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

Area of Science:

• Enzymology
• Structural Biology
• Biochemistry

Background:

• The enzymatic hydrolysis of the nicotinamide-glycosidic bond in nicotinamide adenine dinucleotide (NAD(+)) is hypothesized to involve an oxocarbenium ion-like transition state.
• The transient nature and instability of this ionic intermediate have prevented its direct structural observation.

Purpose of the Study:

• To capture and determine the crystal structure of a transient intermediate in the human CD38 enzymatic reaction pathway.
• To elucidate the catalytic mechanism and stabilization of intermediates in NAD(+) cleavage by CD38.
• To identify potential targets for drug design based on structural insights.

Main Methods:

• Utilized NAD(+) and a surrogate substrate, NGD(+), to capture reaction intermediates.
• Determined crystal structures of human CD38 complexed with substrate, intermediate, and product.
• Analyzed polar interactions and the roles of catalytic residues (Glu(226), Ser(193)) in catalysis and stabilization.

Main Results:

• Successfully captured and determined the crystal structure of a key intermediate in the human CD38-catalyzed NAD(+) cleavage.
• The intermediate is stabilized by polar interactions with the catalytic residue Glu(226), not a covalent bond.
• Identified a regulative role for Ser(193) in catalysis and potential intermediate stabilization.
• Observed product inhibition by ADP-ribose and GDP-ribose through distinct mechanisms.

Conclusions:

• Provided the first structural evidence of a stabilized intermediate in NAD(+) cleavage by human CD38.
• Demonstrated the critical role of polar interactions with Glu(226) in initiating catalysis.
• Offered structural insights into enzyme mechanism, product inhibition, and potential avenues for drug development targeting CD38.