Structural Insight into the Mechanism of c-di-GMP Hydrolysis by EAL Domain Phosphodiesterases

JOURNAL OF MOLECULAR BIOLOGY

卷:402

Article

Tchigvintsev, Anatoli^1,2  Xu, Xiaohui^1,2  Singer, Alexander^1,2  Chang, Changsoo³  Brown, Greg^1,2  Proudfoott, Michael^1,2  Cui, Hong^1,2  Flick, Robert^1,2  Anderson, Wayne F.^4,5  Joachimiak, Andrzej³  Galperin, Michael Y.⁶  Savchenko, Alexei^1,2  Yakunin, Alexander F.^1,2 

[1] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5G 1L6, Canada

[2] Univ Toronto, Dept Chem Engn & Appl Chem, Toronto, ON M5G 1L6, Canada

[3] Argonne Natl Lab, Midwest Ctr Struct Genom & Struct Biol Ctr, Biosci Div, Argonne, IL 60439 USA

[4] Northwestern Univ, Feinberg Sch Med, Dept Mol Pharmacol & Biol Chem, Chicago, IL 60611 USA

[5] Northwestern Univ, Feinberg Sch Med, Midwest Ctr Struct Genom, Chicago, IL 60611 USA

[6] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA

关键词: EAL domain;    c-di-GMP;    phosphodiesterase;    X-ray crystallography;    Thiobacillus denitrificans;   

DOI  :  10.1016/j.jmb.2010.07.050

来源: Elsevier

【 摘 要 】

Cyclic diguanylate (or bis-(3'-5') cyclic dimeric guanosine monophosphate; c-di-GMP) is a ubiquitous second messenger that regulates diverse cellular functions, including motility, biofilm formation, cell cycle progression, and virulence in bacteria. In the cell, degradation of c-di-GMP is catalyzed by highly specific EAL domain phosphodiesterases whose catalytic mechanism is still unclear. Here, we purified 13 EAL domain proteins from various organisms and demonstrated that their catalytic activity is associated with the presence of 10 conserved EAL domain residues. The crystal structure of the TBD1265 EAL domain was determined in free state (1.8 angstrom) and in complex with c-di-GMP (2.35 angstrom), and unveiled the role of conserved residues in substrate binding and catalysis. The structure revealed the presence of two metal ions directly coordinated by six conserved residues, two oxygens of c-di-GMP phosphate, and potential catalytic water molecule. Our results support a two-metal-ion catalytic mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. (c) 2010 Elsevier Ltd. All rights reserved.

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