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 Glu(226) rather than by a covalent linkage. The polar interactions between Glu(226) and the substrate 2',3'-OH groups are essential for initiating catalysis. Ser(193) 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.
Liu
Qun
Q
Macromolecular Diffraction Facility at the Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, Ithaca, NY 14853, USA.
Kriksunov
Irina A
IA
Graeff
Richard
R
Munshi
Cyrus
C
Lee
Hon Cheung
HC
Hao
Quan
Q
D051997:ADP-ribosyl Cyclase 1 / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism*; D019943:Amino Acid Substitution; D001483:Base Sequence; D001665:Binding Sites; D002384:Catalysis; D003080:Cold Temperature; D018360:Crystallography, X-Ray; D036563:Cyclic ADP-Ribose / Q000378:metabolism; D019281:Dimerization; D004795:Enzyme Stability; D018698:Glutamic Acid / Q000378:metabolism; D006156:Guanosine Diphosphate Sugars / Q000378:metabolism; D006801:Humans; D006868:Hydrolysis; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009243:NAD / Q000378:metabolism; D009244:NAD+ Nucleosidase / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid; D012694:Serine / Q000378:metabolism; D055672:Static Electricity; D013379:Substrate Specificity; D014867:Water / Q000737:chemistry
D006156:Guanosine Diphosphate Sugars; C090657:cyclic guanosine diphosphate-ribose; D014867:Water; D009243:NAD; D036563:Cyclic ADP-Ribose; D018698:Glutamic Acid; D012694:Serine; D009244:NAD+ Nucleosidase; D051997:ADP-ribosyl Cyclase 1