Photoaffinity labeling of diphtheria toxin fragment A with 8-azidoadenosyl nicotinamide adenine dinucleotide.

Diphtheria toxin fragment A (DT-A) is an important enzyme in the class of mono(ADP-ribosyl)transferases. To identify peptides and amino acid residues which form the NAD(+) binding site of DT-A using a photoaffinity approach, the photoprobes nicotinamide 8-azidoadenine dinucleotide (8-N(3)-NAD) and nicotinamide 2-azidoadenine dinucleotide (2-N(3)-NAD) were synthesized. Binding studies gave an IC(50) of 2.5 microM for 8-N(3)-NAD and 5.0 microM for 2-N(3)-NAD. Irradiation of DT-A and low concentrations of [alpha-(32)P]-8-N(3)-NAD with short-wavelength UV light resulted in rapid covalent incorporation of the photoprobe into the protein. The photoincorporation was shown to be specific for the active site with a stoichiometry of photoincorporation of 75-80%. After proteolytic digestion of photolabeled DT-A, derivatized peptides were isolated using immobilized boronate affinity chromatography followed by reversed phase HPLC. Radiolabeled peptides originating from two regions of the protein were identified. Chymotryptic digestion produced labeled peptides corresponding to His(21)-Gln(32) and Lys(33)-Phe(53). Lys-C digestion gave overlapping peptides Ser(11)-Lys(33) and Ser(40)-Lys(59). Tyr(27) was identified as the site of photoinsertion within the peptide His(21)-Gln(32) on the basis of the absence of PTH-Tyr at the predicted cycle during sequence analysis and by the lack of predicted chymotryptic cleavage at Tyr(27). Within the second modified peptide Ser(40)-Lys(59), Trp(50) is the most probable site of modification. Identification of Tyr(27) as a site of photoinsertion is in agreement with its placement in the NAD binding site of the X-ray structure of the proenzyme DT-NAD complex [Bell, C. E., and Eisenberg, D. (1996) Biochemistry 35, 1137]. Trp(50) is far from the adenine ring in the crystallographic model; however, site-directed mutagenesis studies suggest that Trp(50) is a major determinant of NAD binding affinity [Wilson, B. A., Blanke, S. R., Reich, K. A., and Collier, R. J. (1994) J. Biol. Chem. 269, 23296-23301].