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. Author manuscript; available in PMC: 2013 Sep 5.
Published in final edited form as: J Mol Biol. 2008 Jun 5;381(1):13–23. doi: 10.1016/j.jmb.2008.05.078

Figure 2.

Figure 2

The putative active site of AlkD. (A) Close-up of the concave cleft shows aromatic and charged residues implicated in nucleobase and DNA binding. Water molecules are shown as red spheres and hydrogen bonds are depicted as black dotted lines. (B) The electron-rich active site of AlkA, showing the conserved Asp238 essential for base excision. (C) 7-methylguanine (7mG) excision by AlkD. Denaturing polyacrylamide gel showing the disappearance of 7mGDNA substrate (S) and appearance of alkaline-cleaved abasic-DNA product (P) as a result of reaction with no enzyme, wild-type AlkD, Asp113Asn, and Arg148Ala mutants for increasing amounts of time. (D) Quantitation of the data in panel C showing the inactivity of the Asp113Asn (squares) and Arg148Ala (triangles) mutants as compared to wild-type AlkD (closed circles). Non-enzymatic 7mG hydrolysis is shown as crosses and dotted line curve fit. Error bars represent the standard deviation from the average of three independent experiments.