179594.fig.004
Figure 4: A schematic representation of models for the nucleotide excision repair pathway controlled by Uvr proteins. All of the predicted protein structures were modeled using SWISS-MODEL. The template structures used in the model building were Geobacillus stearothermophilus UvrA, the N- and C-terminal domain of Thermotoga maritime UvrC, G. stearothermophilus UvrD, Thermus aquaticus DNA polymerase I, Thermus filiformis DNA ligase, and E. coli TRCF. UvrA (TTHA1440; predicted model) and UvrB (TTHA1892; PDB ID: 1D2M) recognize the DNA lesion. In transcribing strand, TRCF (TTHA0889; predicted model) is also involved in recognition of the lesion. UvrC (TTHA1568; predicted model) incises both sides of the lesion. The DNA fragment containing the lesion is excised by UvrD (TTHA1427; predicted model), SSB (TTHA0244; 2CWA), and exonuclease RecJ (TTHA1167; PDB ID: 2ZXO). A new strand is resynthesized by DNA polymerase I (TTHA1054; predicted model) and ligated by DNA ligase (TTHA1097; predicted model).