Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA

Atanu Maiti, Wazo Myint, Tapan Kanai, Krista Delviks-Frankenberry, Christina Sierra Rodriguez, Vinay K. Pathak, Celia A. Schiffer and Hiroshi Matsuo ()
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Atanu Maiti: Frederick National Laboratory for Cancer Research
Wazo Myint: Frederick National Laboratory for Cancer Research
Tapan Kanai: Frederick National Laboratory for Cancer Research
Krista Delviks-Frankenberry: National Cancer Institute at Frederick
Christina Sierra Rodriguez: Frederick National Laboratory for Cancer Research
Vinay K. Pathak: National Cancer Institute at Frederick
Celia A. Schiffer: University of Massachusetts Medical School
Hiroshi Matsuo: Frederick National Laboratory for Cancer Research

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxy-uridine mutations in single-stranded DNA (ssDNA), and capable of restricting replication of HIV-1 by generating mutations in viral genome. The mechanism by which APOBEC3G specifically deaminates 5′-CC motifs has remained elusive since structural studies have been hampered due to apparently weak ssDNA binding of the catalytic domain of APOBEC3G. We overcame the problem by generating a highly active variant with higher ssDNA affinity. Here, we present the crystal structure of this variant complexed with a ssDNA substrate at 1.86 Å resolution. This structure reveals atomic-level interactions by which APOBEC3G recognizes a functionally-relevant 5′-TCCCA sequence. This complex also reveals a key role of W211 in substrate recognition, implicating a similar recognition in activation-induced cytidine deaminase (AID) with a conserved tryptophan.

Date: 2018
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DOI: 10.1038/s41467-018-04872-8

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