Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair

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Abstract
Nucleotide excision repair removes damages from the DNA by incising the damaged strand on the 3′ and 5′ sides of the lesion. In Escherichia coli, the two incisions are made by the UvrC protein, which consists of two functional halves. The N-terminal half contains the catalytic site for 3′ incision and the C-terminal half contains the residues involved in 5′ incision. The genome of E. coli contains an SOS-inducible gene (ydjQ) encoding a protein that is homologous to the N-terminal half of UvrC. In this paper we show that this protein, which we refer to as Cho (UvrC homologue), can incise the DNA at the 3′ side of a lesion during nucleotide excision repair. The incision site of Cho is located 4 nt further away from the damage compared with the 3′ incision site of UvrC. Cho and UvrC bind to different domains of UvrB, which is probably the reason of the shift in incision position. Some damaged substrates that are poorly incised by UvrC are very efficiently incised by Cho. We propose that E. coli uses Cho for repair of such damages in vivo. Initially, most of the lesions in the cell will be repaired by the action of UvrC alone. Remaining damages, that for structural reasons obstruct the 3′ incision by UvrC, will be repaired by the combined action of Cho (for 3′ incision) and UvrC (for 5′ incision).