Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase

  1. Chris Furlan
  2. Nipa Chongdar
  3. Pooja Gupta
  4. Wolfgang Lubitz
  5. Hideaki Ogata
  6. James N Blaza  Is a corresponding author
  7. James A Birrell  Is a corresponding author
  1. University of York, United Kingdom
  2. Max Planck Institute for Chemical Energy Conversion, Germany
  3. Nara Institute of Science and Technology, Japan

Abstract

Electron-bifurcation is a fundamental energy conservation mechanism in nature in which two electrons from an intermediate potential electron donor are split so that one is sent along a high potential pathway to a high potential acceptor and the other is sent along a low potential pathway to a low potential acceptor. This process allows endergonic reactions to be driven by exergonic ones and is an alternative, less recognised, mechanism of energy coupling to the well-known chemiosmotic principle. The electron-bifurcating [FeFe] hydrogenase from Thermotoga maritima (HydABC) requires both NADH and ferredoxin to reduce protons generating hydrogen. The mechanism of electron-bifurcation in HydABC remains enigmatic in spite of intense research efforts over the last few years. Structural information may provide the basis for a better understanding of spectroscopic and functional information. Here, we present a 2.3 Å electron cryo-microscopy structure of HydABC. The structure shows a heterododecamer composed of two independent 'halves' each made of two strongly interacting HydABC heterotrimers connected via a [4Fe-4S] cluster. A central electron transfer pathway connects the active sites for NADH oxidation and for proton reduction. We identified two conformations of a flexible iron-sulfur cluster domain: a 'closed bridge' and an 'open bridge' conformation, where a Zn2+ site may act as a 'hinge' allowing domain movement. Based on these structural revelations, we propose a possible mechanism of electron-bifurcation in HydABC where the flavin mononucleotide serves a dual role as both the electron bifurcation center and as the NAD+ reduction/NADH oxidation site.

Data availability

Protein databank (PDB) files for the four model presented in this manuscript are available at https://www.rcsb.org/ under PDB ID 7P5H (D2 tetramer, 7P8N (Bridge closed forward), 7P91 (Bridge closed reverse), and 7P92 (Open bridge). Cryo-EM maps are available at https://www.ebi.ac.uk/pdbe/emdb/. All other data are available in the main text or the supplementary materials.

Article and author information

Author details

  1. Chris Furlan

    Department of Chemistry, University of York, York, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Nipa Chongdar

    Max Planck Institute for Chemical Energy Conversion, Muelheim an der Ruhr, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Pooja Gupta

    Department of Chemistry, University of York, York, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Wolfgang Lubitz

    Max Planck Institute for Chemical Energy Conversion, Muelheim an der Ruhr, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Hideaki Ogata

    Division of Materials Science, Nara Institute of Science and Technology, Nara, Japan
    Competing interests
    The authors declare that no competing interests exist.
  6. James N Blaza

    Department of Chemistry, University of York, York, United Kingdom
    For correspondence
    jamie.blaza@york.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5420-2116
  7. James A Birrell

    Max Planck Institute for Chemical Energy Conversion, Muelheim an der Ruhr, Germany
    For correspondence
    James.Birrell@cec.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0939-0573

Funding

Deutsche Forschungsgemeinschaft (BI 2198/1-1)

  • Nipa Chongdar
  • James A Birrell

UK Research and Innovation (MR/T040742/1)

  • James N Blaza

Japan Society for the Promotion of Science (JP20H03215)

  • Hideaki Ogata

Max-Planck-Gesellschaft (n/a)

  • Nipa Chongdar
  • Wolfgang Lubitz
  • James A Birrell

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Amie K Boal, Pennsylvania State University, United States

Publication history

  1. Preprint posted: September 13, 2021 (view preprint)
  2. Received: April 8, 2022
  3. Accepted: August 25, 2022
  4. Accepted Manuscript published: August 26, 2022 (version 1)
  5. Version of Record published: September 21, 2022 (version 2)

Copyright

© 2022, Furlan et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Chris Furlan
  2. Nipa Chongdar
  3. Pooja Gupta
  4. Wolfgang Lubitz
  5. Hideaki Ogata
  6. James N Blaza
  7. James A Birrell
(2022)
Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase
eLife 11:e79361.
https://doi.org/10.7554/eLife.79361

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