DNA damage can occur spontaneously or be caused by mutagenic chemicals and physical factors such as radiation and sunlight. These modifications must be corrected to avoid detrimental effects to the cell. One of the primary pathways of DNA repair is NER, in which a stretch of bases harboring the lesion is removed, and the gap is filled by a DNA polymerase. The unique feature of NER is its ability to detect and correct a wide spectrum of DNA modifications of different sizes and chemical structures. NER can target single base modifications, bulky adducts, backbone modifications and inter- or intrastrand cross-links1
. NER was first described in bacteria2
, and its key genes were identified and named uvrA, uvrB
. These proteins are used only by bacteria and some archaea, but the principles of NER are the same in all three kingdoms of life. In eukaryotes, a larger number of proteins are used, and only a few have similarities with the bacterial system4
. In humans, mutations in NER genes lead to several diseases, such as xeroderma pigmentosum with extreme susceptibility to ultraviolet radiation and an increased risk of skin cancer5
, Cockayne syndrome with impaired development, premature aging and sunlight sensitivity and trichothiodystrophy with impaired development and mental retardation6
The first step in NER is damage detection, which is carried out by the UvrA or UvrA–UvrB complex in bacteria1
. The first contacts with the DNA occur through the UvrA protein. When the damage is located, the DNA is handed over to the UvrB protein for damage verification. UvrC nuclease is then recruited and cleaves the DNA at the fourth or fifth phosphate 3′ to the lesion and at the eighth phosphate 5′ to the lesion7
. UvrD helicase removes the excised oligonucleotide, and polymerase I fills the gap. The repair is completed by DNA ligase I, which seals the nick.
The UvrA, UvrB and UvrC proteins have been extensively characterized biochemically. The crystal structures of UvrB show that the protein adopts a helicase fold similar to that of PcrA8-10
. The characteristic feature of the structure is a β-hairpin inserted between the two DNA strands to clamp the substrate11
. UvrC has two separate nuclease domains: an N
-terminal domain resembling GIY-YIG homing endonuclease12,13
that is responsible for 3′ cleavage and a C-terminal domain that adopts the RNase H fold and executes the 5′ cleavage14
UvrA is a dimeric protein that belongs to the ATP-binding cassette (ABC) family of ATPases, together with transporters15,16
and MutS DNA repair protein17,18
. Crystal structures of Bacillus stearothermophilus
UvrA (Bst-UvrA) and Deinococcus radiodurans
UvrA2 (Dr-UvrA2) have recently been reported19,20
. UvrA contains two ATP-binding domains, I and II. Signature domains I and II are inserted into the corresponding ATP-binding domains. The first signature domain also contains two additional insertions, one responsible for UvrB binding19,21
and the other for DNA binding20
. The two composite ATPase active sites are formed between ATP-binding domain I and signature motif II (that is, the proximal site) and between ATP-binding domain II and signature motif I (that is, the distal site). Three structural zinc-binding elements are present in the structure.
UvrA is hypothesized to be the first NER component to detect the DNA lesion, but its mechanism of DNA binding and damage recognition has been unclear. The key unanswered question has been how the markedly wide specificity of UvrA for different types of DNA lesions is achieved. Here we report a crystal structure of Thermotoga maritima UvrA in complex with modified DNA that indicates a mechanism of indirect readout in which UvrA detects DNA modification through deformations of the double helix.