Figure 2

Catalytic mechanism, topology of catalytic domain and contextual inference of Thg1 function. A. Contextual Network of Thg1 domain with the blue edges indicating architectural contexts and the dotted red edges indicate predicted gene neighborhood contexts in prokaryotes. B. Examples of conserved gene neighborhoods of the prokaryotic Thg1 genes. The arrows indicate genes in an operon in the 5'-3' direction. The gene name Thg1 gene and organism from which the representative gene neighborhood has been extracted is shown below each representation. C. Simplified catalytic schemes for the GGDEF and RNA polymerase enzymes are shown along with Thg1 to illustrate the reaction differences. The Thg1 reaction scheme also includes the predicted reaction for the polynucleotide kinase (PNK) present in conserved gene neighborhoods with Thg1. Standard names are used for all enzymes. The "...n" is a placeholder for a polynucleotide chain. D. The topology of the Thg1 catalytic domain is shown as cartoon based on structure prediction and alignment with known RRM-fold polymerase palm domain structures. The conserved residues predicted to be required for catalysis are shown. The C terminal extension is also shown in the colored box. We predict that this extension will be able fold on the rest of the protein to be in proximity with the catalytic site and substrate. E. A phylogenetic tree of the Thg1 proteins was derived using the seed alignment similar to that shown in Fig. 1 with the FastTree program. Only the major phyletic groups supported with bootstrap values greater than 85% are shown. The thickness of a given branch is approximately proportional to the number of proteins contained within it.