AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking

Abstract

E. coli AlkB is a direct DNA/RNA repair protein that oxidatively reverses N1 alkylated purines and N3 alkylated pyrimidines to regular bases. Previous crystal structures have revealed N1-methyl adenine (1-meA) recognition by AlkB and a unique base flipping mechanism, but how the AlkB active site can accommodate bulky base adducts is largely unknown. Employing a previously developed chemical cross-linking technique, we crystallized AlkB with a duplex DNA containing a caged thymine base (cagedT). The structure revealed a flexible hairpin lid and a reorganized substrate recognition loop used by AlkB to accommodate cagedT. These observations demonstrate, at the molecular level, how bulky DNA adducts may be recognized and processed by AlkB.