Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger cyclic di-GMP.
The universal second messenger cyclic di-GMP (cdG) is involved in the regulation of a diverse range of cellular processes in bacteria. The intracellular concentration of the dinucleotide is determined by the opposing actions of diguanylate cyclases and cdG-specific phosphodiesterases (PDEs). Whereas most PDEs have accessory domains that are involved in the regulation of their activity, the regulatory mechanism of this class of enzymes has remained unclear. Here, we use biophysical and functional analyses to show that the isolated EAL domain of a PDE from Escherichia coli (YahA) is in a fast thermodynamic monomer-dimer equilibrium, and that the domain is active only in its dimeric state. Furthermore, our data indicate thermodynamic coupling between substrate binding and EAL dimerization with the dimerization affinity being increased about 100-fold upon substrate binding. Crystal structures of the YahA-EAL domain determined under various conditions (apo, Mg(2+), cdG·Ca(2+) complex) confirm structural coupling between the dimer interface and the catalytic center. The built-in regulatory properties of the EAL domain probably facilitate its modular, functional combination with the diverse repertoire of accessory domains.
Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland.
Amit
A
Sundriyal
Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland.
Claudia
C
Massa
Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland.
Dietrich
D
Samoray
Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland.
Fabian
F
Zehender
Biophysics Facility, University of Basel, CH-4056 Basel, Switzerland.
Timothy
T
Sharpe
Focal Area of Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.
Urs
U
Jenal
Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland. Electronic address: tilman.schirmer@unibas.ch.
Tilman
T
Schirmer
D015106:3',5'-Cyclic-GMP Phosphodiesterases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006868:Hydrolysis; D008969:Molecular Sequence Data; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D015290:Second Messenger Systems
D029968:Escherichia coli Proteins; C062025:bis(3',5')-cyclic diguanylic acid; D015106:3',5'-Cyclic-GMP Phosphodiesterases; C000589035:YahA protein, E coli; D006152:Cyclic GMP
Allosteric Regulation; Bacterial Signal Transduction; Chromatography; Crystal Structure; Phosphodiesterases; Second Messenger; c-di-GMP Signaling