## 6 Global Genome Repair (GGR)
### Two Types of ABC ATPase Sites on UvrA Power Damage Detection and UvrB Binding  
It has been known for nearly 35 years that ATP is involved in steps of NER mediated by UvrA and UvrB [16, 39, 40, 56, 58, 65, 99, 117, 118, 119, 120], however, precise roles for the nucleotide sites have yet to be decisively established. Prior studies have suggested roles for ATP in stability of the UvrA dimer [119, 121, 122], interaction with UvrB [100] and damage discrimination [16, 39, 40, 41, 118, 120], with strong evidence for mixed nucleotide states and cooperativity between sites [40, 46, 118, 120, 122]. Structural and biochemical evidence implicated nucleotide dynamics at the proximal site in interactions with UvrB and DNA [21, 38], while discrimination of native from damaged DNA was hypothesized to involve the distal site [21, 39, 40, 41]. The finding that UvrA may tune its activity depending on the lesion [46], that NER efficiency is dependent on sequence context [123, 124] and that bulky DNA lesions can be repaired in the absence of ATP hydrolysis by UvrA [120] is intriguing and requires further exploration. The extensive structural database of other ABC-family proteins [36, 125] provide a basis for predicting or understanding conformation-switching in UvrA during NER. However, the presence of two types of ATP binding sites in UvrA, which could each transition through three nucleotide states (empty, ADP and ATP) and are coupled, giving rise to eight possible nucleotide combinations [46], underscores challenges in understanding the role of ATP during NER. The current set of eight crystal structures from four bacterial species provide 24 independent views of the NBDs and composite nucleotide-binding sites of UvrA, however, the structural configuration formed in the presence of ATP is currently lacking. This limits efforts to understand how nucleotide binding and hydrolysis are coupled to DNA damage sensing. Superposition of all available nucleotide binding site structures on the ATP binding domains (Figure 4) reveals a low RMSD (proximal: 1.19 A, distal: 1.06 A). With the exception of the conformers that lack nucleotide or are bound to dsDNA, the ABC signature domains are found to populate a narrow range of configurations that are within 1-10\({}^{\circ}\) (average proximal: 4.7\({}^{\circ}\); average distal; 7.6\({}^{\circ}\)) of the reference molecule (PDB entry 2R6F); the corresponding values for sites that lacked nucleotide or are bound to DNA are in the 18-20\({}^{\circ}\) range (Figure 4). Two lines of evidence indicate that UvrA likely undergoes substantial conformational changes during NER. First, restricting dynamics of the \(\beta\)-hairpin in the Zn3 module (Zn3 hp) of UvrA using disulfide cross-linking disrupts its ATPase activity and capacity to load UvrB onto damaged DNA; this dynamism requires a functional distal nucleotide binding site [41]. Second, the NBDs of ABC ATPases in membrane transporters, as exemplified by the TAP transporter [125], have been observed to exhibit significantly larger angular and distance changes during the functional cycle than those currently seen with the current set of UvrA structures. The fact that the nucleotide binding sites of most the available UvrA structures are filled with ADP and the finding that the motion of domains most expected to switch conformation is restricted by crystal contacts limits structural insights into the UvrA ATP cycle during NER. Biochemical and biological studies have, however, provided new and important clues into nucleotide dynamics of UvrA during NER. Detailed analysis of pre-steady state kinetics revealed that UvrA programs differential responses by the proximal and distal ATPase sites to absence of DNA or presence of either native or damaged DNA [46]. The two types of sites were found to bind ATP with a considerable difference in affinity [21; 46; 46]. Figure 4: The proximal and distal nucleotide binding sites of UvrA.