College of Veterinary Medicine, China Agricultural Universitygrid.22935.3f, Beijing, China.
Joint National Laboratory for Antibody Drug Engineering, Henan University, Kaifeng, China.
J Virol. 2022 Jul 13;96(13):e0073622. doi: 10.1128/jvi.00736-22. Epub 2022 Jun 21.
Senecavirus A (SVA) is an emerging picornavirus infecting porcine of all age groups and causing foot and mouth disease (FMD)-like symptoms. One of its key enzymes is the 3C protease (3C), which is similar to other picornaviruses and essential for virus maturation by controlling polyprotein cleavage and RNA replication. In this study, we reported the crystal structure of SVA 3C at a resolution of 1.9 Å and a thorough structural comparison against all published picornavirus 3C structures. Using statistical and graphical visualization techniques, we also investigated the sequence specificity of the 3C. The structure revealed that SVA 3C adopted a typical chymotrypsin-like fold with the S1 subsite as the most conservative site among picornavirus 3C. The surface loop, A1-B1 hairpin, adopted a novel conformation in SVA 3C and formed a positively charged protrusion around S' subsites. Correspondingly, SVA scissile bonds preferred Asp rather than neutral amino acids at P3' and P4'. Moreover, SVA 3C showed a wide range tolerance to P4 residue volume (acceptable range: 67 Å to 141 Å), such as aromatic side chain, in contrast to other picornaviruses. In summary, our results provided valuable information for understanding the cleavage pattern of 3C. Picornaviridae is a group of RNA viruses that harm both humans and livestock. 3C is an essential enzyme for picornavirus maturation, which makes it a promising target for antiviral drug development and a critical component for virus-like particle (VLP) production. However, the current challenge in the development of antiviral drugs and VLP vaccines includes the limited knowledge of how subsite structure determines the 3C cleavage pattern. Thus, an extensive comparative study of various picornaviral 3C was required. Here, we showed the 1.9 Å crystal structure of SVA 3C. The structure revealed similarities and differences in the substrate-binding groove among picornaviruses, providing new insights into the development of inhibitors and VLP.
肠道病毒 A（SVA）是一种新兴的微小 RNA 病毒，感染所有年龄段的猪并引起口蹄疫（FMD）样症状。其关键酶之一是 3C 蛋白酶（3C），它与其他微小 RNA 病毒相似，通过控制多蛋白切割和 RNA 复制，对病毒成熟至关重要。在这项研究中，我们报道了 SVA 3C 的晶体结构，分辨率为 1.9 Å，并与所有已发表的微小 RNA 病毒 3C 结构进行了彻底的结构比较。我们还使用统计和图形可视化技术研究了 3C 的序列特异性。结构表明，SVA 3C 采用了典型的胰凝乳蛋白酶样折叠，其中 S1 亚基是微小 RNA 病毒 3C 中最保守的位点。表面环 A1-B1 发夹在 SVA 3C 中采用了一种新的构象，并在 S'亚基周围形成了一个带正电荷的突起。相应地，SVA 切割键在 P3'和 P4'更喜欢 Asp 而不是中性氨基酸。此外，与其他微小 RNA 病毒相比，SVA 3C 对 P4 残基体积（可接受范围：67 Å 至 141 Å）表现出广泛的容忍度，例如芳香族侧链。总之，我们的结果为理解 3C 的切割模式提供了有价值的信息。微小 RNA 病毒科是一组危害人类和牲畜的 RNA 病毒。3C 是微小 RNA 病毒成熟的必需酶，使其成为抗病毒药物开发的有前途的靶点，也是病毒样颗粒（VLP）生产的关键组成部分。然而，目前在抗病毒药物和 VLP 疫苗开发方面面临的挑战包括对亚基结构如何决定 3C 切割模式的了解有限。因此，需要对各种微小 RNA 病毒 3C 进行广泛的比较研究。在这里，我们展示了 SVA 3C 的 1.9 Å 晶体结构。该结构揭示了微小 RNA 病毒之间底物结合槽的相似性和差异性，为抑制剂和 VLP 的开发提供了新的见解。
