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The APOBEC3C crystal structure and the interface for HIV-1 Vif binding

Nature Structural & Molecular Biology volume 19, pages 1005–1010 (2012)Cite this article

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Abstract

The human apolipoprotein B mRNA-editing enzyme catalytic polypeptide–like 3 (APOBEC3, referred to as A3) proteins are cellular cytidine deaminases that potently restrict retrovirus replication. However, HIV-1 viral infectivity factor (Vif) counteracts the antiviral activity of most A3 proteins by targeting them for proteasomal degradation. To date, the structure of an A3 protein containing a Vif-binding interface has not been solved. Here, we report a high-resolution crystal structure of APOBEC3C and identify the HIV-1 Vif–interaction interface. Extensive structure-guided mutagenesis revealed the role of a shallow cavity composed of hydrophobic or negatively charged residues between the α2 and α3 helices. This region is distant from the DPD motif (residues 128–130) of APOBEC3G that participates in HIV-1 Vif interaction. These findings provide insight into Vif-A3 interactions and could lead to the development of new pharmacologic anti–HIV-1 compounds.

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Figure 1: The X-ray crystal structure of full-length A3C.
Figure 2: Ten A3C residues critical for HIV-1 Vif interaction.
Figure 3: The A3C interface for the HIV-1 Vif interaction.
Figure 4: Analogous residues of A3F and A3DE are involved in the HIV-1 Vif-binding interface.
Figure 5: The effects of mutations at the equivalent residues in A3F on antiviral activity.

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Acknowledgements

We thank A.M. Gronenborn, J.G. Levin and K. Strebel for critical discussions and reading of the manuscript. We also thank K. Tokunaga (National Institute of Infectious Diseases, Tokyo, Japan) for providing the pCAGGS APOBEC3 plasmids. This work was supported in part by a grant from the Ministry of Education, Culture, Sports, Science and Technology of Japan to Y.I. (JSPS KAKENHI 24590568) and by a grant for HIV/AIDS research from the Ministry of Health, Labor and Welfare of Japan to Y.I.

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Authors and Affiliations

  1. Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan

    Shingo Kitamura, Hirotaka Ode, Masaaki Nakashima, Mayumi Imahashi, Yuriko Naganawa, Teppei Kurosawa, Yoshiyuki Yokomaku, Wataru Sugiura & Yasumasa Iwatani

  2. Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Japan

    Shingo Kitamura, Masaaki Nakashima, Teppei Kurosawa, Takashi Yamane, Nobuhisa Watanabe & Atsuo Suzuki

  3. Program in Integrated Molecular Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan

    Mayumi Imahashi, Wataru Sugiura & Yasumasa Iwatani

  4. Synchrotron Radiation Research Center, Nagoya University, Nagoya, Japan

    Nobuhisa Watanabe

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Contributions

S.K., H.O., M.N., T.K., T.Y., N.W., A.S. and Y.I. performed experiments and analysis for the crystal structure determination; S.K., M.N., M.I., Y.N., T.K., Y.Y. and Y.I. performed biochemical experiments; S.K., M.N., M.I., Y.N., Y.Y., W.S. and Y.I. analyzed the biochemical data; Y.I. directed the project; S.K., H.O. and Y.I. wrote the manuscript with all authors' help.

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Correspondence to Yasumasa Iwatani.

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Kitamura, S., Ode, H., Nakashima, M. et al. The APOBEC3C crystal structure and the interface for HIV-1 Vif binding. Nat Struct Mol Biol 19, 1005–1010 (2012). https://doi.org/10.1038/nsmb.2378

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