Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G

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Abstract
The cellular cytosine deaminase APOBEC3G inhibits replication of HIV lacking the viral protein Vif; here the NMR structure of a mutant form of the catalytic domain of APOBEC3G is reported, and a model for the APOBEC–DNA interaction is proposed. The human APOBEC3G (apolipoprotein B messenger-RNA-editing enzyme, catalytic polypeptide-like 3G) protein is a single-strand DNA deaminase that inhibits the replication of human immunodeficiency virus-1 (HIV-1), other retroviruses and retrotransposons1,2,3,4,5,6. APOBEC3G anti-viral activity is circumvented by most retroelements, such as through degradation by HIV-1 Vif7. APOBEC3G is a member of a family of polynucleotide cytosine deaminases, several of which also target distinct physiological substrates. For instance, APOBEC1 edits APOB mRNA and AID deaminates antibody gene DNA8,9,10. Although structures of other family members exist, none of these proteins has elicited polynucleotide cytosine deaminase or anti-viral activity11,12,13,14,15,16. Here we report a solution structure of the human APOBEC3G catalytic domain. Five α-helices, including two that form the zinc-coordinating active site, are arranged over a hydrophobic platform consisting of five β-strands. NMR DNA titration experiments, computational modelling, phylogenetic conservation and Escherichia coli-based activity assays combine to suggest a DNA-binding model in which a brim of positively charged residues positions the target cytosine for catalysis. The structure of the APOBEC3G catalytic domain will help us to understand functions of other family members and interactions that occur with pathogenic proteins such as HIV-1 Vif.