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Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase

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Abstract

Chlorite dismutase (Cld) is a heme enzyme capable of rapidly and selectively decomposing chlorite (ClO2 −) to Cl− and O2. The ability of Cld to promote O2 formation from ClO2 − is unusual. Heme enzymes generally utilize ClO2 − as an oxidant for reactions such as oxygen atom transfer to, or halogenation of, a second substrate. The X-ray crystal structure of Dechloromonas aromatica Cld co-crystallized with the substrate analogue nitrite (NO2 −) was determined to investigate features responsible for this novel reactivity. The enzyme active site contains a single b-type heme coordinated by a proximal histidine residue. Structural analysis identified a glutamate residue hydrogen-bonded to the heme proximal histidine that may stabilize reactive heme species. A solvent-exposed arginine residue likely gates substrate entry to a tightly confined distal pocket. On the basis of the proposed mechanism of Cld, initial reaction of ClO2 − within the distal pocket generates hypochlorite (ClO−) and a compound I intermediate. The sterically restrictive distal pocket probably facilitates the rapid rebound of ClO− with compound I forming the Cl− and O2 products. Common to other heme enzymes, Cld is inactivated after a finite number of turnovers, potentially via the observed formation of an off-pathway tryptophanyl radical species through electron migration to compound I. Three tryptophan residues of Cld have been identified as candidates for this off-pathway radical. Finally, a juxtaposition of hydrophobic residues between the distal pocket and the enzyme surface suggests O2 may have a preferential direction for exiting the active site.

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Abbreviations

ASU:

Asymmetric unit

Cld:

Chlorite dismutase

MES:

2-(N-Morpholino)ethanesulfonate

NCS:

Noncrystallographic symmetry

PDB:

Protein Data Bank

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Acknowledgments

This research was supported by the National Institutes of Health (R01 GM-66569 to C.M.W.; R03 ES-14390 and R01 GM-90260 to J.L.D.), and a Minnesota Partnership for Biotechnology and Medical Genomics grant SPAP-05-0013-P-FY06 to C.M.W. B.R.S. was supported by an Environmental Protection Agency STAR fellowship (FP-91690601-0). Computer resources were provided by the Basic Sciences Computing Laboratory of the University of Minnesota Supercomputing Institute, and we thank Can Ergenekan for his support. X-ray data were collected at the Kahlert Structural Biology Laboratory (KSBL) at The University of Minnesota and beamline 19-ID, Structural Biology Consortium–Collaborative Access Team, at the Advanced Photon Source, Argonne National Laboratory (Argonne, IL, USA). Argonne National Laboratory is operated by University of Chicago Argonne LLC for the US Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. We thank Ed Hoeffner for KSBL support and Steve Ginell and the staff at Sector 19, Advanced Photon Source, for their support.

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Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA

    Brandon R. Goblirsch & Carrie M. Wilmot

  2. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA

    Bennett R. Streit & Jennifer L. DuBois

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  1. Brandon R. Goblirsch
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  2. Bennett R. Streit
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  3. Jennifer L. DuBois
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  4. Carrie M. Wilmot
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Correspondence to Carrie M. Wilmot.

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Goblirsch, B.R., Streit, B.R., DuBois, J.L. et al. Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase. J Biol Inorg Chem 15, 879–888 (2010). https://doi.org/10.1007/s00775-010-0651-0

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