Journal:

Article Title: Transition State Structure for the Hydrolysis of NAD + Catalyzed by Diphtheria Toxin †

doi: 10.1021/ja971317a

Figure Lengend Snippet: Stereodiagram of the transition state structure fitted into active site of DTA. Projection of the electrostatic potentials onto the molecular surface shows the complementarity of the contact site for the transition state. The ball-and-stick figure of the transition state on the lower right shows the orientation of the transition state in the active site. The ring oxygen, O4′, is labeled on the molecular surface. The region of positive potential (solid red) associated with C1′ of the TS is apposed with the negative potential (blue dots) of the carboxylate of Glu148. The negative electrostatic potential of the phosphate oxygens (solid blue) is near the positive potential (red dots) of His21 (not visible behind the phosphate). The proximity of the nucleophile water to the carboxylate of Glu148 raises the possibility that it promotes catalysis as a general base catalyst or by polarizing the H–O bond to enhance the nucleophilicity of the oxygen. The electrostatic potentials were calculated using the Delphi module of the program Insight II (Biosym Technologies, San Diego, CA). Charges were of 1+ were assigned to Lys, Arg, and His21 of DTA, 0.5+ to other His residues, and 1– to Glu and Asp. Point charges on the atoms of the transition state structure were assigned from the natural population analysis90 charges calculated from the wave function as in Figure 7. The molecular surfaces were calculated as the Connolly surfaces,91 but with the atomic radii reduced by a factor of 0.8 so that the surface approximates a smoothed van der Waals surface. The contact site of DTA includes all residues that contribute to the molecular surface surrounding the transition state: Tyr20, His21, Tyr54, Ser55, Thr56, Tyr65, Phe140, Glu148. Secondary structural elements of DTA, as calculated by the Kabsch and Sander criteria,92 are shown, with α-helices in purple and β-strands in blue. The transition state structure from Figure 7 was fitted into the active site cleft by allowing the bond angles between the nicotinamide and ribosyl moieties to vary, as well as the torsional angles about C4′–C5′ and C5′–O5′.

Article Snippet: The electrostatic potentials were calculated using the Delphi module of the program Insight II (Biosym Technologies, San Diego, CA).

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