Citation: Jin Jiaoyu, Yan Xiaoxuan, Liu Yaping, Lan Wenxian, Wang Chunxi, Xu Bin, Cao Chunyang. Recent Advances in the Structural Studies on Cytosine Deaminase APOBEC3 Family Members and Their Nucleic Acid Complexes[J]. Acta Chimica Sinica, ;2019, 77(11): 1089-1098. doi: 10.6023/A19080296 shu

Recent Advances in the Structural Studies on Cytosine Deaminase APOBEC3 Family Members and Their Nucleic Acid Complexes

Jin Jiaoyu ^a,b ,
Yan Xiaoxuan ^b ,
Liu Yaping ^b ,
Lan Wenxian ^b ,
Wang Chunxi ^b ,
Xu Bin ^a,, ,
Cao Chunyang ^b,,

a.
College of Science, Shanghai University, Shanghai 200444
b.
State Key Lab of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032

Corresponding author: Xu Bin, xubin@t.shu.edu.cn Cao Chunyang, ccao@mail.sioc.ac.cn
Received Date: 7 August 2019
Available Online: 9 November 2019

Figures(10)

Apolipoprotein B mRNA catalytically edited protein APOBEC3 (A3) is a family of proteins in the intracellular retrotransposon defense system, including seven members APOBEC3A (A3A), APOBEC3B (A3B), APOBEC3C (A3C), APOBEC3DE (A3DE), APOBEC3F (A3F), APOBEC3G (A3G) and APOBEC3H (A3H) encoded in a tandem array on human chromosome 22. They deaminate cytosine in single-stranded DNA and RNA substrates, which play a variety of roles in human health and disease. Among them, A3DE, A3F, A3G and A3H restrict replication of human immunodeficiency virus-1 (HIV-1) in strains lacking the virus infectivity factor protein (Vif) by deaminating cytidine in virus cDNA. Subsequent replication of the virus cDNA generates the hallmark G-to-A hyper-mutations, causing proviral inactivation. HIV-1 develops countermeasures to antagonize this intrinsic host defense response. Its Vif protein facilitates polyubiquitination of A3 members by recruiting an E3 ubiquitin ligase complex, which results in the proteasomal degradation of A3 proteins. To better understand the deamination mechanism of A3 proteins, we here reviewed the research progress on the structures of free A3 family members and their complexes with single-stranded DNA or double-stranded RNA. It includes the structures of the apo-forms of N- and/or C-termini domains of A3A, A3B, A3C, A3F, A3G and A3H, or the chimeric forms of their functional domains, and their complexes with nucleic acids, which demonstrate the basis of how A3 proteins to identify target base cytosine in hot motifs 5'-TC or 5'-CC in DNA, and then to conduct catalytic deamination. We simply described how the key residues of A3 members are involved in DNA or RNA interactions, the common properties of their structures, and their interactions with DNA or RNA. We partially discussed the interactions between A3 proteins and Vif, therefore, this review might be helpful to rationally design anti-virus drugs to disrupt these interactions. We finally suggested the new research directions about how to make full-length A3 proteins containing N-terminal CD1 and C-terminal CD2 domains, and how to study the interactions between these full-length A3 proteins and nucleic acids through cryo-EM and other techniques.
- APOBEC3,
- cytidine deamination,
- HIV virus,
- nucleic acid,
- structure
1. [1]
  Goila-Gaur, R.; Strebel, K. Retrovirology 2008, 5, 51. doi: 10.1186/1742-4690-5-51
2. [2]
