Exploring APOBEC3 domain structure: impact on recognition of DNA damage

Abstract

Activation-induced deoxycytidine deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3 (APOBEC3, or A3) enzymes are a family of deoxycytidine (dC) deaminases involved in somatic hypermutation (SHM), antibody class switch recombination, and antiviral responses. These enzymes share similar structural features in their single active deoxycytidine deaminase (CD) domain, but some family members (A3B/DE/F/G) possess an additional second regulatory CD domain also known as an N-terminal domain (Ntd). AID/A3s mutate the genome indiscriminately, and A3A, A3B, and A3H haplotype II have been associated with cancer development. Thus, to date the paradigm has been that AID/A3s are pro-tumour factors because they transform healthy DNA into damaged and mutated DNA. However, I observed that the activity of A3A (single domain) and A3B (double domain) is increased if their substrate DNA contains environmentally damaged nucleotides such as 8-Oxo-2’-deoxyguanosine (8oxoG) directly adjacent to the dC (in the -2 or -1 nucleotide position). When exposed to substrates containing damaged nucleotides in positions further downstream, further upstream, or containing a greater concentration of damaged bases, A3A failed to demonstrate an activity increase relative to undamaged and -1 position 8oxoG control substrates whereas A3B exhibited significantly increased activity for all distally damaged substrates compared to controls. I propose that the regulatory Ntd of A3B is a key structural component that accounts for binding distally damaged DNA substrates. The notion that AID/A3s can target pre-damaged DNA in addition to non-damaged healthy DNA is a novel insight in the field; understanding the basis of this phenomenon from both the substrate sequence and enzyme structure point of view would advance our basic knowledge and permit exploration of targeting AID/A3 enzymes in cancer.