Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

The APOBEC-2 crystal structure and functional implications for the deaminase AID

Nature volume 445, pages 447–451 (2007)Cite this article

Abstract

APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA1,2. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies3, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus4,5,6,7. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long α-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The structure of APO2.
Figure 2: The APO2 active site.
Figure 3: Structurally guided mutagenesis of AID impairs deamination activity.
Figure 4: AID HIGM-2 mutations.

Similar content being viewed by others

References

  1. Pham, P., Bransteitter, R. & Goodman, M. F. Reward versus risk: DNA cytidine deaminases triggering immunity and disease. Biochemistry 44, 2703–2715 (2005)

    Article  CAS  Google Scholar 

  2. Conticello, S. G., Thomas, C. J. F., Petersen-Mahrt, S. K. & Neuberger, M. S. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol. Biol. Evol. 22, 367–377 (2004)

    Article  Google Scholar 

  3. Bransteitter, R., Sneeden, J. L., Allen, S., Pham, P. & Goodman, O. M. F. First AID (activation-induced cytidine deaminase) is needed to produce high affinity isotype-switched antibodies. J. Biol. Chem. 281, 16833–16836 (2006)

    Article  CAS  Google Scholar 

  4. Chiu, Y. L. & Greene, W. C. Multifaceted antiviral actions of APOBEC3 cytidine deaminases. Trends Immunol. 27, 291–297 (2006)

    Article  CAS  Google Scholar 

  5. Cullen, B. R. Role and mechanism of action of the APOBEC3 family of antiretroviral resistance factors. J. Virol. 80, 1067–1076 (2006)

    Article  CAS  Google Scholar 

  6. Franca, R., Spadari, S. & Maga, G. APOBEC deaminases as cellular antiviral factors: a novel natural host defense mechanism. Med. Sci. Monit. 12, RA92–RA98 (2006)

    CAS  PubMed  Google Scholar 

  7. Bonvin, M. et al. Interferon-inducible expression of APOBEC3 editing enzymes in human hepatocytes and inhibition of hepatitis B virus replication. Hepatology 43, 1364–1374 (2006)

    Article  CAS  Google Scholar 

  8. Johansson, E., Mejlhede, N., Neuhard, J. & Larsen, S. Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 Å resolution. Biochemistry 41, 2563–2570 (2002)

    Article  CAS  Google Scholar 

  9. Xie, K. et al. The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1. Proc. Natl Acad. Sci. USA 101, 8114–8119 (2004)

    Article  ADS  CAS  Google Scholar 

  10. Teh, A. et al. The 1.48 Å resolution crystal structure of the homotetrameric cytidine deaminase from mouse. Biochemistry 45, 7825–7833 (2006)

    Article  CAS  Google Scholar 

  11. Chung, S. J., Fromme, J. C. & Verdine, G. L. Structure of human cytidine deaminase bound to a potent inhibitor. J. Med. Chem. 48, 658–660 (2005)

    Article  CAS  Google Scholar 

  12. Betts, L., Xiang, S., Short, S. A., Wolfenden, R. & Carter, C. W. Cytidine deaminase. The 2.3 Å crystal structure of an enzyme: transition-state analog complex. Curr. Biol. 235, 635–656 (1994)

    CAS  Google Scholar 

  13. Smith, A. A., Carlow, D. C., Wolfenden, R. & Short, S. A. Mutations affecting transition-state stabilization by residues coordinating zinc at the active site of cytidine deaminase. Biochemistry 33, 6468–6474 (1994)

    Article  CAS  Google Scholar 

  14. Durandy, A., Peron, S. & Fischer, A. Hyper-IgM syndromes. Curr. Opin. Rheumatol. 18, 369–376 (2006)

    Article  CAS  Google Scholar 

  15. Minegishi, Y. et al. Mutations in activation-induced cytidine deaminase in patients with hyper IgM syndrome. Clin. Immunol. 97, 203–210 (2000)

