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X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site

Nature Structural Biology volume 6, pages 448–453 (1999)Cite this article

Abstract

The crystal structure of 5'-nucleotidase (5'-NT) from E. coli, also known as UDP-sugar hydrolase, has been determined at 1.7 Å resolution. Two zinc ions are present in the active site, which is located in a cleft between two domains. The dimetal center and a catalytic Asp-His dyad are the main players in the catalytic mechanism. Structure-based sequence comparisons show that the structure also provides a model for animal 5'-NTs, which together with other ectonucleotidases terminate the action of nucleotides as extracellular signaling substances in the nervous system.

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Figure 1: Protein fold of 5'-nucleotidase (5'–NT).
Figure 2: Active-site region.
Figure 3: Structure-based sequence alignment (see Methods) of selected bacterial and animal 5'-NTs.
Figure 4: Superposition of the active-site structures of E. coli 5'-NT (green), kidney bean purple acid phosphatase (blue, PDB code 4KBP12,13), human calcineurin (yellow, PP-2B, PDB code 1AUI15), and rabbit protein phosphatase 1 (red, PDB code 1FJM14).

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Acknowledgements

We thank W. Saenger for generous support, G. Leonard (ESRF and EMBL, Grenoble, France) for assistance with the MAD measurements, W. Rypniewski for help with the data collection at the EMBL beamline at DESY, Hamburg, and G. Bains for support during the data collection at the ESRF and for helpful comments on the manuscript. This work was supported by a grant from the Deutsche Forschungsgemeinschaft to N.S.

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  1. Abteilung Saenger, Institut für Kristallographie, Freie Universität Berlin, Takustr. 6, Berlin, 14195 , Germany

    Thomas Knöfel & Norbert Sträter

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Correspondence to Norbert Sträter.

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Knöfel, T., Sträter, N. X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site. Nat Struct Mol Biol 6, 448–453 (1999). https://doi.org/10.1038/8253

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