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

Nature Structural and Molecular Biology

Volumn 19, Issue 10, 2012, Pages 1005-1011

  Kitamura, Shingo ^a,b   Ode, Hirotaka ^a   Nakashima, Masaaki ^a,b   Imahashi, Mayumi ^a,c   Naganawa, Yuriko ^a   Kurosawa, Teppei ^a,b   Yokomaku, Yoshiyuki ^a   Yamane, Takashi ^b   Watanabe, Nobuhisa ^b   Suzuki, Atsuo ^b   Sugiura, Wataru ^a,c   Iwatani, Yasumasa ^a,c  

^a NATIONAL HOSPITAL ORGANIZATION NAGOYA MEDICAL CENTER   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

^c NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 3C; HYDROLASE; UNCLASSIFIED DRUG; VIF PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF;

AMINO ACID SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; CYTIDINE DEAMINASE; CYTOSINE DEAMINASE; HELA CELLS; HIV-1; HUMANS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; VIF GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; VIRION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84867229556     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2378     Document Type: Article

References (42)

1. Goila-Gaur, R. & Strebel, K. HIV-1 Vif, APOBEC, and intrinsic immunity. Retrovirology 5, 51 (2008).
2. LaRue, R.S. et al. Guidelines for naming nonprimate APOBEC3 genes and proteins. J. Virol. 83, 494-497 (2009).
3. Wedekind, J.E., Dance, G.S., Sowden, M.P. & Smith, H.C. Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. Trends Genet. 19, 207-216 (2003).
4. Jäger, S. et al. Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature 481, 371-375 (2012).
5. Zhang, W., Du, J., Evans, S.L., Yu, Y. & Yu, X.F. T-cell differentiation factor CBF-β regulates HIV-1 Vif-mediated evasion of host restriction. Nature 481, 376-379 (2012).
6. Marin, M., Rose, K.M., Kozak, S.L. & Kabat, D. HIV-1 Vif protein binds the editing enzyme APOBEC3G and induces its degradation. Nat. Med. 9, 1398-1403 (2003).
7. Sheehy, A.M., Gaddis, N.C. & Malim, M.H. The antiretroviral enzyme APOBEC3G is degraded by the proteasome in response to HIV-1 Vif. Nat. Med. 9, 1404-1407 (2003).
8. Yu, X. et al. Induction of APOBEC3G ubiquitination and degradation by an HIV-1 Vif-Cul5-SCF complex. Science 302, 1056-1060 (2003).
9. Russell, R.A., Smith, J., Barr, R., Bhattacharyya, D. & Pathak, V.K. Distinct domains within APOBEC3G and APOBEC3F interact with separate regions of human immunodeficiency virus type 1 Vif. J. Virol. 83, 1992-2003 (2009).
10. Smith, J.L. & Pathak, V.K. Identification of specific determinants of human APOBEC3F, APOBEC3C, and APOBEC3DE and African green monkey APOBEC3F that interact with HIV-1 Vif. J. Virol. 84, 12599-12608 (2010).
11. Zhen, A., Wang, T., Zhao, K., Xiong, Y. & Yu, X.F. A single amino acid difference in human APOBEC3H variants determines HIV-1 Vif sensitivity. J. Virol. 84, 1902-1911 (2010).
12. Bogerd, H.P., Doehle, B.P., Wiegand, H.L. & Cullen, B.R. A single amino acid difference in the host APOBEC3G protein controls the primate species specificity of HIV type 1 virion infectivity factor. Proc. Natl. Acad. Sci. USA 101, 3770-3774 (2004).
13. Mangeat, B., Turelli, P., Liao, S. & Trono, D. A single amino acid determinant governs the species-specific sensitivity of APOBEC3G to Vif action. J. Biol. Chem. 279, 14481-14483 (2004).
14. Schröfelbauer, B., Chen, D. & Landau, N.R. A single amino acid of APOBEC3G controls its species-specific interaction with virion infectivity factor (Vif). Proc. Natl. Acad. Sci. USA 101, 3927-3932 (2004).
15. Xu, H. et al. A single amino acid substitution in human APOBEC3G antiretroviral enzyme confers resistance to HIV-1 virion infectivity factor-induced depletion. Proc. Natl. Acad. Sci. USA 101, 5652-5657 (2004).
16. Huthoff, H. & Malim, M.H. Identification of amino acid residues in APOBEC3G required for regulation by human immunodeficiency virus type 1 Vif and Virion encapsidation. J. Virol. 81, 3807-3815 (2007).
17. Albin, J.S. et al. A single amino acid in human APOBEC3F alters susceptibility to HIV-1 Vif. J. Biol. Chem. 285, 40785-40792 (2010).
