C11 半胱氨酸蛋白酶 Clostripain 的显微电子数据结构

IF 3.5 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Yasmeen N. Ruma , Guanhong Bu , Johan Hattne , Tamir Gonen
{"title":"C11 半胱氨酸蛋白酶 Clostripain 的显微电子数据结构","authors":"Yasmeen N. Ruma ,&nbsp;Guanhong Bu ,&nbsp;Johan Hattne ,&nbsp;Tamir Gonen","doi":"10.1016/j.yjsbx.2024.100107","DOIUrl":null,"url":null,"abstract":"<div><p>Clostripain secreted from <em>Clostridium histolyticum</em> is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine-specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of <em>C. histolyticum</em> clostripain determined at 2.5 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of clostripain shows a typical Clan CD α/β/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 and 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"10 ","pages":"Article 100107"},"PeriodicalIF":3.5000,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2590152424000126/pdfft?md5=42cb6b31866b2698d485367c031389f5&pid=1-s2.0-S2590152424000126-main.pdf","citationCount":"0","resultStr":"{\"title\":\"MicroED structure of the C11 cysteine protease clostripain\",\"authors\":\"Yasmeen N. Ruma ,&nbsp;Guanhong Bu ,&nbsp;Johan Hattne ,&nbsp;Tamir Gonen\",\"doi\":\"10.1016/j.yjsbx.2024.100107\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Clostripain secreted from <em>Clostridium histolyticum</em> is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine-specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of <em>C. histolyticum</em> clostripain determined at 2.5 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of clostripain shows a typical Clan CD α/β/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 and 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.</p></div>\",\"PeriodicalId\":17238,\"journal\":{\"name\":\"Journal of Structural Biology: X\",\"volume\":\"10 \",\"pages\":\"Article 100107\"},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-07-06\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2590152424000126/pdfft?md5=42cb6b31866b2698d485367c031389f5&pid=1-s2.0-S2590152424000126-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Structural Biology: X\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2590152424000126\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Structural Biology: X","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2590152424000126","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

组织溶解梭菌分泌的梭菌毒素是 CD 族半胱氨酸肽酶 C11 家族的创始成员,而 CD 族半胱氨酸肽酶是众多细菌分泌的一类重要肽酶。梭菌毒素是一种精氨酸特异性内肽酶。由于它具有半胱氨酸肽酶的功效,因此被广泛应用于实验室环境中。尽管梭菌毒素非常重要,但其结构仍未得到解决。在这里,我们描述了利用微晶体电子衍射(MicroED)技术以 2.5 Å 分辨率测定的溶组织胞杆菌梭菌毒素活性形式的首个结构。该结构是通过聚焦离子束研磨后的单个纳米晶体确定的。Clostripain 的结构显示出典型的 Clan CD α/β/α 夹层结构,活性位点中存在 Cys231/His176 催化二元。它有一个大的电负性底物结合袋,显示出它有能力容纳大量不同的底物。残基 452 和 457 之间形成的重链环可能对底物的结合非常重要。总之,这一结果表明了 MicroED 在确定氯特里肽等大分子未知结构方面的重要性,它可进一步用作研究底物结合和设计这类肽酶潜在抑制剂的平台。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

MicroED structure of the C11 cysteine protease clostripain

MicroED structure of the C11 cysteine protease clostripain

Clostripain secreted from Clostridium histolyticum is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine-specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of C. histolyticum clostripain determined at 2.5 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of clostripain shows a typical Clan CD α/β/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 and 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Journal of Structural Biology: X
Journal of Structural Biology: X Biochemistry, Genetics and Molecular Biology-Structural Biology
CiteScore
6.50
自引率
0.00%
发文量
20
审稿时长
62 days
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信