DNA binds in a large cleft composed of three domains. The “palm” domain has important conserved sequence motifs that provide the catalytic active site. The “fingers” are involved in positioning the template correctly at the active site. The “thumb” binds the DNA as it exits the enzyme, and is important in processivity.

TLS Online TPP Program

#Id: 6126

#Unit 3. Fundamental Processes

DNA glycosylases recognize and remove formamidopyrimidine and 8-hydroxyguanine (both arising from purine oxidation), hypoxanthine (arising from adenine deamination), and alkylated bases such as 3-methyladenine and 7-methylguanine.

TLS Online TPP Program

#Id: 6127

#Unit 3. Fundamental Processes

Enzymes that remove bases from DNA are called glycosylases and lyases

TLS Online TPP Program

#Id: 6128

#Unit 3. Fundamental Processes

Glycosylase action is followed by the endonuclease APE1, which cleaves the polynucleotide chain on the 5’ side. This in turn attracts a replication complex including the DNA polymerase d/E and ancillary components, which performs a short synthesis reaction extending for two to 10 nucleotides. The displaced material is removed by the endonuclease FEN1.

TLS Online TPP Program

#Id: 6129

#Unit 3. Fundamental Processes

When the initial removal involves lyase action, the endonuclease APE1 instead recruits DNA polymerase b to replace a single nucleotide. The nick is then sealed by the ligase XRCC1/ligase-3. This is called the short-patch pathway.

TLS Online TPP Program

#Id: 6130

#Unit 3. Fundamental Processes

Alkyladenine DNA glycosylase (AAG), recognizes and removes a variety of alkylated substrates, including 3-methyladenine, 7-methylguanine, and hypoxanthine. 

TLS Online TPP Program

#Id: 6131

#Unit 3. Fundamental Processes

1-methyladenine and 3MC is corrected by an enzyme that uses an oxygenating mechanism alkB by reversal mechanism