Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases

Anatoli Tchigvintsev; Xiaohui Xu; Alexander Singer; Changsoo Chang; Greg Brown; Michael Proudfoot; Hong Cui; Robert Flick; Wayne F. Anderson; Andrzej Joachimiak; Michael Y. Galperin; Alexei Savchenko; Alexander F. Yakunin

doi:10.1016/j.jmb.2010.07.050

Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases

Anatoli Tchigvintsev, Xiaohui Xu, Alexander Singer, Changsoo Chang, Greg Brown, Michael Proudfoot, Hong Cui, Robert Flick, Wayne F. Anderson, Andrzej Joachimiak, Michael Y. Galperin, Alexei Savchenko, Alexander F. Yakunin^*

^*Corresponding author for this work

Biochemistry and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

105 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	524-538
Number of pages	15
Journal	Journal of Molecular Biology
Volume	402
Issue number	3
DOIs	https://doi.org/10.1016/j.jmb.2010.07.050
State	Published - Sep 2010

Funding

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 .

Keywords

C-di-GMP
EAL domain
Phosphodiesterase
Thiobacillus denitrificans
X-ray crystallography

ASJC Scopus subject areas

Structural Biology
Molecular Biology

Access to Document

10.1016/j.jmb.2010.07.050

Cite this

@article{3c94a69516774fbeb5e545ea7303fe3c,

title = "Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases",

abstract = "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 {\AA}) and in complex with c-di-GMP (2.35 {\AA}), 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.",

keywords = "C-di-GMP, EAL domain, Phosphodiesterase, Thiobacillus denitrificans, X-ray crystallography",

author = "Anatoli Tchigvintsev and Xiaohui Xu and Alexander Singer and Changsoo Chang and Greg Brown and Michael Proudfoot and Hong Cui and Robert Flick and Anderson, {Wayne F.} and Andrzej Joachimiak and Galperin, {Michael Y.} and Alexei Savchenko and Yakunin, {Alexander F.}",

note = "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 . ",

year = "2010",

month = sep,

doi = "10.1016/j.jmb.2010.07.050",

language = "English (US)",

volume = "402",

pages = "524--538",

journal = "Journal of Molecular Biology",

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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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DO - 10.1016/j.jmb.2010.07.050

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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 -

Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases

Abstract

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

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Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans

Cite this

Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases

Abstract

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Datasets

Crystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans

Cite this