  Larue, R. S.; Andresdottir, V.; Blanchard, Y.; Conticello, S. G.; Derse, D.; Emerman, M.; Greene, W. C.; Jonsson, S. R.; Landau, N. R.; Lochelt, M.; Malik, H. S.; Malim, M. H.; Munk, C.; O'Brien, S. J.; Pathak, V. K.; Strebel, K.; Wain-Hobson, S.; Yu, X. F.; Yuhki, N.; Harris, R. S. J. Virol. 2009, 83, 494. doi: 10.1128/JVI.01976-08
3. [3]
  Wedekind, J. E. Trends Genet. 2003, 19, 207. doi: 10.1016/S0168-9525(03)00054-4
4. [4]
  Harris, R. S.; Liddament, M. T. Nat. Rev. Immunol. 2004, 4, 868. doi: 10.1038/nri1489
5. [5]
  Kitamura, S.; Ode, H.; Nakashima, M. Nat. Struct. Mol. Biol. 2012, 19, 1005. doi: 10.1038/nsmb.2378
6. [6]
  Mitra, M.; Hercik, K.; Byeon, I. J. L. Nucleic Acids Res. 2014, 42, 1095. doi: 10.1093/nar/gkt945
7. [7]
  Chen, K. M.; Harjes, E.; Gross, P. J.; Fahmy, A.; Lu, Y.; Shindo, K. Seibutsu Butsuri 2008, 48, 116.
8. [8]
  Burns, M. B.; Lackey, L.; Carpenter, M. A.; Rathore, A.; Land, A. M.; Leonard, B. Nature 2013, 494, 366. doi: 10.1038/nature11881
9. [9]
  Shi, K.; Carpenter, M. A.; Kurahashi, K.; Harris, R. S.; Aihara, H. J. Biol. Chem. 2015, 290, 28120. doi: 10.1074/jbc.M115.679951
10. [10]
  Xiao, X.; Yang, H.; Arutiunian, V.; Fang, Y.; Chen, X. S. Nucleic Acids Res. 2017, 45, 7494. doi: 10.1093/nar/gkx362
11. [11]
  Nathans, R.; Cao, H.; Sharova, N.; Ali, A.; Sharkey, M.; Stranska, R. Nat. Biotechnol. 2008, 26, 1187. doi: 10.1038/nbt.1496
12. [12]
  Dang, Y.; Wang, X.; Esselman, W. J.; Zheng, Y. H. J. Virol. 2006, 80, 10522. doi: 10.1128/JVI.01123-06
13. [13]
  Stanley, B. J.; Ehrlich, E. S.; Short, L.; Yu, Y.; Xiong, Y. J. Virol. 2008, 82, 8656. doi: 10.1128/JVI.00767-08
14. [14]
  Seplyarskiy, V. B.; Andrianova, M. A.; Bazykin, G. A. Genome Res. 2017, 27, 175. doi: 10.1101/gr.210336.116
15. [15]
  Zheng, Y. H.; Irwin, D.; Kurosu, T. J. Virol. 2004, 78, 6073. doi: 10.1128/JVI.78.11.6073-6076.2004
16. [16]
  Byeon, I. J. L.; Ahn, J.; Mitra, M.; Byeon, C. H.; Hercík, K.; Hritz, J. Nat. Commun. 2013, 4, 1890. doi: 10.1038/ncomms2883
17. [17]
  Chelico, L.; Prochnow, C.; Erie, D. A. J. Biol. Chem. 2010, 283, 16195.
18. [18]
  Guo, Y.; Dong, L.; Qiu, X.; Wang, Y.; Zhang, B.; Liu, H. Nature 2014, 505(7482), 229. doi: 10.1038/nature12884
19. [19]
  Bohn, M. F. Structure 2013, 21, 1042. doi: 10.1016/j.str.2013.04.010
20. [20]
  Siu, K. K.; Sultana, A.; Azimi, F. Nat. Commun. 2013, 4, 2593. doi: 10.1038/ncomms3593
21. [21]
  Matsui, M.; Shindo, K.; Izumi, T.; Io, K.; Shinohara, M.; Komano, J.; Kobayashi, M.; Kadowaki, N.; Harris, R. S.; Takaori-Kondo, A. Virol. J. 2014, 11, 122. doi: 10.1186/1743-422X-11-122
22. [22]
  Kouno, T.; Luengas, E. M.; Shigematsu, M. Nat. Struct. Mol. Biol. 2015, 22(6), 485. doi: 10.1038/nsmb.3033
23. [23]
  Klarmann, G. J. J. Biol. Chem. 2003, 278, 7902. doi: 10.1074/jbc.M207223200
24. [24]
  Furukawa, A.; Nagata, T.; Matsugami, A. Nucleic Acids Symp. Ser. 2009, 53, 87. doi: 10.1093/nass/nrp044
25. [25]
  Mangeat, B.; Turelli, P.; Caron, G.; Friedli, M.; Perrin, L.; Trono, D. Nature 2003, 4244, 99.
26. [26]
  Peng, G. J. Exp. Med. 2006, 203, 41. doi: 10.1084/jem.20051512
27. [27]
  Chelico, L.; Pham, P.; Calabrese, P.; Goodman, M. F. Nat. Struct. Mol. Biol. 2006, 13, 392 doi: 10.1038/nsmb1086
28. [28]
