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

Kuan Ming Chen, Elena Harjes, Phillip J. Gross, Amr Fahmy, Yongjian Lu, Keisuke Shindo, Reuben S. Harris, Hiroshi Matsuo

Research output: Contribution to journalArticlepeer-review

178 Scopus citations

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. APOBEC3G anti-viral activity is circumvented by most retroelements, such as through degradation by HIV-1 Vif. 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. Although structures of other family members exist, none of these proteins has elicited polynucleotide cytosine deaminase or anti-viral activity. 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.

Original languageEnglish (US)
Pages (from-to)116-119
Number of pages4
JournalNature
Volume452
Issue number7183
DOIs
StatePublished - Mar 6 2008

Bibliographical note

Funding Information:
Acknowledgements We thank R. LaRue, N. Martemyanova, M. Stenglein and S. Wagner for assistance, laboratory members for discussions, V. Pathak for sharing unpublished information, and J. Lipscomb and K. Walters for comments on the manuscript. Key instrumentation was provided by the University of Minnesota NMR Facility (NSF) and Supercomputing Institute, the University of Wisconsin NMRfam (NIH) and the University of Connecticut Analytical Ultracentrifugation Facility. This work was supported by grants from the National Institutes of Health (A.F., H.M. and R.S.H.), the Medica Foundation (MN Partnership for Biotechnology and Medical Genomics (H.M. and R.S.H.)), the University of Minnesota (H.M. and R.S.H.) and the Searle Scholarship Program (R.S.H.).

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