PDBsum entry 1g0s

Hydrolase

PDB id: 1g0s

Contents

Protein chains

201 a.a. *

Waters ×392

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The structure of ADP-Ribose pyrophosphatase reveals the structural basis for the versatility of the nudix family.

Authors

S.B.Gabelli, M.A.Bianchet, M.J.Bessman, L.M.Amzel.

Ref.

Nat Struct Biol, 2001, 8, 467-472. [DOI no: 10.1038/87647]

PubMed id

11323725

Abstract

Regulation of cellular levels of ADP-ribose is important in preventing nonenzymatic ADP-ribosylation of proteins. The Escherichia coli ADP-ribose pyrophosphatase, a Nudix enzyme, catalyzes the hydrolysis of ADP-ribose to ribose-5-P and AMP, compounds that can be recycled as part of nucleotide metabolism. The structures of the apo enzyme, the active enzyme and the complex with ADP-ribose were determined to 1.9 A, 2.7 A and 2.3 A, respectively. The structures reveal a symmetric homodimer with two equivalent catalytic sites, each formed by residues of both monomers, requiring dimerization through domain swapping for substrate recognition and catalytic activity. The structures also suggest a role for the residues conserved in each Nudix subfamily. The Nudix motif residues, folded as a loop-helix-loop tailored for pyrophosphate hydrolysis, compose the catalytic center; residues conferring substrate specificity occur in regions of the sequence removed from the Nudix motif. This segregation of catalytic and recognition roles provides versatility to the Nudix family.

Figure 3.
Figure 3. Coordination of the Gd^3+ in ADPRase. The side chains of the residues involved in ion coordination are shown in all-atom representation. The corresponding portion of the 2F[o] - F[c] electron density map is shown in sky blue. The metal ion is shown in green, and the metal-coordinating waters as red spheres.

Figure 4.
Figure 4. Substrate binding to ADPRase. a, Location of the two equivalent ADPR binding sites in the ADPRase dimer. In each binding site, loop L8 of the opposite monomer is in close proximity to the ribose moiety of ADPR. b, Stereo diagram of one ADPR binding site. Residues of the two monomers contributing to binding are labeled (B: main monomer, A: second monomer). The 2F[o] - F[c] electron density of the ADPR is shown in light blue. Carbons are gray, oxygens red, nitrogens blue, phosphorous yellow, and sulfur green; bound waters (labeled W3 and W4) are shown as red spheres. The adenosine group of the substrate binds to the enzyme in anti conformation (dihedral glycosylic bond is -143°); the adenine ribose ring has C3'-endo puckering and the terminal ribose binds with C2'-endo puckering. c, Interactions between ADPR and ADPRase. The ADPR molecule is drawn with heavy lines. Hydrogen bonds are shown with dashed blue lines; the distances between donors and acceptors are indicated. Amino acids providing van der Waals interactions are shown as decorated arcs. Residue numbers are followed by a letter (A or B) to indicate the monomer. Water molecules W1 to W4 are shown as spheres.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 467-472) copyright 2001.