  Harjes, E.; Gross, P. J.; Chen, K. M.; Lu, Y.; Shindo, K. J. Mol. Biol. 2009, 389, 819. doi: 10.1016/j.jmb.2009.04.031
29. [29]
  Wichroski, M. J.; K. Ichiyama; T. M. Rana. J. Biol. Chem. 2005, 280, 8387.
30. [30]
  Sheehy, A. M.; Gaddis, N. C.; Choi, J. D.; Malim, M. H. Nature 2002, 418, 646. doi: 10.1038/nature00939
31. [31]
  Bennett, R. P.; Presnyak, V.; Wedekind, J. E.; Smith, H. C. J. Biol. Chem. 2008, 283, 7320. doi: 10.1074/jbc.M708567200
32. [32]
  Lu, X.; Zhang, T. L.; Xu, Z. J. Biol. Chem. 2015, 290, 4010. doi: 10.1074/jbc.M114.624262
33. [33]
  Dang, Y.; Siew, L. M.; Wang, X. J.; Han, Y. X.; Lampen, R.; Zheng, Y. H. J. Biol. Chem. 2008, 283, 11606. doi: 10.1074/jbc.M707586200
34. [34]
  Jarmuz, A.; Chester, A.; Bayliss, J.; Gisbourne, J.; Dunham, I.; Scott, J. Genomics 2002, 79, 285. doi: 10.1006/geno.2002.6718
35. [35]
  Holden, L. G.; Prochnow, C.; Chang, Y. P. Nature 2008, 456, 121. doi: 10.1038/nature07357
36. [36]
  Olson, M. E.; Li, M.; Harris, R. S. Chem. Med. Chem. 2013, 8, 112. doi: 10.1002/cmdc.201200411
37. [37]
  Jager, S.; Kim, D. Y.; Hultquist, J. F.; Shindo, K.; Larue, R. S.; Kwon, E. Nature 2012, 481, 371. doi: 10.1038/nature10693
38. [38]
  Mehle, A.; Strack, B.; Ancuta, P.; Zhang, C.; Mcpike, M.; Gabuzda, D. J. Biol. Chem. 2004, 279, 7792. doi: 10.1074/jbc.M313093200
39. [39]
  Marcsisin, S. R.; Engen, J. R. J. Mol. Biol. 2010, 402, 892. doi: 10.1016/j.jmb.2010.08.026
40. [40]
  Bergeron, J. R.; Huthoff, H.; Veselkov, D. A.; Beavil, R. L.; Sanderson, M. R. PLoS Pathog. 2010, 6, e1000925. doi: 10.1371/journal.ppat.1000925
41. [41]
  Reingewertz, T. H.; Shalev, D. E.; Friedler, A. Protein Pept. Lett. 2010, 17, 988. doi: 10.2174/092986610791498876
42. [42]
  Liddament, M. T.; Brown, W. L.; Schumacher, A. J.; Harris, R. S. Curr. Biol. 2004, 14, 1385. doi: 10.1016/j.cub.2004.06.050
43. [43]
  Lu, Z.; Bergeron, J. R. C.; AtkinsLu, Z.; Bergeron, J. R. C.; Atkinson, R. A.; Schaller, T.; Veselkov, D. A.; Oregioni, A. Open. Biol. 2013, 3, 130100. doi: 10.1098/rsob.130100
44. [44]
  Luo, K.; Xiao, Z.; Ehrlich, E.; Yu, Y.; Liu, B.; Zheng, S. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 11444. doi: 10.1073/pnas.0502440102
45. [45]
  Stenglein, M. D.; Burns, M. B.; Li, M.; Lengyel, J.; Harris, R. S. Nat. Struct. Mol. Biol. 2010, 17, 222. doi: 10.1038/nsmb.1744
46. [46]
  Chelico, L.; Pham, P.; Calabrese, P.; Goodman, M. F. Nat. Struct. Mol. Biol. 2006, 13, 392. doi: 10.1038/nsmb1086
47. [47]
  Ronsard, L.; Raja, R.; Panwar, V.; Saini, S.; Mohankumar, K.; Sridharan, S. Sci. Rep. 2015, 5, 15438. doi: 10.1038/srep15438
48. [48]
  Yamanaka, S.; Balestra, M. E.; Ferrell, L. D. Proc. Nat. Acad. Sci. U. S. A. 1995, 92, 8483. doi: 10.1073/pnas.92.18.8483
49. [49]
  Navarro, F.; Bollman, B.; Chen, H. Virology 2005, 333, 374. doi: 10.1016/j.virol.2005.01.011
50. [50]
  Kouno, T.; Silvas, T. V.; Hilbert, B. J.; Shandilya, S. M. D.; Bohn, M. F.; Kelch, B. A.; Royer, W. E.; Somasundaran, M.; Kurt Yilmaz, N.; Matsuo, H.; Schiffer, C. A. Nat. Commun. 2017, 8, 15024. doi: 10.1038/ncomms15024
51. [51]
  Shi, K.; Carpenter, M. A.; Banerjee, S.; Shaban, N. M.; Kurahashi, K.; Salamango, D. J.; McCann, J. L.; Starrett, G. J.; Duffy, J. V.; Demir, O.; Amaro, R. E.; Harki, D. A.; Harris, R. S.; Aihara, H. Nat. Struct Mol. Biol. 2017, 24, 131. doi: 10.1038/nsmb.3344
