Domain structure of Thermus thermophilus UvrB protein. Similarity in domain structure to a helicase

UvrB protein plays an essential role in the prokaryotic excision repair system. UvrB protein shows cryptic ATPase activity, DNA binding, helicase-like activity, and incision activity by interacting with UvrA or UvrC proteins. To reveal the structure-function relationship of this multifunctional protein, the domain structure of Thermus thermophilus UvrB protein (ttUvrB) was studied by limited proteolysis and denaturation experiments. Proteolytic profiles indicated that ttUvrB consists of four domains: the N domain (residues 2-105), M domain (106-455), C1 domain (456-590), and C2 domain (591-665). The properties of the proteolytic fragments indicated the involvement of the respective domains in the functions of the protein as follows: the N and C1 domains are necessary for ATPase activity, the C1 domain is indispensable for DNA binding, and the N and/or M domains are involved in UvrA binding. The structural stability of the C1 and C2 domains was higher than that of the N and M domains, which supports the proposed domain nature of ttUvrB. Based on these results and the crystal structure of PcrA helicase (Subramanya, H. S., Bird, L. E., Brannigan, J. A., and Wigley, D. B. (1996) Nature 384, 379-383), the domain organization of ttUvrB was proposed.