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Fig. 5. Common core structure shared by the DGC domain, the catalytic domain of AC, and the palm domain of DNA polymerase. (a) Stereographic view of the superposition of DGC (green) on AC (blue, PDB ID code 1cjk). Ninety-two Cα were superimposed with an rms deviation (rmsd) of 1.5 Å. The common core is shown in a thicker line. (b) Stereographic view of the superposition of DGC (green) on DNA polymerase I (light blue, PDB ID code 1nk4). Sixty-three Cα were superimposed with an rmsd of 1.7 Å. The common core here is different from the that in a in that DNA polymerase I lacks a β5 strand.

Fig. 6. Product inhibition of PleD at varying GTP concentrations as determined by thin-layer chromatography. Data refer to the initial velocity, i.e., they were acquired at time points before the reaction slowed down due to product inhibition. The values represent the averages of four independent experiments for 10, 31.6, 100, and 316 μM GTP, and two independent experiments for 3.16 μM GTP, respectively. For all substrate concentrations, roughly the same bis-(3′→5′)-cyclic di-GMP (c-diGMP) concentration of 6 μM is required to attain 50% inhibition. Taking into account the enzyme concentration of 5 μM, a K_i of ≈ 0.5 μM corresponding to the bimolecular association reaction: PleD + (c-diGMP)₂ ↔ PleD-(c-diGMP)₂ can be obtained by numerical solution. This assumes that c-diGMP is present as a dimer in solution.