4LYK: Crystal Structure Of The Eal Domain Of C-di-gmp Specific Phosphodiesterase Yaha In Complex With Activating Cofactor Mg++

Citation:
Abstract
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.
PDB ID: 4LYKDownload
MMDB ID: 117061
PDB Deposition Date: 2013/7/31
Updated in MMDB: 2014/05
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
Similar Structures:
Biological Unit for 4LYK: dimeric; determined by author and by software (PISA)
Molecular Components in 4LYK
Label Count Molecule
Proteins (2 molecules)
2
Cyclic Di-gmp Phosphodiesterase Yaha(Gene symbol: yahA)
Molecule annotation
Chemicals (7 molecules)
1
2
2
2
3
3
* Click molecule labels to explore molecular sequence information.

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