AlkA protein is the third Escherichia coli DNA repair protein excising a ring fragmentation product of thymine

Various forms of oxidative stress lead to the formation of damaged bases in cluding N-(2-deoxy-beta -D-erythro-pentofuranosyl)-N-3-(2R-hydroxyisobutyri c acid)-urea or alpha RT, the fragmentation product of thymine formed from 5R-thymidine CS-hydrate upon hydrolysis. It was shown that alpha RT is exci sed by Escherichia coli Fpg and Nth proteins. Here we report that when pres ent in DNA, alpha RT is, in addition, a substrate for the E, coli AlkA prot ein with an apparent K-m value of congruent to 170 nM. alpha RT positioned opposite T, dG, dC, and dA were efficiently excised by AlkA protein from du plex oligodeoxynucleotides in the following order: dA approximate to T much greater than dC approximate to dG. This is the first example of the excisi on of a ring opened form of a pyrimidine by AlkA protein and also the first example where the same DNA base lesion is excised by three different DNA g lycosylases of the base excision repair pathway. The present results sugges t possible structural similarity of the active site between E. coli AlkA, F pg, and Nth proteins.