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. 2008 Oct 20;15(10):1068-78.
doi: 10.1016/j.chembiol.2008.08.007.

Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38

Qun Liu  1 , Irina A Kriksunov, Hong Jiang, Richard Graeff, Hening Lin, Hon Cheung Lee, Quan Hao
Affiliations

Covalent and noncovalent intermediates of an NAD utilizing enzyme, human CD38

Qun Liu et al. Chem Biol. .

Abstract

Enzymatic utilization of nicotinamide adenine dinucleotide (NAD) has increasingly been shown to have fundamental roles in gene regulation, signal transduction, and protein modification. Many of the processes require the cleavage of the nicotinamide moiety from the substrate and the formation of a reactive intermediate. Using X-ray crystallography, we show that human CD38, an NAD-utilizing enzyme, is capable of catalyzing the cleavage reactions through both covalent and noncovalent intermediates, depending on the substrate used. The covalent intermediate is resistant to further attack by nucleophiles, resulting in mechanism-based enzyme inactivation. The noncovalent intermediate is stabilized mainly through H-bond interactions, but appears to remain reactive. Our structural results favor the proposal of a noncovalent intermediate during normal enzymatic utilization of NAD by human CD38 and provide structural insights into the design of covalent and noncovalent inhibitors targeting NAD-utilization pathways.

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Figures

Figure 1
Figure 1. Schematic diagram of the reactions of NAD catalysis
A) Nicotinamide cleavage results in the formation of possible covalent and non-covalent intermediates. B) Reactions of forming cADPR or ADPR from NAD catalyzed by CD38.
Figure 2
Figure 2. Covalent intermediate after the cleavage of nicotinamide
A) Chemical synthesized ara-F-NMN, a mechanism based analogue of substrate NMN. B) Overall structure of CD38 with its catalytic residue Glu226 covalently linked to ara-F-R5P. The two domains of CD38 are differently colored to show that the intermediate is right between the gulf of two domains. The covalent linkage is shown as sticks. C) A stereo presentation of active site structure showing the trapping of intermediate species ara-F-R5P. The 2Fo-Fc omit electron densities (with ara-F-R5P omitted during the calculation of the electron density map) for the trapped covalent intermediate is shown as gray isomesh at 1.0 σ. The active site residues are shown as sticks with their carbons atoms in gray. Ara-F-R5P, the remaining moiety after the release of leaving group nicotinamide from substrate, is also shown as sticks but with their carbon atoms in green. The covalent bond length between Glu226 and ara-F-R5P is 1.6 Å. Polar interactions between protein and ara-F-R5P are drawn as cyan dashed lines. Four water molecules observed in the active site are shown as red spheres.
Figure 3
Figure 3. Dynamics of covalent intermediate
A) Structure of ara-F-R5P/Nic complex. With the pre-existence of covalent ara-F-R5P intermediate in the active site, nicotinamide, at high concentration, can bind to the active site through polar interactions to Glu146 and Asp155, and hydrophobic stacking interactions to Trp189. The 2Fo-Fc omit density covering ara-F-R5P and Glu226 is shown as gray isomesh contoured at 1.0 σ; the Fo-Fc electron density covering nicotinamide is show as purple isomesh contoured at 2.5 σ. Nicotinamide is 3.7 Å away to the reaction center atom C1′. B) Structural comparison of two covalent intermediates, with and without nicotinamide, to show the rearrangement of the covalent intermediate. Intermediate without nicotinamide (marine carbon atoms) was superimposed on intermediate (green carbon atoms) with the disturbance of high concentration of nicotinamide. Upon the binding of nicotinamide, the covalent ara-F-R5P intermediate dynamically rotates its arabinyl sugar group 90° around a free phosphate-sugar bond. Accordingly, four water molecules (marine spheres) are evacuated from the active site by this rotational movement.
Figure 4
Figure 4. Non-covalent intermediate trapped by GTP
A) The GTP complex. GTP alone can inhibit CD38 by occupying the nicotinamide binding site defined by residues Glu146, Asp155, and Trp189. The Fo-Fc omit (with GTP omitted from the calculation of the electron density map) electron density is shown as gray isomesh contoured at 2.5 σ covering GTP. B) The non-covalent R5PI intermediate trapped by GTP. The non-covalent R5P intermediate (R5PI) is show as sticks with its carbon green. R5PI forms two hydrogen bonds with the catalytic residues Glu226 and Trp125 main chain nitrogen. The Fo-Fc omit electron density is shown as gray isomesh contoured at 2.8 σ. The GTP molecule in the active site (yellow sticks) has almost the same conformation as in the GTP complex shown in A). The phosphate group of R5PI forms extensive H-bonds to residues Ser126, Arg127, Phe222, and Thr221. C) A R5P-GTP adduct in which R5PI is attacked by GTP from the β-face to form a covalent bond. The bond distance between C1′ and GTP O6 is 1.9 Å. The Fo-Fc omit electron density (with R5P-GTP omitted from the calculation of the electron density map) is shown as gray isomesh and contoured at 2.8 σ. D) Structural comparison of covalent and non-covalent intermediates. The covalent intermediate (green carbon sticks) with nicotinamide trapped in the active site is used for the superimposition with R5PI intermediate (gray carbon sticks). Essential active site residues Glu146, Asp155, Trp189, and Ser193 align quite well whereas the catalytic residue Glu226 rotates its carboxylate group by 30° in order to form a covalent intermediate with ara-F-R5P.
Figure 5
Figure 5. Structural determinants for nicotinamide-glycosidic bond cleavage
A) NMN/E226Q complex. Substrate NMN is shown as sticks with its carbon atoms green. The Fo-Fc omit electron density (with NMN omitted from the calculation of the map) is shown as gray isomesh contoured at 2.5 σ. The nicotinamide moiety of NMN is recognized by its interactions to Glu-146, Asp-155, and Trp-189. Dashed lines colored in cyan show the specific polar interactions between NMN and the enzyme. B) NMN/wtCD38 complex. The presentation scheme is the same as A). C) Stereo representation of the structural comparison of the NMN/wtCD38 complex with the ara-F-R5P/nicotinamide complex. Both complexes are shown as sticks with green carbon for the NMN/wtCD38 complex and gray/magenta/yellow carbon for the ara-F-R5P/nicotinamide/wtCD38 tertiary complex. The alignment of both structures shows the structural determinants for the enzymatic cleavage of nicotinamide.
Figure 6
Figure 6. Rational designs of covalent and non-covalent inhibitors based on mechanism of catalysis
A) Covalent inhibitors of 2'-substitutions of arabino configuration. B) Covalent inhibitors of 2'- substitutions of ribose configuration. Among these potential inhibitors, 2'-substitution by an -NH2 group might not be a good covalent intermediate as it can likely form an H-bond with the catalytic residue Glu226 to stabilize a non-covalent intermediate. C) Non-covalent inhibitors: R5P-Guanine based inhibitors.
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