Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces.

Shivender Shandilya, University of Massachusetts Medical School
Madhavi N. L. Nalam, University of Massachusetts Medical School
Ellen A. Nalivaika, University of Massachusetts Medical School
Phillip J. Gross, University of Minnesota
Johnathan C. Valesano, University of Minnesota
Keisuke Shindo, University of Minnesota
Ming Li, University of Minnesota
Mary Munson, University of Massachusetts Medical School
William E. Royer, University of Massachusetts Medical School
Elena Harjes, University of Minnesota
Takahide Kono, University of Minnesota - Twin Cities
Hiroshi Matsuo, University of Minnesota
Reuben S. Harris, University of Minnesota
Mohan Somasundaran, University of Massachusetts Medical School
Celia A. Schiffer, University of Massachusetts Medical School

Abstract

APOBEC3G is a DNA cytidine deaminase that has antiviral activity against HIV-1 and other pathogenic viruses. In this study the crystal structure of the catalytically active C-terminal domain was determined to 2.25 A. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second beta strand and a lengthening of the second alpha helix. Oligomerization is postulated to be critical for the function of APOBEC3G. In this structure, four extensive intermolecular interfaces are observed, suggesting potential models for APOBEC3G oligomerization. The structural and functional significance of these interfaces was probed by solution NMR and disruptive variants were designed and tested for DNA deaminase and anti-HIV activities. The variant designed to disrupt the most extensive interface lost both activities. NMR solution data provides evidence that another interface, which coordinates a novel zinc site, also exists. Thus, the observed crystallographic interfaces of APOBEC3G may be important for both oligomerization and function.