Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding

Xiang Fang; Guoliang Lu; Yanchun Deng; Sa Yang; Chunsheng Hou; Peng Gong

doi:10.1016/j.virs.2023.05.002

August 2023

. doi: 10.1016/j.virs.2023.05.002

Citation: Xiang Fang, Guoliang Lu, Yanchun Deng, Sa Yang, Chunsheng Hou, Peng Gong. Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding .VIROLOGICA SINICA, 2023, 38(4) : 531-540. http://dx.doi.org/10.1016/j.virs.2023.05.002

在一种双顺反子病毒依赖RNA的RNA聚合酶的晶体结构中观察到的亚结构非常规构象提示该蛋白N端延伸区对蛋白整体正确折叠的贡献

方翔 ^a,c ,
逯国亮 ^a ,
邓炎春 ^b ,
杨卅 ^d ,
侯春生 ^b,, ,
龚鹏 ^a,c,e,,

中国科学院武汉病毒研究所;中国农业科学院蜜蜂研究所;中国农业科学院麻类作物研究所;中国科学院大学

通讯作者： 侯春生, houchunsheng@caas.cn; 龚鹏, gongpeng@wh.iov.cn
收稿日期： 2023-04-03
录用日期： 2023-05-04

摘要

双顺反子病毒科包含多种昆虫病原。这类病毒包含一条正链RNA基因组，由病毒编码的依赖RNA的RNA聚合酶（RdRP）3D^pol进行基因组复制。与小RNA病毒科如脊髓灰质炎病毒（PV）的3D^pol相比，双顺反子病毒科中的代表以色列急性麻痹病毒（IAPV）3D^pol的有一段长约40个氨基酸残基的氨基端延伸区（NE）。截至目前，双顺反子病毒科RdRP的结构特征与催化机制仍不明晰。本文报道了分别命名为Δ85和Δ40的两种截短体形式IAPV 3D^pol的晶体结构，这两种截短体都缺失NE区域， 3D^pol在这两个结构中呈现出三种构象状态。IAPV 3D^pol的手掌区和拇指区结构在很大程度上与PV 3D^pol一致。然而，在所有的IAPV结构中，RdRP手指区均呈现部分无序状态，多个RdRP亚结构的构象及亚结构间的相互作用存在差异。尤其在Δ40结构的一种构象状态中，基序B-中指区域发生了较大幅度的构象变化，而此前曾报道的基序A的一种非常规构象在所有的IAPV结构中都能观察到。以上这些实验数据一方面展现了RdRP多个亚结构固有的构象多样性，另一方面也提示NE区域对IAPV RdRP的正确折叠可能存在贡献。
- 以色列急性麻痹病毒
- , 脊髓灰质炎病毒
- , 依赖RNA的RNA聚合酶
- , 晶体结构
- , 催化基序

Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding

Xiang Fang ^a,c ,
Guoliang Lu ^a ,
Yanchun Deng ^b ,
Sa Yang ^d ,
Chunsheng Hou ^b,, ,
Peng Gong ^a,c,e,,

a. Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China;
b. Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China;
c. University of Chinese Academy of Sciences, Beijing, 100049, China;
d. Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China;
e. Hubei Jiangxia Laboratory, Wuhan, 430207, China

Corresponding author: Chunsheng Hou, houchunsheng@caas.cn Peng Gong, gongpeng@wh.iov.cn
Received Date: 03 April 2023
Accepted Date: 04 May 2023

Abstract

The Dicistroviridae is a virus family that includes many insect pathogens. These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase (RdRP) also named 3D^pol. Compared with the Picornaviridae RdRPs such as poliovirus (PV) 3D^pol, the Dicistroviridae representative Israeli acute paralysis virus (IAPV) 3D^pol has an additional N-terminal extension (NE) region that is about 40-residue in length. To date, both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive. Here we reported crystal structures of two truncated forms of IAPV 3D^pol, namely Δ85 and Δ40, both missing the NE region, and the 3D^pol protein in these structures exhibited three conformational states. The palm and thumb domains of these IAPV 3D^pol structures are largely consistent with those of the PV 3D^pol structures. However, in all structures, the RdRP fingers domain is partially disordered, while different conformations of RdRP substructures and interactions between them are also present. In particular, a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of the Δ40 structure, while a previously documented alternative conformation of motif A was observed in all IAPV structures. These experimental data on one hand show intrinsic conformational variances of RdRP substructures, and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.
- Israeli acute paralysis virus (IAPV)
- , Poliovirus
- , RNA-dependent RNA polymerase (RdRP)
- , Crystal structure
- , Catalytic motif

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