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Crystal structure of a human mitochondrial deoxyribonucleotidase

Nature Structural Biology volume 9, pages 779–787 (2002)Cite this article

Abstract

5′ nucleotidases are ubiquitous enzymes that dephosphorylate nucleoside monophosphates and participate in the regulation of nucleotide pools. The mitochondrial 5′-(3′) deoxyribonucleotidase (dNT-2) specifically dephosphorylates dUMP and dTMP, thereby protecting mitochondrial DNA replication from excess dTTP. We have solved the structure of dNT-2, the first of a mammalian 5′ nucleotidase. The structure reveals a relationship to the HAD family, members of which use an aspartyl nucleophile as their common catalytic strategy, with a phosphoserine phosphatase as the most similar neighbor. A structure-based sequence alignment of dNT-2 with other 5′ nucleotidases also suggests a common origin for these enzymes. Here we study the structures of dNT-2 in complex with bound phosphate and beryllium trifluoride plus thymidine as model for a phosphoenzyme–product complex. Based on these structures, determinants for substrate specificity recognition and the catalytic action of dNT-2 are outlined.

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Figure 1: Structure and sequence alignment of the dNT-2.
Figure 2: Comparison of the dNT-2 structure with PSP (PDB entry 1F5S).
Figure 3: Detailed view of the active site of dNT-2.
Figure 4: Structure of dNT-2 in complex with thymidine and BeF3.
Figure 5: A proposal for a general catalytic mechanism for the soluble nucleotidases.

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Acknowledgements

We thank in particular M. Bennet and X.-D. Su for advice on data collection and phasing. We also thank people at the Max Lab, Y. Cerenius for technical assistance, the staff at ESRF for technical assistance and G. Leonard for help with preliminary MAD data processing. We are grateful to K.-M. Larsson, M. Högbom and P. Stenmark for help with data collection. This work was supported by grants from Theleton Italia (V.B.), AIRC Associazione Italiana per la Ricerca sul Cancro (V.B.), the Swedish Research Council (P.N.), the Swedish Cancer Society (P.N.) and from the European community.

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Authors and Affiliations

  1. Department of Biochemistry and Biophysics, Stockholm University, S-106 91, Stockholm, Sweden

    Agnes Rinaldo-Matthis & Pär Nordlund

  2. Department of Biology, University of Padova, I-35131, Padova, Italy

    Chiara Rampazzo, Peter Reichard & Vera Bianchi

  3. Department of Biochemistry, Medical Nobel Institute, MBB, Karolinska Institute, S-171 77, Stockholm, Sweden

    Peter Reichard

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Correspondence to Pär Nordlund.

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Rinaldo-Matthis, A., Rampazzo, C., Reichard, P. et al. Crystal structure of a human mitochondrial deoxyribonucleotidase. Nat Struct Mol Biol 9, 779–787 (2002). https://doi.org/10.1038/nsb846

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