Structural basis for the mechanistic understanding of human CD38-controlled multiple catalysis

The enzymatic cleavage of the nicotinamide-glycosidic bond on nicotinamide adenine dinucleotide (NAD⁺) has been proposed to go through an oxocarbenium ion-like transition state. Because of the instability of the ionic intermediate, there has been no structural report on such a transient reactive species. Human CD38 is an ectoenzyme that can use NAD⁺ to synthesize two calcium-mobilizing molecules. By using NAD⁺ and a surrogate substrate, NGD⁺, we captured and determined crystal structures of the enzyme complexed with an intermediate, a substrate, and a product along the reaction pathway. Our results showed that the intermediate is stabilized by polar interactions with the catalytic residue Glu²²⁶ rather than by a covalent linkage. The polar interactions between Glu²²⁶ and the substrate 2′,3′-OH groups are essential for initiating catalysis. Ser¹⁹³ was demonstrated to have a regulative role during catalysis and is likely to be involved in intermediate stabilization. In addition, a product inhibition effect by ADP-ribose (through the reorientation of the product) or GDP-ribose (through the formation of a covalently linked GDP-ribose dimer) was observed. These structural data provide insights into the understanding of multiple catalysis and clues for drug design.