Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA

Abstract

ABSTRACTAPOBEC3F (A3F) demonstrates antivirus activity through its A3F‐CD2 domain catalyzing deamination of cytidine in target motif 5’‐TC in viral cDNA during reverse transcription. But structural basis is unclear. Previously, chimeric A3F‐CD2 (i.e., A3Fc‐CD2, where residues 195—217 of A3F‐CD2 were replaced with residues 197—221 of A3G‐CD2) was found soluble with deamination activity. Here, we report crystal structures of A3Fc‐CD2 in complexes with single‐stranded DNA (5’‐ATTTT5C6A7A8T9T‐3’ and 5’‐ATTTT5C6A7A8C9T‐3’) at resolutions of 1.98 Å and 2.30 Å, respectively. They demonstrate that one molecular DNA binds two A3Fc‐CD2 molecules (monomers A and B) at two sites, distinct from the reported complex structure of human A3F‐CD2 with a 10‐dT DNA. The first site is formed by residues Tyr333, Lys358 and Tyr359 in monomer A, far away from Zn2+ binding motif, interacting with bases dT5, dC6 and dA7 through π‐π stacking and hydrogen bonds. The second site is composed of Trp277, Y307YFW310 near to Zn2+ binding region in monomer B, interacting with base dA8, mainly through π‐π stacking and hydrophobic interactions, determining deamination preference of DNA sequence. Subsequent biochemical investigations further confirm the contribution of these residues to DNA binding and deamination activities. These studies are helpful to understand the mechanism how A3F‐CD2 catalyzes cytidine deamination.