18. Chen, K.M. et al. Structure of the DNA deaminase domain of the HIV-1 restriction factor APOBEC3G. Nature 452, 116-119 (2008).
19. Furukawa, A. et al. Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G. EMBO J. 28, 440-451 (2009).
20. Holden, L.G. et al. Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications. Nature 456, 121-124 (2008).
21. Shandilya, S.M. et al. Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. Structure 18, 28-38 (2010).
22. Betts, L., Xiang, S., Short, S.A., Wolfenden, R. & Carter, C.W.J. Cytidine deaminase. The 2.3 Å crystal structure of an enzyme: transition-state analog complex. J. Mol. Biol. 235, 635-656 (1994).
23. Prochnow, C., Bransteitter, R., Klein, M.G., Goodman, M.F. & Chen, X.S. The APOBEC-2 crystal structure and functional implications for the deaminase AID. Nature 445, 447-451 (2007).
24. Krzysiak, T.C., Jung, J., Thompson, J., Baker, D. & Gronenborn, A.M. APOBEC2 is a monomer in solution: implications for APOBEC3G models. Biochemistry 51, 2008-2017 (2012).
25. Iwatani, Y. et al. HIV-1 Vif-mediated ubiquitination/degradation of APOBEC3G involves four critical lysine residues in its C-terminal domain. Proc. Natl. Acad. Sci. USA 106, 19539-19544 (2009).
26. Russell, R.A. & Pathak, V.K. Identification of two distinct human immunodeficiency virus type 1 Vif determinants critical for interactions with human APOBEC3G and APOBEC3F. J. Virol. 81, 8201-8210 (2007).
27. Larue, R.S., Lengyel, J., Jónsson, S.R., Andrésdó ttir, V. & Harris, R.S. Lentiviral Vif degrades the APOBEC3Z3/APOBEC3H protein of its mammalian host and is capable of cross-species activity. J. Virol. 84, 8193-8201 (2010).
28. Kitamura, S., Ode, H. & Iwatani, Y. Structural features of antiviral APOBEC3 proteins are linked to their functional activities. Front. Microbiol. 2, 258 (2011).
29. Hultquist, J.F., Binka, M., Larue, R.S., Simon, V. & Harris, R.S. Vif proteins of human and simian immunodeficiency viruses require cellular CBFβ to degrade APOBEC3 restriction factors. J. Virol. 86, 2874-2877 (2012).
30. He, Z., Zhang, W., Chen, G., Xu, R. & Yu, X.F. Characterization of conserved motifs in HIV-1 Vif required for APOBEC3G and APOBEC3F interaction. J. Mol. Biol. 381, 1000-1011 (2008).
31. Pery, E., Rajendran, K.S., Brazier, A.J. & Gabuzda, D. Regulation of APOBEC3 proteins by a novel YXXL motif in human immunodeficiency virus type 1 Vif and simian immunodeficiency virus SIVagm Vif. J. Virol. 83, 2374-2381 (2009).
32. Schröfelbauer, B., Senger, T., Manning, G. & Landau, N.R. Mutational alteration of human immunodeficiency virus type 1 Vif allows for functional interaction with nonhuman primate APOBEC3G. J. Virol. 80, 5984-5991 (2006).
33. Tian, C. et al. Differential requirement for conserved tryptophans in human immunodeficiency virus type 1 Vif for the selective suppression of APOBEC3G and APOBEC3F. J. Virol. 80, 3112-3115 (2006).
34. Stauch, B. et al. Model structure of APOBEC3C reveals a binding pocket modulating ribonucleic acid interaction required for encapsidation. Proc. Natl. Acad. Sci. USA 106, 12079-12084 (2009).
35. Kao, S. et al. The human immunodeficiency virus type 1 Vif protein reduces intracellular expression and inhibits packaging of APOBEC3G (CEM15), a cellular inhibitor of virus infectivity. J. Virol. 77, 11398-11407 (2003).
36. Kinomoto, M. et al. All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition. Nucleic Acids Res. 35, 2955-2964 (2007).
37. Nguyen, K.L. et al. Codon optimization of the HIV-1 vpu and vif genes stabilizes their mRNA and allows for highly efficient Rev-independent expression. Virology 319, 163-175 (2004).
38. Otwinowski, Z. & Minor, W. Processing of X-Ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
39. Vargin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-1025 (1997).
40. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
41. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255 (1997).
42. Roos, J.W., Maughan, M.F., Liao, Z., Hildreth, J.E. & Clements, J.E. LuSIV cells: a reporter cell line for the detection and quantitation of a single cycle of HIV and SIV replication. Virology 273, 307-315 (2000).