on the native lesion-recognition complex (LRC) of hOGG116 and prepared the corresponding mutant proteins, containing a single cysteine at the relevant positions

Summary

Introduction

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. Using DXL technology, we have previously found an X-ray structure of bacterial 8-oxoguanine DNA glycosylase, MutM, interrogating a fully intrahelical lesion oxoG22.

Results

Conclusion