Prof. Dr. Tilman Schirmer

University of Basel
Klingelbergstrasse 50 / 70
CH - 4056 Basel
Biozentrum, Room 311 Phone: +41 61 267 20 89
Curriculum Vitae

Administrative Assistant

Marlise Frick
Biozentrum, Room 308
Phone: +41 61 267 20 81
Fax: +41 61 267 21 09

Research group Tilman Schirmer

Molecular mechanisms of c-di-GMP signal transduction and AMP transferases

Fig. 1: Dinucleotide c-di-GMP bound to phosphodiesterase YkuI from B. subtilis. The scissile bond is indicated by the arrow, the catalytic magnesium ion (magenta) is found at the bottom of the binding site.

We are employing crystallographic and biochemical/ biophysical techniques to reveal the structural basis for the catalysis and regulation of c-di-GMP related proteins. Our second focus is on bacterial type IV secretion system (T4SS) effector proteins with AMP transferase activity.

Diguanylate cyclases and regulation of c-di-GMP synthesis

Recent discoveries show that a novel second messenger, c-di-GMP, is extensively used by bacteria to control multicellular behavior, such as biofilm formation. Condensation of two GTP to the dinucleotide is catalyzed by GGDEF domains that usually occur in combination with sensory and/or regulatory modules. The opposing phosphodiesterase activity is provided by EAL domains that are also regulated.

In collaboration with the Jenal group (Biozentrum) and based on crystallographic studies we have elucidated the catalytic and regulatory mechanisms of PleD, an essential part of the signaling pathway regulating the developmental cycle of Caulobacter crescentus. More recently, we have determined the structure of the putative c-di-GMP specific phosphodiesterase YkuI in complex with c-di-GMP, which allowed us to propose the catalytic mechanism of EAL domains. Moreover, the structure provided clues about how this class of enzymes may be regulated in a modular and universal fashion by sensory domains.

Fig. 2: An AMP transferase with Fic fold. Also shown, the ATP/Mg++ in the putative active site. Adopted rom Palanivelu et al. (2011).

Effector proteins of the type IV secretion system

Type IV secretion systems (T4SS) are utilized by many bacterial pathogens for the delivery of virulence proteins or protein-DNA complexes into their eukaryotic target cells. Together with the Dehio group (Biozentrum) we are working on a class of effector proteins that are composed of a Fic and a BID domain responsible for pathogenic action in the host cell and translocation, respectively.

Only recently, it has become apparent that the Fic domain catalyzes AMP transfer onto host target protein(s) to subvert cellular function. From a Fic crystal structure (truncated BepA from Bartonella henselae) we were able to deduce the mechanisms of catalysis and target positioning. Currently, we are investigating Fic inhibition that - depending on the protein - is caused by an α-helix that interferes with productive binding of the ATP substrate or, inter-molecularly, by complex formation with an anti-toxin. Interestingly, both inhibition mechanisms are structurally related. This knowledge may be utilized for drug development to target Fic proteins of bacterial pathogens.

Fig. 3: KdgM porin folded to a small 12-stranded hollow β-barrel.


Porins are integral membrane proteins from the outer membrane of Gram-negative bacteria. They allow the uptake of nutrients by passive diffusion through an intrinsic pore that extends along the axis of the transmembrane β-barrel structure. After extensive work on the general trimeric porins OmpF and OmpC from E. coli, we have recently determined the high-resolution 12-stranded β-barrel structures of NanC from E. coli and KdgM from Dickeya dadantii, representatives of a porin family that is specific for the translocation of negatively charged poly-saccharides. We are now studying the molecular details of translocation of oligogalacturonate, the degradation product of pectin, through KdgM.