Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces

Shivender M D Shandilya; Madhavi N L Nalam; Ellen A. Nalivaika; Phillip J. Gross; Johnathan C. Valesano; Keisuke Shindo; Ming Li; Mary Munson; William E. Royer; Elena Harjes; Takahide Kono; Hiroshi Matsuo; Reuben Harris; Mohan Somasundaran; Celia A. Schiffer

doi:10.1016/j.str.2009.10.016

Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces

Shivender M D Shandilya, Madhavi N L Nalam, Ellen A. Nalivaika, Phillip J. Gross, Johnathan C. Valesano, Keisuke Shindo, Ming Li, Mary Munson, William E. Royer, Elena Harjes, Takahide Kono, Hiroshi Matsuo, Reuben Harris, Mohan Somasundaran, Celia A. Schiffer

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106 Scopus citations

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 Å. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second β strand and a lengthening of the second α 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.

Original language	English (US)
Pages (from-to)	28-38
Number of pages	11
Journal	Structure
Volume	18
Issue number	1
DOIs	https://doi.org/10.1016/j.str.2009.10.016
State	Published - Jan 13 2010

Bibliographical note

Funding Information:
The authors would like to thank K. Romano, S. Mittal, and M. Kolli for assistance with data collection; R. Bandaranayake for assistance with initial data processing; and R. Tomaino for assistance with mass spectrometry. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Basic Energy Sciences, Office of Science, under Contract No. DE-AC02-06CH11357. Use of the BioCARS Sector 14 was supported by the National Institutes of Health, National Center for Research Resources, under grant number RR007707. This work was supported by grants from the National Institutes of Health (A1067021 and GM65347 to C.A.S; AI073167 to H.M.; and AI064046 to R.S.H.). The University of Minnesota Supercomputing Institute and NMR Core (NSF BIR-961477) provided key instrumentation. All mass spectrometry analyses were performed at the Taplin Biological Mass Spectrometry Facility of Harvard Medical School.

Keywords

DNA
PROTEINS

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Shandilya, S. M. D., Nalam, M. N. L., 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., Somasundaran, M., & Schiffer, C. A. (2010). Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces. Structure, 18(1), 28-38. https://doi.org/10.1016/j.str.2009.10.016

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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 {\AA}. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second β strand and a lengthening of the second α 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.",

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AU - Shandilya, Shivender M D

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AU - Nalivaika, Ellen A.

AU - Gross, Phillip J.

AU - Valesano, Johnathan C.

AU - Shindo, Keisuke

AU - Li, Ming

AU - Munson, Mary

AU - Royer, William E.

AU - Harjes, Elena

AU - Kono, Takahide

AU - Matsuo, Hiroshi

AU - Harris, Reuben

AU - Somasundaran, Mohan

AU - Schiffer, Celia A.

N1 - Funding Information: The authors would like to thank K. Romano, S. Mittal, and M. Kolli for assistance with data collection; R. Bandaranayake for assistance with initial data processing; and R. Tomaino for assistance with mass spectrometry. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Basic Energy Sciences, Office of Science, under Contract No. DE-AC02-06CH11357. Use of the BioCARS Sector 14 was supported by the National Institutes of Health, National Center for Research Resources, under grant number RR007707. This work was supported by grants from the National Institutes of Health (A1067021 and GM65347 to C.A.S; AI073167 to H.M.; and AI064046 to R.S.H.). The University of Minnesota Supercomputing Institute and NMR Core (NSF BIR-961477) provided key instrumentation. All mass spectrometry analyses were performed at the Taplin Biological Mass Spectrometry Facility of Harvard Medical School.

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N2 - 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 Å. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second β strand and a lengthening of the second α 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.

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Crystal Structure of the APOBEC3G Catalytic Domain Reveals Potential Oligomerization Interfaces

Abstract

Bibliographical note

Keywords

UN SDGs

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