细菌转录抑制因子 NrdR--灵活的多因素核苷酸传感器

Inna Rozman Grinberg, Ornella Bimai, Saher Shahid, Lena Philipp, Markel Martinez-Carranza, Ipsita Banerjee, Daniel Lundin, Pal Stenmark, Britt-Marie Sjoberg, Derek T. Logan
{"title":"细菌转录抑制因子 NrdR--灵活的多因素核苷酸传感器","authors":"Inna Rozman Grinberg, Ornella Bimai, Saher Shahid, Lena Philipp, Markel Martinez-Carranza, Ipsita Banerjee, Daniel Lundin, Pal Stenmark, Britt-Marie Sjoberg, Derek T. Logan","doi":"10.1101/2024.09.04.609659","DOIUrl":null,"url":null,"abstract":"NrdR is a bacterial transcriptional repressor consisting of a Zn-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two \"NrdR boxes\" upstream of ribonucleotide reductase operons, of which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, where we identified a new box. We show that E. coli NrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus dATP or equivalent diphosphate combinations. No other combination of nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high resolution crystal structures of an NrdR. We have also determined cryo-EM structures of DNA-bound EcoNrdRATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATPcones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that when loaded with the correct nucleotides adapt to an optimal promoter binding conformation.","PeriodicalId":501048,"journal":{"name":"bioRxiv - Biophysics","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Bacterial transcriptional repressor NrdR - a flexible multifactorial nucleotide sensor\",\"authors\":\"Inna Rozman Grinberg, Ornella Bimai, Saher Shahid, Lena Philipp, Markel Martinez-Carranza, Ipsita Banerjee, Daniel Lundin, Pal Stenmark, Britt-Marie Sjoberg, Derek T. Logan\",\"doi\":\"10.1101/2024.09.04.609659\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"NrdR is a bacterial transcriptional repressor consisting of a Zn-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two \\\"NrdR boxes\\\" upstream of ribonucleotide reductase operons, of which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, where we identified a new box. We show that E. coli NrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus dATP or equivalent diphosphate combinations. No other combination of nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high resolution crystal structures of an NrdR. We have also determined cryo-EM structures of DNA-bound EcoNrdRATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATPcones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that when loaded with the correct nucleotides adapt to an optimal promoter binding conformation.\",\"PeriodicalId\":501048,\"journal\":{\"name\":\"bioRxiv - Biophysics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-09-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"bioRxiv - Biophysics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1101/2024.09.04.609659\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"bioRxiv - Biophysics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2024.09.04.609659","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

摘要

NrdR 是一种细菌转录抑制因子,由一个 Zn-ribbon 结构域和一个 ATP-cone 结构域组成。了解其作用机制有助于设计新型抗菌药物。NrdR 与核糖核苷酸还原酶操作子上游的两个 "NrdR 框 "特异性结合,大肠杆菌有三个 "NrdR 框":nrdHIEF、nrdDG 和 nrdAB。我们的研究表明,大肠杆菌 NrdR(EcoNrdR)与 ATP 加 dATP 或等效二磷酸组合时,与所有三个位点的结合强度相似。没有其他核苷酸组合能促进与 DNA 的结合。我们展示了 EcoNrdR-ATP-dATP 和 EcoNrdR-ADP-dATP 的晶体结构,这是 NrdR 的首个高分辨率晶体结构。我们还测定了与 DNA 结合的 EcoNrdRATP-dATP 和新型 EcoNrdR-ATP 细丝的冷冻电镜结构。四聚体形式的 EcoNrdR 涉及成对的 Zn-ribbon 结构域和 ATP-cones 之间的交替相互作用。这些结构揭示了 ATP-cones 与 Zn-ribbon domains 的相对取向具有相当大的灵活性。与 DNA 结合的 EcoNrdR-ATP-dATP 的结构表明,在与 DNA 结合的同时,ATP-锥体和 Zn-ribbon 之间发生了显著的构象重排,而 ATP 锥体则保持相同的相对方向。与此相反,ATP 负载的 EcoNrdR 细丝显示出 ATP-锥对的重排,并封存了 NrdR 的 DNA 结合残基,使其无法与 DNA 结合。我们的研究结果与之前的结构和生化研究相结合,表明 EcoNrdR 结构具有高度灵活性,当负载正确的核苷酸时,可适应最佳的启动子结合构象。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Bacterial transcriptional repressor NrdR - a flexible multifactorial nucleotide sensor
NrdR is a bacterial transcriptional repressor consisting of a Zn-ribbon domain followed by an ATP-cone domain. Understanding its mechanism of action could aid the design of novel antibacterials. NrdR binds specifically to two "NrdR boxes" upstream of ribonucleotide reductase operons, of which Escherichia coli has three: nrdHIEF, nrdDG and nrdAB, where we identified a new box. We show that E. coli NrdR (EcoNrdR) has similar binding strength to all three sites when loaded with ATP plus dATP or equivalent diphosphate combinations. No other combination of nucleotides promotes binding to DNA. We present crystal structures of EcoNrdR-ATP-dATP and EcoNrdR-ADP-dATP, which are the first high resolution crystal structures of an NrdR. We have also determined cryo-EM structures of DNA-bound EcoNrdRATP-dATP and novel filaments of EcoNrdR-ATP. Tetrameric forms of EcoNrdR involve alternating interactions between pairs of Zn-ribbon domains and ATP-cones. The structures reveal considerable flexibility in relative orientation of ATP-cones vs Zn-ribbon domains. The structure of DNA-bound EcoNrdR-ATP-dATP shows that significant conformational rearrangements between ATP-cones and Zn-ribbons accompany DNA binding while the ATPcones retain the same relative orientation. In contrast, ATP-loaded EcoNrdR filaments show rearrangements of the ATP-cone pairs and sequester the DNA-binding residues of NrdR such that they are unable to bind to DNA. Our results, in combination with a previous structural and biochemical study, point to highly flexible EcoNrdR structures that when loaded with the correct nucleotides adapt to an optimal promoter binding conformation.
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
自引率
0.00%
发文量
0
×
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