ADP-ribose diphosphatase

It is a structurally conserved loop-helix-loop motif that creates a scaffold for metal binding and pyrophosphatase chemistry in the enzyme.

As noted earlier, the Nudix fold is the catalytic part of the enzyme, but both domains are involved in the active site and they both help with the attachment and coordination of H2O, Mg2+, and the ADP-ribose substrate.

A glutamate side chain (E162) will deprotonate the water molecule, and then the hydroxide ion will attack nucleophilically.

This evidence is a refutation of a previous study that suggested that hydrolysis of ADP-ribose could proceed by nucleophilic attack at either alpha- or beta- phosphate (Gabelli, et al. 2001).

After the water molecule attacks, an intermediate is formed, and then ribose 5-phosphate is kicked off as a leaving group.

The hydrolysis of ADPR is catalyzed by E162, which improves the nucleophilicity of the water molecule in the active site by deprotonating it.

Thus, it is believed that ADPRase functions in general as a house-cleaning enzyme to eliminate potentially deleterious ADP-ribose from the cell.

But in mammalian cells, there is only an indirect evidence linking ADPRase to a detoxifying role, and this comes from studies of the very specific rat liver ADPRibase-I by cytotoxic agents.

This shows the full enzyme with ADP-Ribose bound in the active site pocket. Blue and red areas on the surface represent polar residues that assist in the creation of the active site pocket. [1] From PDB : 1KHZ ​.
This shows how H-bonds and Mg 2+ coordinate and hold the AMPCPR substrate (an analog of ADP-ribose) in complex with the enzyme. Active site amino acids are shown, as well as two important active site water molecules. [2] From PDB : 1KHZ ​.
This shows how two Mg 2+ coordinate the attacking water molecule and how the third Mg 2+ bridges the two phosphates on ADP-ribose. Distances between the Mg 2+ and the substrate are shown in angstroms. H-bonds to the catalytic glutamate are also shown. [3] From PDB : 1KHZ ​.