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Crystal structures of APOBEC3G N-domain alone and its complex with DNA

Author

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  • Xiao Xiao

    (Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California
    Molecular and Computational Biology Program, University of Southern California)

  • Shu-Xing Li

    (Molecular and Computational Biology Program, University of Southern California
    Center of Excellence in NanoBiophysics, University of Southern California)

  • Hanjing Yang

    (Molecular and Computational Biology Program, University of Southern California)

  • Xiaojiang S. Chen

    (Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California
    Molecular and Computational Biology Program, University of Southern California
    Center of Excellence in NanoBiophysics, University of Southern California
    Norris Comprehensive Cancer Center, University of Southern California)

Abstract

APOBEC3G (A3G) is a potent restriction factor of HIV-1. The N-terminal domain of A3G (A3G-CD1) is responsible for oligomerization and nucleic acid binding, both of which are essential for anti-HIV activity. As a countermeasure, HIV-1 viral infectivity factor (Vif) binds A3G-CD1 to mediate A3G degradation. The structural basis for the functions of A3G-CD1 remains elusive. Here, we report the crystal structures of a primate A3G-CD1 (rA3G-CD1) alone and in complex with single-stranded DNA (ssDNA). rA3G-CD1 shares a conserved core structure with the previously determined catalytic APOBECs, but displays unique features for surface charge, dimerization and nucleic acid binding. Its co-crystal structure with ssDNA reveals how the conformations of loops and residues surrounding the Zn-coordinated centre (Zn-centre) change upon DNA binding. The dimerization interface of rA3G-CD1 is important for oligomerization, nucleic acid binding and Vif-mediated degradation. These findings elucidate the molecular basis of antiviral mechanism and HIV-Vif targeting of A3G.

Suggested Citation

  • Xiao Xiao & Shu-Xing Li & Hanjing Yang & Xiaojiang S. Chen, 2016. "Crystal structures of APOBEC3G N-domain alone and its complex with DNA," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12193
    DOI: 10.1038/ncomms12193
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    Cited by:

    1. Hanjing Yang & Kyumin Kim & Shuxing Li & Josue Pacheco & Xiaojiang S. Chen, 2022. "Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Hanjing Yang & Josue Pacheco & Kyumin Kim & Ayub Bokani & Fumiaki Ito & Diako Ebrahimi & Xiaojiang S. Chen, 2024. "Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    3. Stefan Harjes & Harikrishnan M. Kurup & Amanda E. Rieffer & Maitsetseg Bayarjargal & Jana Filitcheva & Yongdong Su & Tracy K. Hale & Vyacheslav V. Filichev & Elena Harjes & Reuben S. Harris & Geoffrey, 2023. "Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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