Crystal structures reveal the distinct features of the 2'-dG-III riboswitch in the purine riboswitch family.

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-07-19 DOI:10.1093/nar/gkaf702

Ke Chen,Wenjian Liao,Jiali Wang,Yangyi Ren,Zhizhong Lu,Xuemei Peng,Jia Wang,Lin Huang

{"title":"Crystal structures reveal the distinct features of the 2'-dG-III riboswitch in the purine riboswitch family.","authors":"Ke Chen,Wenjian Liao,Jiali Wang,Yangyi Ren,Zhizhong Lu,Xuemei Peng,Jia Wang,Lin Huang","doi":"10.1093/nar/gkaf702","DOIUrl":null,"url":null,"abstract":"Purine riboswitches, located in the 5'-untranslated regions of bacterial messenger RNA, regulate gene expression by sensing purines and their derivatives. A class of the guanine-I riboswitch variants was recently reported to be the third class of 2'-deoxyguanosine (2'-dG) riboswitch termed 2'-dG-III riboswitch. Here we present the crystal structures of the 2'-dG-III riboswitch bound with 2'-dG, guanosine, or guanine. Despite similarities in secondary and overall structures to other purine riboswitches, the 2'-dG-III riboswitch exhibits unique features in its loop-loop interaction, three-way junction, and ligand binding. The 2'-dG-III riboswitch exhibits a tuning fork-like structure with a unique six-tiered interaction within the three-way junction. The second, third, and fourth tiers form the ligand-binding pocket, with a consistent binding mode for the guanine moiety of all three ligands. Structural and biochemical analyses reveal detailed interactions between the 2'-dG-III riboswitch and different ligands, providing insights into its regulatory mechanisms in purine metabolism.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"12 1","pages":""},"PeriodicalIF":16.6000,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nucleic Acids Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/nar/gkaf702","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Purine riboswitches, located in the 5'-untranslated regions of bacterial messenger RNA, regulate gene expression by sensing purines and their derivatives. A class of the guanine-I riboswitch variants was recently reported to be the third class of 2'-deoxyguanosine (2'-dG) riboswitch termed 2'-dG-III riboswitch. Here we present the crystal structures of the 2'-dG-III riboswitch bound with 2'-dG, guanosine, or guanine. Despite similarities in secondary and overall structures to other purine riboswitches, the 2'-dG-III riboswitch exhibits unique features in its loop-loop interaction, three-way junction, and ligand binding. The 2'-dG-III riboswitch exhibits a tuning fork-like structure with a unique six-tiered interaction within the three-way junction. The second, third, and fourth tiers form the ligand-binding pocket, with a consistent binding mode for the guanine moiety of all three ligands. Structural and biochemical analyses reveal detailed interactions between the 2'-dG-III riboswitch and different ligands, providing insights into its regulatory mechanisms in purine metabolism.

查看原文本刊更多论文

晶体结构揭示了2'-dG-III核糖开关在嘌呤核糖开关家族中的独特特征。

嘌呤核糖开关位于细菌信使RNA的5'-非翻译区，通过感知嘌呤及其衍生物来调节基因表达。一类鸟嘌呤- 1核糖开关变体最近被报道为第三类2'-脱氧鸟嘌呤（2'-dG）核糖开关，称为2'-dG- iii核糖开关。在这里，我们展示了与2'-dG，鸟苷或鸟嘌呤结合的2'-dG- iii核糖开关的晶体结构。尽管二级和整体结构与其他嘌呤核开关相似，但2'-dG-III核开关在环-环相互作用、三向连接和配体结合方面表现出独特的特征。2'-dG-III核糖开关显示出一个音叉状结构，在三向结内具有独特的六层相互作用。第二层、第三层和第四层形成配体结合袋，对所有三种配体的鸟嘌呤部分具有一致的结合模式。结构和生化分析揭示了2'-dG-III核开关与不同配体之间的详细相互作用，为其在嘌呤代谢中的调节机制提供了见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.