Damage recognition in nucleotide excision repair

Abstract

The initial damage recognizing complex in bacterial nucleotide excision repair consists of two UvrA and two UvrB molecules. Of these proteins UvrB is the main damage recognition protein and is capable of recognizing various structurally unrelated types of damage. To do so, the protein must recognize a common alteration of the DNA structure induced by these different damages. For UvrB sterical hindrance of the present DNA modification prevents it from passing behind a _-hairpin structure present in the protein, thereby conferring damage recognition. Upon stalling of the protein at the site of damage in this way we show that two nucleotides become extrahelical: the nucleotide directly 3__ to the lesion and its base-pairing partner in the non-damaged strand. In contrast to other repair enzymes however the damaged nucleotide itself does not become extrahelical. Flipping in one of the two DNA strands has been shown to be important in preventing stable binding of the protein to undamaged DNA. Flipping in the other DNA strand however is required for efficient 3__ incision by UvrC, the nuclease of the system. A second incision at the 5__ side of the damage by the same protein facilitates removal of the damage-containing DNA oligonucleotide.