Figure 4.

Mapping of chemical shift perturbations upon binding of DNA, surface electrostatic potential and proposed position of a substrate cytidine. (A) Chemical shift perturbations observed for the wild-type deaminase domain upon binding of 10-mer DNA. The residues exhibiting combined chemical shift perturbations as to H^N and N of >0.03 p.p.m. and 0.02–0.03 p.p.m. are coloured red and yellow, respectively. The residues whose ¹H–¹⁵N correlation peaks either disappeared or became notably weak, the relative intensity in a free state to that in a complex state being greater than 1.2, are coloured blue. (B) Chemical shift perturbations observed for the mutant deaminase domain upon binding of 21-mer DNA. The residues exhibiting combined chemical shift perturbations of >0.03 p.p.m. and 0.02–0.03 p.p.m. are coloured red and yellow, respectively. The structure and perturbation data reported for the mutant deaminase domain (Chen et al, 2008) were used to make this figure. (C) Left, the perturbations for the wild-type deaminase domain mapped on the surface representation; right, positive and negative surface potentials of the wild-type deaminase domain represented in blue and red, respectively. (D) A close-up of the deduced key interactive region of the wild-type APOBEC3G deaminase domain, with the proposed position of a substrate cytidine indicated by a dashed circle, viewed from two different angles. (E) Three possible positions of ssDNA relative to the APOBEC3G deaminase domain. Right, the position proposed by Chen et al, 2008 (dashed vertical line in blue) and that by Holden et al, 2008 (dashed kinked horizontal line in green); left, the third possible position.