TY - JOUR
T1 - Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases
AU - Tchigvintsev, Anatoli
AU - Xu, Xiaohui
AU - Singer, Alexander
AU - Chang, Changsoo
AU - Brown, Greg
AU - Proudfoot, Michael
AU - Cui, Hong
AU - Flick, Robert
AU - Anderson, Wayne F.
AU - Joachimiak, Andrzej
AU - Galperin, Michael Y.
AU - Savchenko, Alexei
AU - Yakunin, Alexander F.
N1 - Funding Information:
We thank all members of the Ontario Center for Structural Proteomics in Toronto for help with the conduct of experiments and for discussions. We acknowledge the support of Genome Canada (through the Ontario Genomics Institute) and the Protein Structure Initiative of the National Institutes of Health (Midwest Center for Structural Genomics, National Institutes of Health grant GM074942 to A.J.). The use of the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science. The use of Structural Biology Center beamlines was supported by the Office of Biological and Environmental Research under contract DE-AC02-06CH11357. M.Y.G. was supported by the Intramural Research Program of the National Library of Medicine , National Institutes of Health .
PY - 2010/9
Y1 - 2010/9
N2 - 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 Å) and in complex with c-di-GMP (2.35 Å), 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.
AB - 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 Å) and in complex with c-di-GMP (2.35 Å), 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.
KW - C-di-GMP
KW - EAL domain
KW - Phosphodiesterase
KW - Thiobacillus denitrificans
KW - X-ray crystallography
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U2 - 10.1016/j.jmb.2010.07.050
DO - 10.1016/j.jmb.2010.07.050
M3 - Article
C2 - 20691189
AN - SCOPUS:77956921553
SN - 0022-2836
VL - 402
SP - 524
EP - 538
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 3
ER -