Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA

Human APOBEC3G (A3G) inhibits the replication of human immunodeficiency virus-1 by deaminating cytidine at the 3'-end in the target motif 5'-CCC-3' in viral cDNA during reverse transcription. It in vitro deaminates two consecutive cytidines in a 3'- > 5' order. Although a crystal structure of the A3G catalytic domain (A3G-CD2) with DNA was reported, it is unknown why residues involved in enzymatic reaction are distributed widely. Here, we introduced an iodine atom into the C-5 position of cytidine (dC(6)(I)) in DNA 5'-ATTC(4)C(5)C(6)(I)A(7)ATT-3' (TCCC6I). It switches the deamination sequence preference from CCC to TCC, although small dC(6)(I) deamination was observed. Solution structures of A3G-CD2 in complexes with products DNA TCUC6I and TCUU6I indicate that the substrate DNA binds A3G-CD2 in TCC and CCC modes. The dC(6) deamination correlates with the 4th base type. The CCC mode favours dC(6) deamination, while the TCC mode results in dC(5) deamination. These studies present an extensive basis to design inhibitors to impede viral evolvability.