Proposed translocation mechanism of UvrB. (a) Proposed rigid body movement of RecA-like domains upon ATP-binding and ATP-hydrolysis. (b) Interactions between the inner strand and two nucleic acid binding sites in domains 1a and 3. For clarity, only 8-nucleotide stretch of the inner strand is shown. Nucleotides in contact with helicase motifs are shown in colors while others are shown in white. The Interactions are represented in dashed lines in all panels. (c) F527 (red) lodged deeply in the minor groove. Helicase motifs and F-loop are colored in blue and pink, respectively. (d) DNA bubble (green) flanked by F527 on one end and the β
-hairpin on the other in two orthogonal views. Domains 1a, 1b, and 2 are omitted for clarity. (e) Superposition of domain 3 of UvrB in the absence (grey; PDB ID, 1D9Z) [16
] and presence of dsDNA substrate (cyan). Motif V, which undergoes conformational transition upon DNA binding, is highlighted in yellow. (f) The ATPase site of UvrB bound to ATP in the absence of dsDNA (PDB ID, 1D9Z) [16
]. (g) The activated ATPase site in the UvrB-dsDNA-ADP·Pi structure.