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O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas

Nature Catalysis volume 5, pages 807–817 (2022)Cite this article

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Abstract

Ni–Fe carbon monoxide dehydrogenases (CODHs) are nearly diffusion-limited biocatalysts that oxidize CO. Their O2 sensitivity, however, is a major drawback for industrial applications. Here we compare the structures of a fast CODH with a high O2 sensitivity (ChCODH-II) and a slower CODH with a lower O2 sensitivity (ChCODH-IV) (Ch, Carboxydothermus hydrogenoformans). Some variants obtained by simple point mutations of the bottleneck residue (A559) in the gas tunnel showed 61–148-fold decreases in O2 sensitivity while maintaining high turnover rates. The variant structure A559W showed obstruction of one gas tunnel, and molecular dynamics supported the locked position of the mutated side chain in the tunnel. The variant was exposed to different gas mixtures, from simple synthetic gas to sophisticated real flue from a steel mill. Its catalytic properties remained unchanged, even at high O2 levels, and the efficiency was maintained for multiple cycles of CO detoxification/regeneration.

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Fig. 1: Discovery of the bottleneck for the O2 response in Ni–Fe CODHs.
Fig. 2: O2 sensitivity of Ni–Fe CODHs and its variants.
Fig. 3: Structures of less O2-sensitive ChCODH-II variants.
Fig. 4: Efficient CO removal of ChCODH-II A559W.
Fig. 5: Repeated reuse of immobilized A559W.

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Data availability

The datasets generated during and/or analysed during the current study are available from the corresponding authors upon reasonable request. MD trajectories of a total of 5 ns are available on Zenodo at https://doi.org/10.5281/zenodo.6865415. The atomic coordinates and structure factors for the ChCODH-II A559 variants have been deposited in the Protein Data Bank under accession codes PDB 7ERR, 7XDM, 7XDN and 7XDP.

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Acknowledgements

This research was supported by the C1 Gas Refinery Program and the Engineering Research Center Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Science, ICT & Future Planning (2015M3D3A1A01064919 and 2020R1A5A1019631, respectively).

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Author notes

  1. These authors contributed equally: Suk Min Kim, Jinhee Lee, Sung Heuck Kang, Yoonyoung Heo.

  2. These authors jointly supervised this work: Hyung Ho Lee, Yong Hwan Kim.

Authors and Affiliations

  1. School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea

    Suk Min Kim, Jinhee Lee, Sung Heuck Kang & Yong Hwan Kim

  2. School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea

    Sung Heuck Kang & Ji-Sook Hahn

  3. Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea

    Yoonyoung Heo, Hye-Jin Yoon & Hyung Ho Lee

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Contributions

Y.H.K. and S.M.K. conceived and planned all the experiments. S.M.K. performed the bioinformatic analysis and gene cloning. S.M.K. and J.L. performed the biochemical characterization, kinetic analysis and feasibility evaluation, all under the supervision of Y.H.K. S.M.K. and S.H.K. engineered the gas tunnels and performed their structural analysis. Y.H.K., S.M.K. and J.-S.H. wrote the manuscript. H.H.L., H.-J.Y. and Y.H. determined the crystal structure. Y.H.K., H.H.L. and J.-S.H. reviewed the manuscript.

Corresponding authors

Correspondence to Hyung Ho Lee or Yong Hwan Kim.

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Nature Catalysis thanks Tristan Wagner, Anna Rovaletti, Stephen Ragsdale and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Kim, S.M., Lee, J., Kang, S.H. et al. O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas. Nat Catal 5, 807–817 (2022). https://doi.org/10.1038/s41929-022-00834-y

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