52. [52]
  Fang, Y.; Xiao, X.; Li, S.; Wolfe, A.; Chen, X. S. J. Mol. Biol. 2018, 430, 87. doi: 10.1016/j.jmb.2017.11.007
53. [53]
  Cheng, C.; Zhang, T.; Wang, C. X.; Lan, W.; Ding, J.; Cao, C. Y. Chin. J. Chem. 2018, 36, 1241. doi: 10.1002/cjoc.201800508
54. [54]
  Xiao, X.; Li, S. X.; Yang, H.; Chen, X. S. Nat. Commun. 2016, 7, 12193. doi: 10.1038/ncomms12193
55. [55]
  Maiti, A.; Myint, W.; Kanai, T.; Delviks-Frankenberry, K.; Sierra Rodriguez, C.; Pathak, V. K.; Schiffer, C. A.; Matsuo, H. Nat. Commun. 2018, 9, 2460. doi: 10.1038/s41467-018-04872-8
56. [56]
  Yan, X. X.; Lan, W. X.; Wang, C. X.; Cao, C. Y. Chem. Asian J. 2019, 14, 2235. doi: 10.1002/asia.201900480
57. [57]
  Bohn, J. A.; Thummar, K.; York, A.; Raymond, A.; Brown, W. C.; Bieniasz, P. D.; Hatziioannou, T.; Smith, J. L. Nat. Commun. 2017, 8, 1021. doi: 10.1038/s41467-017-01309-6
58. [58]
  Nadine, M. S.; Shi, K.; Lauer, K. V.; Brown, W. L.; Aihara, H.; Harris, R. S. Mol. Cell 2018, 69, 75. doi: 10.1016/j.molcel.2017.12.010
59. [59]
  Matsuoka, T.; Nagae, T.; Ode, H.; Awazu, H.; Kurosawa, T.; Hamano, A.; Matsuoka, K.; Hachiya, A.; Imahashi, M.; Yokomaku, Y.; Watanabe, N.; Iwatani, Y. Nucleic Acids Res. 2018, 46, 10368. doi: 10.1093/nar/gky676
1. [1]
  Peng ZHOU , Xiao CAI , Qingxiang MA , Xu LIU . Effects of Cu doping on the structure and optical properties of Au₁₁(dppf)₄Cl₂ nanocluster. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1254-1260. doi: 10.11862/CJIC.20240047
2. [2]
  Qiuyu Ming , Huijun Jiang , Zhihao Zhang . A Sightseeing Tour of Folic Acid Processing Plant. University Chemistry, 2024, 39(9): 11-15. doi: 10.12461/PKU.DXHX202404092
3. [3]
  Maitri Bhattacharjee , Rekha Boruah Smriti , R. N. Dutta Purkayastha , Waldemar Maniukiewicz , Shubhamoy Chowdhury , Debasish Maiti , Tamanna Akhtar . Synthesis, structural characterization, bio-activity, and density functional theory calculation on Cu(Ⅱ) complexes with hydrazone-based Schiff base ligands. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1409-1422. doi: 10.11862/CJIC.20240007
4. [4]
  Haitang WANG , Yanni LING , Xiaqing MA , Yuxin CHEN , Rui ZHANG , Keyi WANG , Ying ZHANG , Wenmin WANG . Construction, crystal structures, and biological activities of two Ln^Ⅲ₃ complexes. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1474-1482. doi: 10.11862/CJIC.20240188
5. [5]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
6. [6]
  Yanxin Wang , Hongjuan Wang , Yuren Shi , Yunxia Yang . Application of Python for Visualizing in Structural Chemistry Teaching. University Chemistry, 2024, 39(3): 108-117. doi: 10.3866/PKU.DXHX202306005
7. [7]
  Yuqiao Zhou , Weidi Cao , Shunxi Dong , Lili Lin , Xiaohua Liu . Study on the Teaching Reformation of Practical X-ray Crystallography. University Chemistry, 2024, 39(3): 23-28. doi: 10.3866/PKU.DXHX202303003
8. [8]
  Qilong Fang , Yiqi Li , Jiangyihui Sheng , Quan Yuan , Jie Tan . Magical Pesticide Residue Detection Test Strips: Aptamer-based Lateral Flow Test Strips for Organophosphorus Pesticide Detection. University Chemistry, 2024, 39(5): 80-89. doi: 10.3866/PKU.DXHX202310004
9. [9]
