Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F

• Published in: Nature communications Vol. 4; no. 1; p. 2593
• Main Authors: Siu, Karen K., Sultana, Azmiri, Azimi, Farshad C., Lee, Jeffrey E.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 2013; Nature Publishing Group
• Subjects: 631/337; Amino Acid Sequence; APOBEC Deaminases; Binding Sites; Crystallography, X-Ray; Cytidine Deaminase; Cytosine Deaminase - chemistry; Cytosine Deaminase - genetics; Cytosine Deaminase - metabolism; Deoxyribonucleic acid; DNA; DNA, Single-Stranded - chemistry; DNA, Single-Stranded - metabolism; Drug resistance; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression; HIV-1 - chemistry; HIV-1 - metabolism; Host-Pathogen Interactions; Humanities and Social Sciences; Humans; Immune response; Models, Molecular; Molecular Sequence Data; multidisciplinary; Mutagenesis, Site-Directed; Mutation; Protein Binding; Protein Interaction Domains and Motifs; Protein Isoforms - chemistry; Protein Isoforms - genetics; Protein Isoforms - metabolism; Proteins; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Science; Science (multidisciplinary); Static Electricity; vif Gene Products, Human Immunodeficiency Virus - chemistry; vif Gene Products, Human Immunodeficiency Virus - genetics; vif Gene Products, Human Immunodeficiency Virus - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms3593

The human APOBEC3 family of DNA cytosine deaminases serves as a front-line intrinsic immune response to inhibit the replication of diverse retroviruses. APOBEC3F and APOBEC3G are the most potent factors against HIV-1. As a countermeasure, HIV-1 viral infectivity factor (Vif) targets APOBEC3s for proteasomal degradation. Here we report the crystal structure of the Vif-binding domain in APOBEC3F and a novel assay to assess Vif-APOBEC3 binding. Our results point to an amphipathic surface that is conserved in APOBEC3s as critical for Vif susceptibility in APOBEC3F. Electrostatic interactions likely mediate Vif binding. Moreover, structure-guided mutagenesis reveals a straight ssDNA-binding groove distinct from the Vif-binding site, and an ‘aromatic switch’ is proposed to explain DNA substrate specificities across the APOBEC3 family. This study opens new lines of inquiry that will further our understanding of APOBEC3-mediated retroviral restriction and provides an accurate template for structure-guided development of inhibitors targeting the APOBEC3-Vif axis. APOBEC3F is a DNA cytosine deaminase involved in restriction of HIV-1, but its activity can be suppressed by the viral protein Vif. Here, the authors provide insights into the interaction between these two proteins by determining the structure of the APOBEC3F Vif-binding domain.