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Breaking down the second messenger c-di-GMP

In collaboration with the MCSG structure genomics center in Argonne, USA, researchers at the Biozentrum, University of Basel, have revealed the structure and mechanism of one of the key enzymes determining the level of the second messenger c-di-GMP in bacterial cells. This sets the basis for the rational design of novel antibiotics. The study is published in the current issue of Journal of Biological Chemistry.

Second messengers are small diffusible signaling molecules that, as part of signaling cascades, can activate specific receptors to elicit a cellular response. Only recently it has been recognized that the dinucleotide cyclic di-GMP plays a central role in the transition between a motile and sessile life-style in bacteria. Related to this, the second messenger c-di-GMP is involved in the regulation of acute and chronic virulence properties in pathogenic bacteria, such as biofilm formation. Since c-di-GMP signaling occurs only in bacteria, the enzymes and receptors involved in this signal pathway are attractive targets for the development of novel antibiotics.

The cellular concentration of c-di-GMP is determined by the action of two antagonistic enzyme activities. Diguanylate cyclases condense two GTP molecules into c-di-GMP, whereas specific phosphodiesterases break up the cyclic dinucleotide into its linear form. Both enzymes typically carry additional domains that, directly or indirectly, sense input signals and, in response, control the activity of the catalytic domains.

In an earlier collaboration at the Biozentrum, the groups of Tilman Schirmer and Urs Jenal determined the structure of a diguanylate cyclase (PleD from Caulobacter crescentus) and unraveled its catalytic and regulatory mechanisms. Now, in collaboration with Wayne F. Anderson from the Midwest Center of Structural Genomics in Argonne (USA), the structure of a c-di-GMP specific phosphodiesterase (YkuI from Bacillus subtilis) in complex with its substrate c-di-GMP has been unraveled, The structure, that they found, suggests a metal dependent catalytic mechanism and sets the basis for rational design of specific inhibitors.

The phosphodiesterase is organized as a tight dimer with crosswise contacts between its catalytic and sensing domain. How the binding of a (yet unknown) ligand to the sensor domain controls catalytic activity is the subject of on-going investigations. According to the scientists, the structure, in combination with functional data, suggests a mutual rearrangement of the two catalytic domains upon signal input, a mechanism that may be operational in a large variety of c-di-GMP specific phosphodiesterases.

Original article:
George Minasov, Sivaraman Padavattan, Ludmilla Shuvalova, Joseph S. Brunzelle, Darcie J. Miller, Arnaud Baslé, Claudia Massa, Frank R. Collart, Tilman Schirmer, and Wayne F. Anderson. Crystal structures of YkuI and its complex with second messenger c-di-GMP suggests catalytic mechanism of phosphodiester bond cleavage by EAL domains. J. Biol. Chem., Vol. 284, Issue 19, 13174-13184, May 8, 2009.

Additional information:
Chan, C., R. Paul, D. Samoray, N. C. Amiot, B. Giese, U. Jenal, and T. Schirmer. 2004. Structural basis of activity and allosteric control of diguanylate cyclase. Proc. Natl. Acad. Sci. U.S.A., 101:17084-9.

Wassmann, P., C. Chan, R. Paul, A. Beck, H. Heerklotz, U. Jenal, and T. Schirmer. 2007. Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure, 15:915-27.

Contact: Communications