Biochemical and functional characterization of an endonuclease III from Thermococcus barophilus Ch5

Endonuclease III (EndoIII) is a bifunctional DNA glycosylase that is essential to excise thymine glycol (Tg) from DNA. Although EndoIII is widespread in bacteria, eukarya and Archaea, our understanding on archaeal EndoIII function remains relatively incomplete due to the limited reports. Herein, we characterized an EndoIII from the hyperthermophilic euryar-chaeon Thermococcus barophilus Ch5 (Tba-EndoIII) biochemically, demonstrating that the enzyme can excise Tg from dsDNA and display maximum activity at 50 similar to 70 degrees C and at pH 6.0 similar to 9.0 without the requirement of a divalent metal ion. Importantly, Tba-EndoIII differs from other reported archaeal EndoIII homologues in thermostability and salt requirement. As observed in other EndoIII homologues, the conserved residues D155 and H157 in Helix-hairpin-Helix motif of Tba-EndoIII are essential for Tg excision. Intriguingly, we first dissected that the conserved residues C215 and C221 in the Fe-S cluster loop in Tba-EndoIII are involved in intermediate formation and Tg excision. Additionally, we first revealed that the conserved residue L48 is flexible for intermediate formation and AP cleavage, but plays no detectable role in Tg excision. Overall, our work has revealed additional archaeal EndoIII function and catalytic mechanism.

Automated summary

In this study, we characterized an EndoIII enzyme from a hyperthermophilic archaeon and demonstrated its ability to excise Tg from DNA. We also found that this enzyme has unique thermostability and salt requirement compared to other archaeal EndoIII homologues. Our study provides insights into the additional function and catalytic mechanism of archaeal EndoIII.