Structural basis of substrate specificity in human cytidine deaminase family APOBEC3s

• Published in: The Journal of biological chemistry Vol. 297; no. 2; p. 100909
• Main Authors: Hou, Shurong, Lee, Jeong Min, Myint, Wazo, Matsuo, Hiroshi, Kurt Yilmaz, Nese, Schiffer, Celia A.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.08.2021; American Society for Biochemistry and Molecular Biology
• Subjects: Amino Acid Sequence; APOBEC Deaminases - chemistry; APOBEC Deaminases - genetics; APOBEC Deaminases - immunology; APOBEC Deaminases - metabolism; APOBEC3; ASBMB Award; Catalytic Domain; Crystallography, X-Ray; DNA, Single-Stranded - chemistry; DNA, Single-Stranded - genetics; DNA, Single-Stranded - metabolism; Humans; Models, Molecular; molecular dynamics simulation; molecular modeling; Mutation; Neoplasms - genetics; Neoplasms - immunology; Neoplasms - metabolism; Neoplasms - pathology; Protein Binding; specificity; structural analysis; Substrate Specificity; APOBEC3; CTD; structural analysis; molecular modeling; pMD; molecular dynamics simulation; CBE; specificity; ssDNA; NTD
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1016/j.jbc.2021.100909

The human cytidine deaminase family of APOBEC3s (A3s) plays critical roles in both innate immunity and the development of cancers. A3s comprise seven functionally overlapping but distinct members that can be exploited as nucleotide base editors for treating genetic diseases. Although overall structurally similar, A3s have vastly varying deamination activity and substrate preferences. Recent crystal structures of ssDNA-bound A3s together with experimental studies have provided some insights into distinct substrate specificities among the family members. However, the molecular interactions responsible for their distinct biological functions and how structure regulates substrate specificity are not clear. In this study, we identified the structural basis of substrate specificities in three catalytically active A3 domains whose crystal structures have been previously characterized: A3A, A3B- CTD, and A3G-CTD. Through molecular modeling and dynamic simulations, we found an interdependency between ssDNA substrate binding conformation and nucleotide sequence specificity. In addition to the U-shaped conformation seen in the crystal structure with the CTC0 motif, A3A can accommodate the CCC0 motif when ssDNA is in a more linear (L) conformation. A3B can also bind both U- and L-shaped ssDNA, unlike A3G, which can stably recognize only linear ssDNA. These varied conformations are stabilized by sequence-specific interactions with active site loops 1 and 7, which are highly variable among A3s. Our results explain the molecular basis of previously observed substrate specificities in A3s and have implications for designing A3-specific inhibitors for cancer therapy as well as engineering base-editing systems for gene therapy.