3IR2

Crystal structure of the APOBEC3G catalytic domain

Summary for 3IR2

• Entry DOI: 10.2210/pdb3ir2/pdb
• Related: 2KEM
• Descriptor: DNA dC->dU-editing enzyme APOBEC-3G, ZINC ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: apobec3g, antiviral defense, host-virus interaction, hydrolase, metal-binding, nucleus
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: Q9HC16
• Total number of polymer chains: 2
• Total formula weight: 48557.27

Authors

Shandilya, S.M.D.,Schiffer, C.A. (deposition date: 2009-08-21, release date: 2010-01-12, Last modification date: 2023-09-06)

Primary citation

Shandilya, S.M.,Nalam, M.N.,Nalivaika, E.A.,Gross, P.J.,Valesano, J.C.,Shindo, K.,Li, M.,Munson, M.,Royer, W.E.,Harjes, E.,Kono, T.,Matsuo, H.,Harris, R.S.,Somasundaran, M.,Schiffer, C.A.
Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces.
Structure, 18:28-38, 2010

PubMed 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.

PubMed: 20152150
DOI: 10.1016/j.str.2009.10.016

Experimental method

X-RAY DIFFRACTION (2.25 Å)