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The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family

Nature Structural Biology volume 8, pages 467–472 (2001)Cite this article

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 1.9Å, 2.7Å and 2.3Å, 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.

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Figure 1: Structure of the apo ADPRase dimer.
Figure 2: Structure of the Nudix motif and the complete Nudix fold.
Figure 3: Coordination of the Gd3+ in ADPRase.
Figure 4: Substrate binding to ADPRase.

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Acknowledgements

Support was provided by NIGMS grants to L.M.A. and M.J.B. S.B.G was supported by an NSF graduate fellowship. Beamlines X25, X8C and X9B of National Synchrotron Light Source, Brookhaven National Laboratory are gratefully acknowledged. We thank D. Leahy for carefully reading the manuscript.

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Authors and Affiliations

  1. Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, 21205, Maryland, USA

    Sandra B. Gabelli, Mario A. Bianchet & L. Mario Amzel

  2. Department of Biology and McCollum-Pratt Institute, Johns Hopkins University, Baltimore, 21218, Maryland, USA

    Maurice J. Bessman

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  1. Sandra B. Gabelli
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  2. Mario A. Bianchet
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  3. Maurice J. Bessman
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Correspondence to L. Mario Amzel.

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Gabelli, S., Bianchet, M., Bessman, M. et al. The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family. Nat Struct Mol Biol 8, 467–472 (2001). https://doi.org/10.1038/87647

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