Figure 3
DNA bending and a flip-out mechanism for base excision by the helix–hairpin–helix DNA glycosylase, Escherichia coli AlkA
Thomas Hollis, Yoshitaka Ichikawa and Tom Ellenberger
- The EMBO Journal (2000) 19, 758 - 766
- doi:10.1093/emboj/19.4.758
(A) The binding surface of AlkA colored according to its electrostatic potential (blue, positively charged; red, negatively charged) shows a relatively uncharged surface contacting the DNA. The intercalating Leu125 is indicated by an asterisk, and the catalytic Asp238 is indicated by the small red patch above the asterisk and adjacent to Leu125. (B) A rotated view of the AlkA–DNA complex showing that the abasic 1-azaribose has been rotated out of the DNA and into the aromatic active site cleft of the enzyme. Leu125 has been inserted into the gap created by the flipped out nucleotide. The minor groove has been widened substantially by the protein, contributing to the significant distortion of the DNA. Figures 3 and 6 were generated with the program GRASP (Nicholls et al., 1993).
