Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain

Hanjing Yang, Josue Pacheco, Kyumin Kim, Ayub Bokani, Fumiaki Ito, Diako Ebrahimi and Xiaojiang S. Chen ()
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Hanjing Yang: University of Southern California
Josue Pacheco: University of Southern California
Kyumin Kim: University of Southern California
Ayub Bokani: CQUniversity
Fumiaki Ito: University of Southern California
Diako Ebrahimi: Texas Biomedical Research Institute
Xiaojiang S. Chen: University of Southern California

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: Abstract APOBEC3G, part of the AID/APOBEC cytidine deaminase family, is crucial for antiviral immunity. It has two zinc-coordinated cytidine-deaminase domains. The non-catalytic N-terminal domain strongly binds to nucleic acids, whereas the C-terminal domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains is not fully understood. Here, we show that DNA editing function of rhesus macaque APOBEC3G on linear and hairpin loop DNA is enhanced by AA or GA dinucleotide motifs present downstream in the 3’-direction of the target-C editing sites. The effective distance between AA/GA and the target-C sites is contingent on the local DNA secondary structure. We present two co-crystal structures of rhesus macaque APOBEC3G bound to ssDNA containing AA and GA, revealing the contribution of the non-catalytic domain in capturing AA/GA DNA. Our findings elucidate the molecular mechanism of APOBEC3G’s cooperative function, which is critical for its antiviral role and its contribution to mutations in cancer genomes.

Date: 2024
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DOI: 10.1038/s41467-024-52671-1

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