Figure 2: A schematic representation of models for direct reversal of DNA damage. The structure of the ATL proteins was modeled by SWISS-MODEL (the template structure is Sulfolobus tokodaii Ogt) [19, 20]. AGT, Ada, and AlkB are not conserved in T. thermophilus. (a) Cyclobutane pyrimidine dimers are recognized by photolyase (TTHB102; PDB ID: 1IQR) and repaired by photolyase. (b) 𝑂 6 -methylguanines are recognized by AGT (PDB ID: 1EH6) in most species and by the C-terminal domain of Ada (PDB ID: 1SFE) in E. coli. Methyl phosphotriesters are recognized by the N-terminal domain of Ada (PDB ID: 1WPK) in E. coli. These enzymes directly accept a methyl group, and the alkyl adducts are removed from the DNA. (c) 𝑂 6 -alkyl adducts including 𝑂 6 -methylguanines are recognized by ATL proteins (TTHA1564; predicted model) in several species. It is predicted that NER proteins are involved in this pathway after recognition of the adducts by ATL proteins. (d) 𝑁 1 -methyladenines and 𝑁 3 -methylcytosines are recognized by AlkB (PDB ID: 2IUW). Methyl group transfer by AlkB depends on 𝛼 -ketoglutarate and Fe(II).