1. Department of Biochemistry, Molecular Biology and Biophysics,
2. Institute for Molecular Virology and,
3. Arnold and Mabel Beckman Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
4. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
5. These authors contributed equally to this work.

Correspondence to: Reuben S. Harris^1,2,3Hiroshi Matsuo^1,2 Correspondence and requests for materials should be addressed to H.M. (Email: matsu029@umn.edu) or R.S.H. (Email: rsh@umn.edu).

Abstract

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 retrotransposons^{1, 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 DNA^{8, 9, 10}. Although structures of other family members exist, none of these proteins has elicited polynucleotide cytosine deaminase or anti-viral activity^{11, 12, 13, 14, 15, 16}. Here we report a solution structure of the human APOBEC3G catalytic domain. Five -helices, including two that form the zinc-coordinating active site, are arranged over a hydrophobic platform consisting of five -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.