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Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

Abstract

The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding1,2,3,4. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded β-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous ‘substrate groove’ around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure6. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.

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Figure 1: The X-ray structure of enzymatically active APOBEC3G-CD2.
Figure 2: Structural comparison of APOBEC3G-CD2 with APOBEC2.
Figure 3: Predicted substrate groove and deamination activity of APOBEC3G mutants.

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Protein Data Bank

Data deposits

The atomic coordinates and the structure of APOBEC3G-CD2 have been deposited in the Protein Data Bank under accession number 3E1U.

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Acknowledgements

We thank the staff at the Berkeley Laboratory’s Advanced Light Source (ALS) BL8.2.1 and Advanced Photon Source 19ID in Argonne National Laboratory for assistance in data collection, and M. Klein and other members of the X.S.C. laboratory for help and discussion. This work is supported in part by CBM graduate training grants to L.G.H. and Y.P.C., and by National Institutes of Health grants to M.F.G. and X.S.C.

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Correspondence to Xiaojiang S. Chen.

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This file contains Supplementary Table 1, Supplementary Figures 1-3 with Legends and Supplementary Notes (PDF 348 kb)

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Holden, L., Prochnow, C., Chang, Y. et al. Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications. Nature 456, 121–124 (2008). https://doi.org/10.1038/nature07357

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