Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains
Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains
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DOI：
10.1074/jbc.m808221200
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发表时间：
2009-05-08
影响因子：
4.8
通讯作者：
Anderson, Wayne F.
中科院分区：
文献类型：
--
作者：
Minasov, George;Padavattan, Sivaraman;Anderson, Wayne F.
环二gmp （c-di-GMP）是一种普遍存在的细菌第二信使，参与调节细胞表面相关性状和感染的持久性。无处不在的GGDEF和EAL结构域分别催化c-二gmp的合成和降解，它们与调控结构域以不同的组合形式出现。研究了枯草芽孢杆菌全长YkuI的晶体结构，它由一个EAL结构域和一个c端PAS-like结构域组成，并与c-di-GMP和Ca2+配合。EAL结构域呈三磷酸异构酶桶状折叠，具有一条反平行的β -链。与c-di-GMP-Ca2+的配合物确定了位于β -桶c末端的推定磷酸二酯酶的活性位点。EAL基序是活性位点的一部分，该基序的Glu-33参与阳离子配位。该配合物的结构允许提出一种磷酸二酯酶机制，其中二价阳离子和一般碱Glu-209激活催化水分子对磷进行亲核在线攻击。c端结构域与pas折叠非常相似。它的口袋状结构可以容纳一种未知的配体。YkuI通过EAL-EAL和反EAL-PAS-like结构域关联形成紧密二聚体。本文讨论了EAL-EAL界面可能的调控意义以及c-di- gmp特异性磷酸二酯酶的感觉域和催化域之间信号转导的机制。
Cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of cell surface-associated traits and the persistence of infections. Omnipresent GGDEF and EAL domains, which occur in various combinations with regulatory domains, catalyze c-di-GMP synthesis and degradation, respectively. Thecrystal structure of full-length YkuI from Bacillus subtilis, composed of an EAL domain and a C-terminal PAS-like domain, has been determined in its native form and in complex with c-di-GMP and Ca2+. The EAL domain exhibits a triose-phosphate isomerase-barrel fold with one antiparallel beta-strand. The complex with c-di-GMP-Ca2+ defines the active site of the putative phosphodiesterase located at the C-terminal end of the beta-barrel. The EAL motif is part of the active site with Glu-33 of the motif being involved in cation coordination. The structure of the complex allows the proposal of a phosphodiesterase mechanism, in which the divalent cation and the general base Glu-209 activate a catalytic water molecule for nucleophilic in-line attack on the phosphorus. The C-terminal domain closely resembles the PAS-fold. Its pocket-like structure could accommodate a yet unknown ligand. YkuI forms a tight dimer via EAL-EAL and trans EAL-PAS-like domain association. The possible regulatory significance of the EAL-EAL interface and a mechanism for signal transduction between sensory and catalytic domains of c-di-GMP-specific phosphodiesterases are discussed.