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Structural basis of enzymatic benzene ring reduction

Nature Chemical Biology volume 11, pages 586–591 (2015)Cite this article

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A Corrigendum to this article was published on 17 September 2015

An Erratum to this article was published on 18 August 2015

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Abstract

In chemical synthesis, the widely used Birch reduction of aromatic compounds to cyclic dienes requires alkali metals in ammonia as extremely low-potential electron donors. An analogous reaction is catalyzed by benzoyl–coenzyme A reductases (BCRs) that have a key role in the globally important bacterial degradation of aromatic compounds at anoxic sites. Because of the lack of structural information, the catalytic mechanism of enzymatic benzene ring reduction remained obscure. Here, we present the structural characterization of a dearomatizing BCR containing an unprecedented tungsten cofactor that transfers electrons to the benzene ring in an aprotic cavity. Substrate binding induces proton transfer from the bulk solvent to the active site by expelling a Zn2+ that is crucial for active site encapsulation. Our results shed light on the structural basis of an electron transfer process at the negative redox potential limit in biology. They open the door for biological or biomimetic alternatives to a basic chemical synthetic tool.

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Figure 1: Chemical Birch reduction of benzoic acid and enzymatic benzoyl-CoA reduction.
Figure 2: Bam(BC)2 overall structure and redox center arrangement.
Figure 3: Analysis of the bisWPT cofactor.
Figure 4: The BamBCisol and BamBCCoA states.
Figure 5: Molecular basis of the proton-coupled electron transfer steps.

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Change history

  • 07 July 2015

    In the version of this article initially published online, the final intermediate in Figure 1a was originally depicted as a fully delocalized radical anion, which was incorrect. The error has been corrected for the print, PDF and HTML versions of this article.

  • 21 July 2015

    In the version of this article initially published, the PDB code for the structure of BamBC as isolated was listed as 4Z4O, which was incorrect. The correct code is 4Z40. The error has been corrected for the PDF and HTML versions of this article.

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Acknowledgements

This work was funded by the German Research Foundation (DFG) in the SPP1319 (BO 1565/10-2 and ER 222/5), by the European Cooperation in Science and Technology Action CM1201 and the Swiss National Foundation for Scientific Research (SNF) (Doc.Mobility grant nos. P1SKP3-148452 and P1SKP3-155073). Work at the University of Saskatchewan was supported by the Canadian Research Chairs Program (G.N.G.), the Natural Sciences and Engineering Research Council of Canada and the Canadian Institutes of Health Research. J.J.H.C. is a CIHR-Training grant in Health Research Using Synchrotron Techniques (THRUST) Associate. The Stanford Synchrotron Radiation Lightsource is supported by the US Department of Energy and the National Institutes of Health. Work at the Helmholtz Center for Environmental Research, Leipzig, Germany (Department of Analytical Chemistry), was funded by the German Federal Ministry of Education and Research. Work at the University of Strasbourg was supported by the Centre International de Recherche aux Frontières de la Chimie (RFC) and the Centre National des Recherches Scientifiques (CNRS). We thank H. Michel for continuous support and the staff of beamline PXII at the Swiss Light Source for help during data collection.

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Author notes

  1. Tobias Weinert and Simona G Huwiler: These authors contributed equally to this work.

Authors and Affiliations

  1. Max Planck Institute of Biophysics, Frankfurt, Germany

    Tobias Weinert, Sina Weidenweber & Ulrich Ermler

  2. Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany

    Simona G Huwiler, Johannes W Kung & Matthias Boll

  3. Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg–CNRS, Strasbourg, France

    Petra Hellwig

  4. Department of Analytical Chemistry, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany

    Hans-Joachim Stärk

  5. Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany

    Till Biskup & Stefan Weber

  6. Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

    Julien J H Cotelesage & Graham N George

  7. Canadian Light Source, Saskatoon, Saskatchewan, Canada

    Julien J H Cotelesage

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Contributions

T.W. crystallized the enzyme collected, processed and refined X-ray data, and prepared figures; S.G.H. purified and characterized the enzyme, performed kinetic assays, prepared samples for spectroscopic analyses (EPR, FT-IR, EXAFS and ICP-MS) and carried out CN analyses and EPR measurements; S. Weidenweber processed and refined X-ray data; J.W.K. purified and characterized the enzyme, performed kinetic assays, and prepared samples for ICP-MS analyses; J.J.H.C. and G.N.G. collected and modeled EXAFS data; H.-J.S. conducted ICP-MS analyses; P.H. performed and interpreted FT-IR analyses; T.B. and S. Weber conducted and interpreted EPR measurements; U.E. and M.B. designed the study, analyzed data and wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Ulrich Ermler or Matthias Boll.

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Supplementary Results, Supplementary Figures 1–8 and Supplementary Tables 1–4 (PDF 1018 kb)

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Weinert, T., Huwiler, S., Kung, J. et al. Structural basis of enzymatic benzene ring reduction. Nat Chem Biol 11, 586–591 (2015). https://doi.org/10.1038/nchembio.1849

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