    Article  CAS  Google Scholar 

  16. Anant, S. et al. ARCD-1, an apobec-1-related cytidine deaminase, exerts a dominant negative effect on C to U RNA editing. Am. J. Cell Physiol. 281, C1904–C1916 (2001)

    Article  CAS  Google Scholar 

  17. Jarmuz, A. et al. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics 79, 285–296 (2002)

    Article  CAS  Google Scholar 

  18. Shindo, K. et al. The enzymatic activity of CEM15/Apobec-3G is essential for the regulation of the infectivity of HIV-1 virion but not a sole determinant of its antiviral activity. J. Biol. Chem. 278, 44412–44416 (2003)

    Article  CAS  Google Scholar 

  19. Wiegand, H. L., Doehle, B. P., Bogerd, H. P. & Cullen, B. R. A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins. EMBO J. 23, 2451–2458 (2004)

    Article  CAS  Google Scholar 

  20. Opi, S. et al. Monomeric APOBEC3G is catalytically active and has antiviral activity. J. Virol. 80, 4673–4682 (2006)

    Article  CAS  Google Scholar 

  21. Navarro, F. et al. Complementary function of the two catalytic domains of APOBEC3G. Virology 333, 374–386 (2005)

    Article  CAS  Google Scholar 

  22. Wang, J. et al. Identification of a specific domain required for dimerization of activation-induced cytidine deaminase. J. Biol. Chem. (in the press).

  23. Teng, B. et al. Mutational analysis of apolipoprotein B mRNA editing enzyme (APOBEC1): structure-function relationships of RNA editing and dimerization. J. Lipid Res. 40, 623–635 (1999)

    CAS  PubMed  Google Scholar 

  24. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  Google Scholar 

  25. Terwilliger, T. C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. 55, 849–861 (1999)

    Article  CAS  Google Scholar 

  26. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. 58, 1772–1779 (2002)

    Article  Google Scholar 

  27. Terwilliger, T. C. Maximum-likelihood density modification. Acta Crystallogr. 56, 965–972 (2000)

    CAS  Google Scholar 

  28. Bransteitter, R., Pham, P., Scharff, M. D. & Goodman, M. F. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc. Natl Acad. Sci. USA 100, 4102–4107 (2003)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank L. Chen for comments on the manuscript. We also thank G. Wang from Chen lab and the staff at ALS LBL8.2.1, BL8.2.2 and APS 19id in the Argonne National Laboratory for assistance in data collection. This work was supported in part by National Institutes of Health grants to M.F.G. and X.S.C. and an NIH-NIA Predoctoral Traineeship to R.B. The structure of APO2 has been uploaded to the Protein Data Bank under accession number 2NYT and to the Research Collaboratory for Structural Bioinformatics (RCSB) under accession number RCSB040471.

Author information

Author notes

  1. Courtney Prochnow and Ronda Bransteitter: These authors contributed equally to this work.

Authors and Affiliations

  1. Molecular and Computational Biology, University of Southern California Los Angeles, California, 90089, USA

    Courtney Prochnow, Ronda Bransteitter, Michael G. Klein, Myron F. Goodman & Xiaojiang S. Chen

Authors
  1. Courtney Prochnow
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ronda Bransteitter
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael G. Klein
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Myron F. Goodman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiaojiang S. Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiaojiang S. Chen.

Ethics declarations

Competing interests

The structure of APO2 has been uploaded to the Protein Data Bank under accession number 2NYT and to the Research Collaboratory for Structural Bioinformatics (RCSB) under accession number RCSB040471. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1 which is consisting of data collection, phasing and refinement statistics (MIR) for the Apo2 structure. Methods provide information about the Apo2 protein purification and crystallization, Apo2 structure determination and refinement, construction of AID mutants and AID deamination reaction. (PDF 138 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Prochnow, C., Bransteitter, R., Klein, M. et al. The APOBEC-2 crystal structure and functional implications for the deaminase AID. Nature 445, 447–451 (2007). https://doi.org/10.1038/nature05492

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature05492

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing