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Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae

Nature Structural Biology volume 9, pages 966–972 (2002)Cite this article

Abstract

Here we report the structure of acireductone dioxygenase (ARD), the first determined for a new family of metalloenzymes. ARD represents a branch point in the methionine salvage pathway leading from methylthioadenosine to methionine and has been shown to catalyze different reactions depending on the type of metal ion bound in the active site. The solution structure of nickel-containing ARD (Ni-ARD) was determined using NMR methods. X-ray absorption spectroscopy, assignment of hyperfine shifted NMR resonances and conserved domain homology were used to model the metal-binding site because of the paramagnetism of the bound Ni2+. Although there is no structure in the Protein Data Bank within 3 Å r.m.s deviation of that of Ni-ARD, the enzyme active site is located in a conserved double-stranded b-helix domain. Furthermore, the proposed Ni-ARD active site shows significant post-facto structural homology to the active sites of several metalloenzymes in the cupin superfamily.

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Figure 1
Figure 2: Relevant sequence alignments for modeling of the Ni-ARD active site.
Figure 3: Comparison of homologous residues in jack bean canavalin and Ni-ARD.
Figure 4: Structure of Ni-ARD.
Figure 5: Active site of Ni-ARD, showing conserved acidic residues in orange, conserved basic residues in cyan and conserved aromatic residues (and backbone) in purple.
Figure 6: Proposed mechanisms for ARD (Ni-type) and ARD′ (Fe-type) catalysis of acireductone oxidation, with rationale for 1,2 (ARD) versus 1,3 (ARD′) activation.

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GenBank/EMBL/DDBJ

Protein Data Bank

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Acknowledgements

This work was supported by the U.S. Public Health Service. The 600 MHz NMR spectrometer used was purchased via a grant from the National Science Foundation (T.C.P.). The authors thank G. Wagner (Harvard Medical School) for access to his 750 MHz NMR spectrometer.

Author information

Author notes

  1. Michael J. Maroney

    Present address: Department of Chemistry, University of Massachusetts, Amherst, 01003-9336, Massachusetts, USA

  2. Huaping Mo

    Present address: Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, Indiana, 46285, USA

  3. Faizah Al-Mjeni

    Present address: Department of Chemistry, College of Science, Sultan Qaboos University, P.O. Box 36, Al-Khod, PC123, Sultanate of Oman

Authors and Affiliations

  1. Department of Chemistry, Brandeis University, MS 015, 415 South Street, Waltham, 02454-9110, Massachusetts, USA

    Thomas C. Pochapsky, Susan Sondej Pochapsky, Tingting Ju & Huaping Mo

  2. Department of Chemistry, University of Massachusetts, Amherst, 01003-9336, Massachusetts, USA

    Faizah Al-Mjeni

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  1. Thomas C. Pochapsky
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Correspondence to Thomas C. Pochapsky.

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Pochapsky, T., Pochapsky, S., Ju, T. et al. Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat Struct Mol Biol 9, 966–972 (2002). https://doi.org/10.1038/nsb863

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