Conformational change-induced repeat domain expansion regulates Rap phosphatase quorum-sensing signal receptors.
Conformational change-induced repeat domain expansion regulates Rap phosphatase quorum-sensing signal receptors.
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DOI：
10.1371/journal.pbio.1001512
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发表时间：
2013
期刊：
影响因子：
9.8
通讯作者：
Neiditch MB
中科院分区：
文献类型：
--
作者：
Parashar V;Jeffrey PD;Neiditch MB
结构-功能研究揭示hojavascript：popupCustomFlags（'pbiology'，%2013052，%20 'Submission'）是细菌细胞-细胞信号肽家族，其功能机制是调节其细胞质靶受体。被称为RNPP蛋白的革兰氏阳性群体感应受体的大家族由与Rap、NprR、PlcR和PrgX蛋白同源的受体组成，这些受体由输入的寡肽自诱导物调节。Rap蛋白是磷酸酶和转录抗激活剂，NprR、PlcR和PrgX蛋白是DNA结合转录因子。尽管其明显的重要性，寡肽受体调节的机制基础在很大程度上是未知的。在这里，我们报告的X-射线晶体结构的枯草芽孢杆菌群体感应受体RapJ在复杂的中央重要的寡肽自诱导能力和孢子形成因子（CSF，也称为PhrC），一个成员的Phr家族的群体感应信号。此外，我们提出了RapI的晶体结构。RapJ-PhrC、RapI、RapH-Spo 0 F和RapF-ComAC晶体结构的比较揭示了Phr活性的机理基础。更具体地，当与靶蛋白复合时，Rap蛋白由通过柔性含螺旋接头连接至N-末端3-螺旋束的C-末端三肽重复（TPR）结构域组成。在不存在靶蛋白或调节肽的情况下，Rap蛋白3-螺旋束采用不同的构象。然而，在肽结合构象中，Rap蛋白N-末端3-螺旋束和接头经历了根本的构象变化，形成TPR样折叠，并与现有的C-末端TPR结构域合并。据我们所知，这是构象变化诱导的重复结构域扩展的第一个例子。此外，在Phr结合时，整个Rap蛋白沿TPR超螺旋轴沿着压缩，产生新的分子内接触，将Rap蛋白锁定在非活性状态。考虑到TPR蛋白不经历大的构象变化是公认的教条，Rap蛋白在构象上是柔性的事实是令人惊讶的。重复蛋白被广泛用作开发设计的亲和试剂的支架，我们建议Rap蛋白可用作工程新的配体可切换亲和试剂的支架。被称为群体感应的细菌细胞-细胞通信过程调节重要的社会行为，包括抗生素产生、运动性、毒力、生物膜形成、孢子形成、生物发光和遗传能力。革兰氏阳性菌分泌寡肽群体感应信号，结合到膜结合和胞质受体。寡肽群体感应信号如何调节其靶受体的活性以前在很大程度上是未知的。在这里，我们表明，蛋白质属于家庭的细菌群体感应受体被称为说唱磷酸酶进行了显着的监管构象变化后，结合寡肽信号。更具体地说，在寡肽信号的情况下，Rap蛋白由两个不同的结构域组成：由三螺旋束组成的N-末端结构域和包含七个类似的螺旋-转角-螺旋重复序列的阵列的超螺旋C-末端结构域。柔性的含螺旋的接头区连接这些结构域。然而，在与调节寡肽的复合物中，Rap蛋白结构域和接头区重排，合并形成由9个螺旋-转角-螺旋重复组成的单一连续超螺旋结构。据我们所知，这代表了构象变化诱导的重复结构域扩展的第一个例子。本文提出的结构-功能研究为能够靶向由Rap蛋白和类似细菌受体介导的细胞-细胞信号传导的抗菌肽和肽模拟物的合理开发奠定了基础。
Structure-function studies reveal hojavascript:popupCustomFlags(‘pbiology’,%2013052,%20‘Submission’)w a family of bacterial cell-cell signaling peptides function mechanistically to regulate their cytoplasmic target receptors. The large family of Gram-positive quorum-sensing receptors known as the RNPP proteins consists of receptors homologous to the Rap, NprR, PlcR, and PrgX proteins that are regulated by imported oligopeptide autoinducers. Rap proteins are phosphatases and transcriptional anti-activators, and NprR, PlcR, and PrgX proteins are DNA binding transcription factors. Despite their obvious importance, the mechanistic basis of oligopeptide receptor regulation is largely unknown. Here, we report the X-ray crystal structure of the Bacillus subtilis quorum-sensing receptor RapJ in complex with the centrally important oligopeptide autoinducer competence and sporulation factor (CSF, also termed PhrC), a member of the Phr family of quorum-sensing signals. Furthermore, we present the crystal structure of RapI. Comparison of the RapJ-PhrC, RapI, RapH-Spo0F, and RapF-ComAC crystal structures reveals the mechanistic basis of Phr activity. More specifically, when complexed with target proteins, Rap proteins consist of a C-terminal tetratricopeptide repeat (TPR) domain connected by a flexible helix-containing linker to an N-terminal 3-helix bundle. In the absence of a target protein or regulatory peptide, the Rap protein 3-helix bundle adopts different