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Connecting the geometric and electronic structures of the nitrogenase iron–molybdenum cofactor through site-selective 57Fe labelling

Nature Chemistry volume 15, pages 658–665 (2023)Cite this article

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Abstract

Understanding the chemical bonding in the catalytic cofactor of the Mo nitrogenase (FeMo-co) is foundational for building a mechanistic picture of biological nitrogen fixation. A persistent obstacle towards this goal has been that the 57Fe-based spectroscopic data—although rich with information—combines responses from all seven Fe sites, and it has therefore not been possible to map individual spectroscopic responses to specific sites in the three-dimensional structure. Here we have addressed this challenge by incorporating 57Fe into a single site of FeMo-co. Spectroscopic analysis of the resting state informed on the local electronic structure of the terminal Fe1 site, including its oxidation state and spin orientation, and, in turn, on the spin-coupling scheme for the entire cluster. The oxidized resting state and the first intermediate in nitrogen fixation were also characterized, and comparisons with the resting state provided molecular-level insights into the redox chemistry of FeMo-co.

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Fig. 1: Employing site-selective isotopic labelling to understand the mechanism of biological nitrogen fixation.
Fig. 2: Postbiosynthetic incorporation of 57Fe into FeMo-co.
Fig. 3: Preparation and characterization of site-selectively labelled holo-NifDK samples.
Fig. 4: Characterization of the NifDK–M(57Fe1) sample.
Fig. 5: Redox changes at the Fe1 site of FeMo-co as revealed through studies of NifDK–M(57Fe1).

Data availability

Data supporting the findings of this work are available within the article and its Supplementary Information. Data supporting the current study are also available from the corresponding author upon request. PDB 3U7Q was used in the preparation of Fig. 1.

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Acknowledgements

We acknowledge the National Institutes of Health (GM141203 to D.L.M.S. and GM111097 to B.M.H.), the MIT Research Support Committee (to D.L.M.S.) and the National Science Foundation (MCB-1908587 to B.M.H.) for funding. We thank N. Thompson for helpful discussions as well as D. Dean and V. Cash for providing the Azotobacter vinelandii strains used in this work. Support for the ICP-MS instrument was provided by a core centre grant (P30-ES002109) from the National Institute of Environmental Health Sciences, NIH.

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Authors and Affiliations

  1. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA

    Edward D. Badding, Suppachai Srisantitham & Daniel L. M. Suess

  2. Department of Chemistry, Northwestern University, Evanston, IL, USA

    Dmitriy A. Lukoyanov & Brian M. Hoffman

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E.D.B., S.S. and D.A.L. performed the experiments. All authors contributed to the design of the study, data analysis and paper writing.

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Correspondence to Daniel L. M. Suess.

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Badding, E.D., Srisantitham, S., Lukoyanov, D.A. et al. Connecting the geometric and electronic structures of the nitrogenase iron–molybdenum cofactor through site-selective 57Fe labelling. Nat. Chem. 15, 658–665 (2023). https://doi.org/10.1038/s41557-023-01154-9

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