  Yinyin Qian , Rui Xu . Utilizing VESTA Software in the Context of Material Chemistry: Analyzing Twin Crystal Nanostructures in Indium Antimonide. University Chemistry, 2024, 39(3): 103-107. doi: 10.3866/PKU.DXHX202307051
10. [10]
  Qiying Xia , Guokui Liu , Yunzhi Li , Yaoyao Wei , Xia Leng , Guangli Zhou , Aixiang Wang , Congcong Mi , Dengxue Ma . Construction and Practice of “Teaching-Learning-Assessment Integration” Model Based on Outcome Orientation: Taking “Structural Chemistry” as an Example. University Chemistry, 2024, 39(10): 361-368. doi: 10.3866/PKU.DXHX202311007
11. [11]
  Zhijun Huang , Jiawei Li , Mojin Lu , Fa Zhou , Limiao Chen , Jianhan Huang , Younian Liu . Spying Operation of the Rabies Virus. University Chemistry, 2024, 39(9): 164-169. doi: 10.12461/PKU.DXHX202403026
12. [12]
  Peng XU , Shasha WANG , Nannan CHEN , Ao WANG , Dongmei YU . Preparation of three-layer magnetic composite Fe₃O₄@polyacrylic acid@ZiF-8 for efficient removal of malachite green in water. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 544-554. doi: 10.11862/CJIC.20230239
13. [13]
  Liyang ZHANG , Dongdong YANG , Ning LI , Yuanyu YANG , Qi MA . Crystal structures, luminescent properties and Hirshfeld surface analyses of three cadmium(Ⅱ) complexes based on 2-(3-(pyridin-2-yl)-1H-pyrazol-1-yl)benzoate. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1943-1952. doi: 10.11862/CJIC.20240079
14. [14]
  Yan Liu , Yuexiang Zhu , Luhua Lai . Introduction to Blended and Small-Class Teaching in Structural Chemistry: Exploring the Structure and Properties of Crystals. University Chemistry, 2024, 39(3): 1-4. doi: 10.3866/PKU.DXHX202306084
15. [15]
  Di Yang , Jiayi Wei , Hong Zhai , Xin Wang , Taiming Sun , Haole Song , Haiyan Wang . Rapid Detection of SARS-CoV-2 Using an Innovative “Magic Strip”. University Chemistry, 2024, 39(4): 373-381. doi: 10.3866/PKU.DXHX202312023
16. [16]
  Zheqi Wang , Yawen Lin , Shunliu Deng , Huijun Zhang , Jinmei Zhou . Antiviral Strategies: A Brief Review of the Development History of Small Molecule Antiviral Drugs. University Chemistry, 2024, 39(9): 85-93. doi: 10.12461/PKU.DXHX202403108
17. [17]
  Zitong Chen , Zipei Su , Jiangfeng Qian . Aromatic Alkali Metal Reagents: Structures, Properties and Applications. University Chemistry, 2024, 39(8): 149-162. doi: 10.3866/PKU.DXHX202311054
18. [18]
  Bairu Meng , Zongji Zhuo , Han Yu , Sining Tao , Zixuan Chen , Erik De Clercq , Christophe Pannecouque , Dongwei Kang , Peng Zhan , Xinyong Liu . Design, synthesis, and biological evaluation of benzo[4,5]thieno[2,3-d]pyrimidine derivatives as novel HIV-1 NNRTIs. Chinese Chemical Letters, 2024, 35(6): 108827-. doi: 10.1016/j.cclet.2023.108827
19. [19]
  Kun WANG , Wenrui LIU , Peng JIANG , Yuhang SONG , Lihua CHEN , Zhao DENG . Hierarchical hollow structured BiOBr-Pt catalysts for photocatalytic CO₂ reduction. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1270-1278. doi: 10.11862/CJIC.20240037
20. [20]
  Dongju Zhang . Exploring the Descriptions and Connotations of Basic Concepts of Teaching Crystal Structures. University Chemistry, 2024, 39(3): 18-22. doi: 10.3866/PKU.DXHX202304003

Get Citation

PDF

XML

Metrics

PDF Downloads(29)
Abstract views(1913)
HTML views(485)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142