conformations. However, in the peptide-bound conformation, the Rap protein N-terminal 3-helix bundle and linker undergo a radical conformational change, form TPR-like folds, and merge with the existing C-terminal TPR domain. To our knowledge, this is the first example of conformational change-induced repeat domain expansion. Furthermore, upon Phr binding, the entire Rap protein is compressed along the TPR superhelical axis, generating new intramolecular contacts that lock the Rap protein in an inactive state. The fact that Rap proteins are conformationally flexible is surprising considering that it is accepted dogma that TPR proteins do not undergo large conformational changes. Repeat proteins are widely used as scaffolds for the development of designed affinity reagents, and we propose that Rap proteins could be used as scaffolds for engineering novel ligand-switchable affinity reagents. The bacterial cell–cell communication process known as quorum sensing regulates important social behaviors including antibiotic production, motility, virulence, biofilm formation, sporulation, bioluminescence, and genetic competence. Gram-positive bacteria secrete oligopeptide quorum-sensing signals that bind to membrane-bound and cytosolic receptors. How oligopeptide quorum-sensing signals regulate the activity of their target receptors was previously largely unknown. Here we show that proteins belonging to the family of bacterial quorum-sensing receptors known as the Rap phosphatases undergo a remarkable regulatory conformational change upon binding oligopeptide signals. More specifically, in the absence of the oligopeptide signal, Rap proteins consist of two distinct domains: an N-terminal domain consisting of a three-helix bundle, and a superhelical C-terminal domain comprising an array of seven similar helix-turn-helix repeats. A flexible helix-containing linker region connects these domains. In complex with the regulatory oligopeptide, however, the Rap protein domains and linker region rearrange, merging to form a single continuous superhelical structure consisting of nine helix-turn-helix repeats. To our knowledge, this represents the first example of conformational change-induced repeat domain expansion. The structure-function studies presented here set the stage for the rational development of antimicrobial peptides and peptide-mimetics capable of targeting cell–cell signaling mediated by Rap proteins and similar bacterial receptors.
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影响因子：
6.8
作者：
Grove, Tijana Z.;Cortajarena, Aitziber L.;Regan, Lynne
通讯作者：
Regan, Lynne
影响因子：
64.5
作者：
BURBULYS, D;TRACH, KA;HOCH, JA
通讯作者：
HOCH, JA
DOI：
10.1099/00221287-136-5-905
发表时间：
1990-05-01
期刊：
JOURNAL OF GENERAL MICROBIOLOGY
影响因子：
--
作者：
GLEAVE, AP;MOUNTAIN, A;THOMAS, CM
通讯作者：
THOMAS, CM
DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH
影响因子：
64.8
作者：
DiMaio, Frank;Terwilliger, Thomas C.;Read, Randy J.;Wlodawer, Alexander;Oberdorfer, Gustav;Wagner, Ulrike;Valkov, Eugene;Alon, Assaf;Fass, Deborah;Axelrod, Herbert L.;Das, Debanu;Vorobiev, Sergey M.;Iwai, Hideo;Pokkuluri, P. Raj;Baker, David
通讯作者：
Baker, David