Crystal Structures of Human CD38 in Complex with NAADP and ADPRP

Abstract

Mobilization of intracellular Ca 2+ stores is a critical process for many cell activities. Nicotinic acid adenine dinucleotide phosphate (NAADP) is a novel second messenger that can mobilize acidic calcium stores, such as the endo-lysosomes. It is thus functionally distinct from the two other Ca 2+ signaling messengers, cyclic ADP-ribose and inositol trisphosphate, which target the Ca 2+ stores in the endoplasmic reticulum. Human CD38, a multifunctional protein having both receptor and enzymatic roles in almost all cell types, has been shown to catalyze both the synthesis and degradation of NAADP. Here, we present the first image of this novel messenger in complex with human CD38 as captured by X-ray crystallography. The results provide insight into the degradation mechanism of NAADP by human CD38.

Cyclic Adenosine 5′-Diphosphate Ribose Analogs without a “Southern” Ribose Inhibit ADP-ribosyl Cyclase–Hydrolase CD38

“…One of these waters forms H-bonds to Leu123, Leu145, and the ribose 2′-OH that is consistent with other reported CD38 crystal structures. 54 Notably, in the 3U4H crystal with 8-NH 2 -cIDPR, the remaining water molecule lies within 3 Å of the hypoxanthine carbonyl group. This water is not observed in the complex of the hydrolyzed ligand 7a (PDB code 4TMF); thus, we postulate that donation of a proton from this water molecule could be enzyme-assisted in the active site.…”

“…Addition of water to C-1′ has occurred to generate the hydrolyzed product, and the -OH group is attached to the α-face of the ribose, as has been observed previously for NAD + hydrolysis products captured by crystallization. 53 , 54 Such observations are at odds with both the proposed ionic or covalent hydrolysis mechanisms, which predict a predominantly or entirely β-product, respectively. 55 Notably, the hydrolyzed ligand still occupies the catalytic site in the same manner as the cADPR, except that the hypoxanthine base has rotated in the binding pocket after hydrolysis.…”

Synthesis of the Ca2+-mobilizing messengers NAADP and cADPR by intracellular CD38 enzyme in the mouse heart: Role in β-adrenoceptor signaling

“…The pyridine ring of SAN4825 also showed π–π stacking with Trp-193 of mouse CD38. These π–π interactions were also observed in the crystal structure of wild-type human CD38 in complex with the NAADP analogue and ADPRP ( 40 ).…”

“…4 C ). Further superimposition of the binding conformation of SAN4825 in mouse CD38 with the binding conformations of an NAADP analogue and ADPRP in human CD38 (PDB code 4F46 ( 40 )) suggests that SAN4825 occupies the same binding site as these substrates, in close proximity to Glu-230 of mouse CD38 ( Fig. 4 C ).…”

“…The blind docking results from the SwissDock server also predicted a single inhibitory binding site for SAN4825, and this site corresponds to the enzymatic active site of CD38. These SAN4285–CD38 binding conformations showed some resemblance to the native binding conformation between CD38 and its substrates, such as NAD, nicotinamide mononucleotide (NMN), cADRP, and NAADP ( 40 , 50 , 51 ).…”