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

doi:10.6023/A19080296

化学学报 ›› 2019, Vol. 77 ›› Issue (11): 1089-1098.DOI: 10.6023/A19080296 上一篇下一篇

综述

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

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摘要/Abstract

载脂蛋白B mRNA催化编辑蛋白APOBEC3（简称为A3）是细胞内逆转录转座子防御系统中一类家族蛋白，它通过对底物单链DNA和RNA中胞嘧啶的脱氨基化在人类的健康和疾病中发挥多种多样的作用.部分人源A3家族蛋白通过对病毒基因组中的胞嘧啶脱氨基化产生尿嘧啶，使逆转录病毒人类免疫缺陷病毒（HIV-1）基因组发生G→A碱基突变，致使HIV-1基因组不能执行正常的功能而抑制HIV-1病毒复制.作为反保护措施，HIV-1病毒利用自身的Vif蛋白（viral infectivity factor）结合人源A3蛋白，通过泛素化标记使A3蛋白降解，从而保证病毒感染.为更好理解A3蛋白催化胞嘧啶脱氨基化机制及抗病毒机制，综述了A3家族蛋白结构、它们对DNA或者RNA进行脱氨基化反应特点和它们与核酸复合物结构的研究进展，对A3家族蛋白参与脱氨基化反应的关键残基如何与核酸碱基相互作用等作了简单概括，相互作用的共同特征进行简要总结，对后期如何利用冷冻电镜技术开展全长A3蛋白相关工作做了展望.本文也部分讨论了A3蛋白如何与Vif相互作用，因此本综述对针对这些相互作用合理设计抗病毒药物有一定帮助.

关键词: APOBEC3, 胞嘧啶脱氨基化, HIV病毒, 核酸, 结构

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

引用此文

金交羽, 严小璇, 刘亚平, 蓝文贤, 王春喜, 许斌, 曹春阳. 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[J]. 化学学报, 2019, 77(11): 1089-1098.

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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图/表 10

图 1. A3家族蛋白结构域组成与分类: (A) A3家族蛋白CD1与CD2分类; (B) A3家族蛋白结构域按Z1、Z2、Z3进行分类; (C)三类Z区域的氨基酸序列比对[2], 与Zn2+配位的氨基酸上面标了星号

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

图 2. A3家族催化ssDNA中胞嘧啶脱氨基化可能机制[4]

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

图 3. A3家族蛋白氨基酸序列对比图. Clustal Omega的氨基酸比对结果的图上方显示了二级结构(α螺旋、β折叠及loop).其中, A3蛋白中序列保守的氨基酸H70、W98、Y130(在A3A中的编号)均参与了DNA特异性识别

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

图 4. A3A突变体E72A/C171A与ssDNA复合物晶体结构(PDB号5KEG)[50]. (A)复合物结构cartoon显示模式; (B)A3A与靶核苷酸碱基(dC0)之间相互作用的立体图; (C) H29侧链与底物DNA之间的相互作用.图中A3A为绿色, DNA为橙色, 图中灰色和红色球分别代表锌离子和水分子, 橙色和黑色虚线分别代表氢键和π-轨道作用.图B和C中氨基酸与碱基以球棍模式显示

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

图 5. A3B嵌合体与ssDNA复合物晶体结构(PDB号5TD5)[51]. (A) cartoon模式显示的复合物结构; (B)A3B活性位点和DNA作用细节.图中A3B为绿色, DNA为橙色, 灰色和红色球分别代表锌离子和水分子, 橙色虚线代表氢键

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

图 6. A3F-CD2与ssDNA复合物晶体结构[52, 53]. (A)以cartoon模式显示的A3F-CD2与poly-dT ssDNA复合物晶体结构(PDB号5W2M), 四个单体A3F-CD2结构分别用绿色, 淡紫色, 金黄色, 淡蓝色显示, DNA用橙色显示; (B) A3F-CD2与poly-dT ssDNA复合物晶体结构表面电势图(蓝色为正电荷、红色为负电荷). (C)A3F-CD2氨基酸Y333(淡蓝色、紫色、绿色与黄色显示)与DNA碱基dT(橙色显示)之间的相互作用细节图.氨基酸与碱基均以球棍模式显示; (D)以cartoon模式显示的嵌合体A3Fc-CD2二聚体与底物DNA的复合物晶体结构(PDB号5ZVA). A3Fc-CD2单体用绿色和淡蓝色表示. (E)图D中A3Fc-CD2单体a残基Y333、Y359与K358形成第一个DNA结合位点; (F)图D中A3Fc-CD2单体b残基W277、Y307、Y308、F309和W310形成第二个DNA结合位点.图中灰色和红色球分别代表锌离子和水分子, 橙色和黑色虚线分别代表氢键和π-轨道相互作用

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

图 7. rA3G-CD1与ssDNA复合物晶体结构[54]. (A) rA3G-CD1二聚体与底物DNA的复合物结构(PDB号5K83);两个rA3G-CD1单体分别用绿色与紫色表示. (B) rA3G-CD1和ssDNA复合物晶体结构中单体rA3G-CD1结构(绿色)与自由态rA3G-CD1 (即apo rA3G-CD1, 灰色)结构重叠图; Loop-1, loop-3, loop-5, loop-7分别简称为LP1, LP3, LP5, LP7.红色箭头表示结合DNA后loop, β1和β2构象的变化. (C) poly- dT结合锌离子中心的细节图.图中DNA为橙色.灰色和红色球分别代表锌离子和水分子, 图C中橙色和黑色虚线分别代表氢键和π-轨道相互作用

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

图 8. A3G-CDT2*与ssDNA复合物晶体结构(PDB号6BUX)[55]. (A)以cartoon模式显示的复合物结构; (B, C, D) A3G-CDT2*与碱基dC-2、dT-3、dC0和dA+1之间相互作用细节图(球棍模式显示).图中A3G-CDT2*为绿色, DNA为橙色.灰色和红色球分别代表锌离子和水分子, 橙色和黑色虚线分别代表氢键和π-轨道相互作用

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

图 9. A3G-CD2与DNA的NMR溶液结构[56]. (A)脱氨基化产物TCUU6I DNA以CCC模式结合A3G-CD2的复合物结构(PDB号6K3J); (B)脱氨基化产物TCUC6I DNA以TCC模式结合A3G-CD2的复合物结构(PDB号6K3K).图中A3G-CD2为绿色, DNA为橙色, 灰色球代表锌离子

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

图 10. 不同来源的A3H与不同dsRNA复合物晶体结构[57~59]. (A)猪尾猴源A3H二聚体与底物RNA复合物结构(PDB号5W3V)A3H单体用绿色和紫色表示, dsRNA显示为橙色; (B)人源A3H二聚体与底物RNA复合物结构(PDB号6BOB)A3H显示为绿色, dsRNA显示为橙色. (C)黑猩猩A3H(cpzA3H)二聚体与双链RNA复合物晶体结构(PDB号5Z98). A3H不同单体用草绿色和浅紫色表示, dsRNA为橙色.所有图中灰色球代表锌离子

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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