179594.fig.003
Figure 3: General mechanism of the BER pathway in T. thermophilus. UDGA, UDGB, and AlkA are monofunctional DNA glycosylases. UDGA (PDB ID: 1UI0) and UDGB (PDB ID: 2DDG) remove uracil from DNA. AlkA removes 3-methyladenine in E. coli. MutY and EndoIII are bifunctional DNA glycosylases and have both DNA glycosylase and AP lyase activities. MutY removes adenine opposite 8-oxoG, and EndoIII removes pyrimidine residues damaged by ring saturation, fragmentation, and contraction [41], by which 3 -phospho 𝛼 , 𝛽 -unsaturated aldehyde ( 3 -PUA) remains. MutM (PDB ID: 1EE8) is a trifunctional DNA glycosylase that removes 8-oxoG from oxidatively damaged DNA and 3 -phosphate remains. An AP site resulting from DNA glycosylase activity is processed by EndoIV or multifunctional DNA glycosylases. EndoIV has both AP endonuclease activity and 3 -esterase activity in E. coli [42, 43]. PolX or MutM removes 5 -dRP by dRP lyase activity. In addition, 5 - 3 exonuclease (RecJ) may have dRPase activity. The resulting gap is filled by PolI or PolX followed by sealing of the nick by LigA. The structures of AlkA, EndoIII, MutY, PolI, PolX, and LigA were obtained using SWISS-MODEL [19, 20] (PDB ID: 2H56, 2ABK, 3FSP, 1TAU, 2W9M, and 1V9P, resp.) based on amino acids sequences of T. thermophilus HB8.