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

doi:10.6023/A19080296

Acta Chimica Sinica ›› 2019, Vol. 77 ›› Issue (11): 1089-1098.DOI: 10.6023/A19080296 Previous Articles Next Articles

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胞嘧啶脱氨基化酶APOBEC3家族及其与核酸复合物结构研究进展

金交羽^a^b, 严小璇^b, 刘亚平^b, 蓝文贤^b, 王春喜^b, 许斌^a*(), 曹春阳^b*()

^a 上海大学理学院化学系上海 200444
^b 中国科学院上海有机化学研究所生命有机化学国家重点实验室上海 200032

投稿日期:2019-08-07 发布日期:2019-08-15
通讯作者: 许斌,曹春阳 E-mail:xubin@t.shu.edu.cn;ccao@mail.sioc.ac.cn
作者简介:金交羽, 女, 上海大学和中科院上海有机所2017级联合培养在读硕士研究生, 主要研究方向为APOBEC3胞嘧啶脱氨基化酶的结构与机理|许斌, 男, 上海大学化学系教授、博导. 2000年获中国科学院上海有机化学研究所理学博士(导师:麻生明院士); 2000~2002年, 在美国国立卫生研究院(NIH)进行博士后研究, 从事基于嘌呤受体的激动剂和拮抗剂的设计与合成(导师: K. A. Jaconson). 2002~2005年, 于美国VivoQuest公司担任高级研究员, 从事抗丙型肝炎药物的设计和合成; 2005年底加入上海大学化学系; 2007年入选上海市“浦江人才”计划.曾获宝钢优秀教师奖、ACP Advanced Research Network Lectureship Award、Asia Core Program Lectureship Award等荣誉.研究方向: (1)惰性化学键可控转化; (2)新型药物分子的设计与合成|曹春阳, 男, 1970年8月出生. 2001年博士毕业于中国科学院上海有机化学研究所, 随后在美国约翰霍普金斯大学医学院做博士后与研究助理, 2005年12月至2006年08月, 转至美国Salk生物研究院结构生物学中心做助理研究员.现任中国科学院上海有机化学研究所“百人计划”研究员, 是上海市“浦江计划”获得者.研究方向:以健康与疾病导向的、以NMR为主要技术手段的化学生物学与结构生物学.内容包括: (1)与癌症或者HIV病毒感染等相关蛋白质与核酸特异性作用机制与功能研究; (2)以与癌症或者HIV病毒感染等相关核酸或蛋白质为靶标, 进行药物分子设计与筛选; (3)基于核磁共振波谱学的蛋白质高效表达新技术新方法研究.
基金资助:
科技部重点研发(No.2017YFE0108200);中国科学院战略性先导科技专项（B类）(XDB 20000000);国家自然科学基金(No.21778065);国家自然科学基金(No.21807105);国家自然科学基金(No.91753119)

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

Received:2019-08-07 Published:2019-08-15
Contact: Xu Bin,Cao Chunyang E-mail:xubin@t.shu.edu.cn;ccao@mail.sioc.ac.cn

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.

Key words: APOBEC3, cytidine deamination, HIV virus, nucleic acid, structure

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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.

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Fig. & Tab. 10

Figure 1. Classification and nomination of the functional domain of A3 family members. (A) The classification of CD1 and CD2 domains of A3 family members; (B) A3 family is classified according to Z1, Z2, Z3; (C) Sequence alignment of three types of Z regions[2], in which residues ligated with Zn2+were marked with star

Figure 2. The possible mechanism of cytosine deamination catalyzed by A3 family members[4]

Figure 3. The sequence alignment of A3 family protein. Clustal Omega amino acids alignment showing secondary structures (α-helices, β-strand and loop). In A3 members, conserved residues H70, W98 and Y130 (in A3A) are all involved in DNA interactions

Figure 4. The crystal structure of A3A E72A/C171A variant in complex with ssDNA (PDB code 5KEG)[50]. (A) Complex structure was displayed in cartoon mode; (B) Interactions between A3A and the target nucleotide base (dC0); (C) Interactions between H29 side chain and the substrate DNA. A3A structure is shown in green, and the DNA is shown in orange; in all picture, Zn2+ ion and water (W) are indicated by grey and red spheres, hydrogen bonds and π-orbital interaction are depicted by orange and black dashed lines. The structures of residues and bases in (B) and (C) were shown in stick mode

