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

Research output: Contribution to journalArticlepeer-review

80 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 languageEnglish (US)
Pages (from-to)524-538
Number of pages15
JournalJournal of Molecular Biology
Volume402
Issue number3
DOIs
StatePublished - Sep 2010

Keywords

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

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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