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. Author manuscript; available in PMC: 2017 Jul 1.
Published in final edited form as: DNA Repair (Amst). 2016 May 13;43:48–56. doi: 10.1016/j.dnarep.2016.05.029

Figure 1. AID crystal structure.

Figure 1

a) Sequence differences at the N-terminus between AID and AIDv. b) Ribbon diagram of the crystal structure of the MBP-AIDv(Δ15) fusion protein. The MBP is colored metallic blue (with bound maltotetraose in yellow) and the AID is colored peach. c) Residues that were modified in AID for solubility purposes are colored cornflower blue. d) Active site region of AIDv with a dUMP (cyan) superimposed in to the active site from a crystal structure of deoxycytidylate deaminase from bacteriophage S-TIM5 (pdb 4P9C). Active site residues chelating the Zn ion and the proposed proton shuttle (E58) are shown in magenta. A water molecule coordinating the Zn ion is also shown (red). e) Interactions of the substrate binding loop. Residues Tyr114 base stacks with Phe115 and is in position to form a perpendicular base-stacking arrangement with the substrate dC. Leu113 and Cys116 cap off a hydrophobic pocket consisting of residues from beta strand 5, helix 4, and the C-terminal helix 6. Cys116 is sandwiched between residues L113 and Pro123 that define the ends of the substrate binding loop. Glu122 forms a potential hydrogen bond with the backbone amide from Tyr88 at the top of helix 3. These interactions may help maintain the loops conformation. In all figures the Zn ion is colored green and the substrate loop is colored orange.