Figure 5. Crystal structure of chimeric A3B variant in complex with ssDNA (PDB code 5TD5)[51]. (A) Complex structure was displayed in cartoon mode; (B) Interactions between A3B active site and DNA. A3B is in green, DNA is shown in orange, Zn2+ ion and water (W) are indicated by grey and red spheres, and hydrogen bonds is depicted by orange dashed lines, respectively

Figure 6. Crystal structure of A3B in complex with ssDNA[52, 53]. (A) Crystal structure of A3F-CD2 tetramer and substrate DNA(PDB code 5W2M), four A3F-CD2 monomers are in green, lavender, golden yellow, light blue, respectively, and DNA is in orange; (B) Electrostatic surface of crystal structure of A3F-CD2 in complex with DNA (blue is positive charge, red is negative charge). (C) Residue Y333 in each A3F-CD2 (cyan, green, pink and yellow) stacks with base dT in DNA (orange). (D) Crystal structure of chimeric A3Fc-CD2 dimer in complex with ssDNA (PDB code 5ZVA), two A3Fc-CD2 monomers are in green and light blue, respectively; (E) Residues Y333, K358 and K359 in A3Fc-CD2 monomer a form the first DNA binding site; (F) Residues W277, Y307, Y308, F309 and W310 in A3Fc-CD2 monomer b form the second DNA binding site. Zn2+ion and water (W) are indicated by spheres colored grey and red, respectively, hydrogen bonds and π-orbital interaction are depicted by orange and black dashed lines, respectively

Figure 7. The crystal structure of rA3G-CD1 in complex with ssDNA[54]. (A) Complex structure of rA3G-CD2 dimer and substrate DNA (orange) (PDB code 5K83); The two rA3G-CD1monomers are shown in green and purple, respectively. (B) Superimposition of bound rA3G-CD1 (green) and apo rA3G-CD1 (grey). loop-1, loop-3, loop-5 and loop-7 were referred as LP1, LP3, LP5 and LP7, respectively. Red arrows indicate the major conformational shifts of loop, β1and β2 upon DNA binding. (C) Interaction between poly-dT and zinc ion binding pocket. In all figures, DNA is in orange. Zn2+ion and water (W) are indicated by spheres colored grey and red, respectively, hydrogen bonds and π-orbital interaction are depicted by orange and black dashed lines, respectively

Figure 8. The crystal structure of A3G-CD2 variant A3G-CDT2* in complex with ssDNA (PDB code 6BUX)[55]. (A) Complex structure was displayed in cartoon mode; (B, C, D) Interactions between bases dC-2, dT-3, dC0 and dA+1 (in orange stick) in DNA and residues (in green stick) in A3G-CDT2*. In all picture, A3G-CDT2* is in green, and DNA is in orange; Zn2+ion and water (W) are indicated by grey and red spheres, respectively, hydrogen bonds and π-orbital interaction are depicted by orange and black dashed lines, respectively

Figure 8. NMR solution structure of A3G-CD2 and ssDNA[56]. (A) Deamination product TCUU6I ssDNA binds to A3G-CD2 in a CCC mode (PDB code 6K3J). (B) Deamination product TCUC6I ssDNA binds to A3G-CD2 in a TCC mode (PDB code 6K3K). In all picture, A3G-CD2 is shown in green, and the DNA is shown in orange, Zn2+ion is indicated by grey spheres

Figure 10. Crystal complex structures of A3H from different hosts and dsRNA[57~59]. (A) Complex structure of pig-tailed macaque A3H and dsRNA (PDB code 5W3V), two A3H monomers are in green and purple, and dsRNA is in orange, respectively; (B) Complex structure of human A3H and dsRNA (PDB code 6BOB), A3H is in green and dsRNA is in orange, respectively. (C) Complex structure of chimpanzee A3H and dsRNA (PDB code 5Z98), two A3H monomers are in grass and lilac, dsRNA is in orange, respectively. In all pictures, Zn2+ion is indicated by grey spheres

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胞嘧啶脱氨基化酶APOBEC3家族及其与核酸复合物结构研究进展

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

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