Structural analysis of the active site and DNA binding of human cytidine deaminase APOBEC3B

Abstract

APOBEC3s proteins (A3s), a family of human cytidine deaminases, protect the host cell from endogenous retro‐elements and exogenous viral infections by introducing hypermutations. However, their ability to mutate genomic DNA makes them a potential cancer source. Of the 7 human A3s, A3A, A3B and A3H have been implicated as an endogenous cause for multiple cancers. Among all A3s, A3B and A3A share highest sequence identity, but have distinct deamination activities with A3B about 15‐fold lower activity compared to A3A. Over the past few years, our lab along with other groups has determined several structures of apo as well as DNA‐bound A3A and A3B complexes. These structures revealed the molecular determinants of nucleotide specificity and importance of the loops around the active site, including the critical loop 1, in DNA binding. However, the current A3B‐DNA co‐crystal structure is that of a chimera with loop 1 from A3A. Hence, the molecular mechanism for how A3B binds to DNA within the context of native loop 1 and how A3B regulates its deamination activity resulting in much lower activity compared to A3A still remain unknown. Here we identified an auto‐inhibited mode of A3B that restricts its activity, revealed the molecular mechanism for DNA binding to A3B, as well as the sequence specificity upstream of substrate cytidine. Using structural analysis and molecular dynamics, we revealed a unique hydrogen bonding network in A3B loop 1. This network auto‐inhibits A3B's activity by locking the active site in a DNA‐binding incompatible mode. In addition, the critical residues for DNA binding to A3B have been identified through molecular modeling and simulations. The results were verified experimentally by binding assays with different engineered A3B mutants. Overall, structural analysis of the active site and DNA binding of A3B demonstrate how A3B structurally regulates its deamination activity and will potentially lead to discovering A3B‐specific inhibitors that may be developed as anti‐cancer drugs to benefit cancer therapeutics.Support or Funding InformationNIH R01GM118474This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.