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Structural basis for bacterial energy extraction from atmospheric hydrogen.

<div class='caption-title'>a, Gas chromatography analysis of the H2 concentration of the headspace of sealed vials containing Huc or no enzyme, with 200 μM menadione as the electron acceptor. Huc can oxidize H2 below atmospheric concentrations (violet line) to the limit of detection (green line). conc., concentration. b, Gas chromatography analysis of vials containing Huc, E. coli Hyd1, or no enzyme, with 200 μM NBT as the electron acceptor. Huc—but not Hyd1—can oxidize H2 at sub-atmospheric levels. c, Michaelis–Menten kinetics of H2 oxidation by Huc in buffer with different percentages of O2 saturation, with 200 μM menadione (the 0% O2 comprises degassed buffer with traces of O2). d, Michaelis–Menten kinetics of Huc H2 consumption in buffer with different electron acceptors, degassed but with traces of O2. In a–d, data are mean ± s.d. Vmax, maximum velocity. e, Cyclic voltammogram of an immobilized Huc protein film in a 100% H2 atmosphere. Eonset is the Huc onset potential determined from the average of four experiments (a single representative curve is shown for clarity). η is the estimated Huc overpotential compared to the 2H+/H2 redox couple potential (E2H+/H20′). The midpoint potentials of benzyl viologen (EBV2+/BV⋅+0′) and menaquinone (EMQ/MQH20′) are indicated. SHE, standard hydrogen electrode. f, Cyclic voltammogram of an immobilized Huc protein film with a gas mixture flushing through the headspace comprising argon, N2 and the indicated level of H2. The dashed vertical lines indicate the potential of the 2H+/H2 couple and Huc onset potential, calculated for 5% H2 at ambient pressure. Scans were recorded in the order of low to high H2. The inset plot shows a zoomed view of the voltage response of Huc at low H2 partial pressures.</div>
<div class='caption-title'>Huc forms an 833-kDa oligomer comprising HucS, HucL and HucM.</div>
<div class='caption-title'>a, A stereo view of the Huc [NiFe] cluster under ambient air. b, The structure of the three HucS [3Fe–4S] clusters. c, High-temperature (30K) EPR spectra of Huc in the as-isolated oxidized state (Huc-Air) and the H2-reduced state (Huc-H2). The isotropic signal at g = 2.03 (g is the Landé factor) is associated with the oxidized [3Fe–4S]+ clusters, which disappears in Huc-H2 owing to reduction of the clusters. No signal attributable to reduced [4Fe–4S]+ clusters is discernible in the H2-treated form of Huc. d, FTIR spectra of oxidized Huc isolated in ambient air, showing that the [NiFe] active site of the enzyme adopts an oxidized state consistent with an Ni-B state. e, The Huc [NiFe] active site, showing the relative distances between the Ni-B state hydroxyl ligand and the Ni and Fe ions of the cluster. f, The HucSL dimer, showing the location and width of the hydrophobic gas channels that provide substrate access to the [NiFe] active site. g, Left, plot of distance versus time, showing the closest distance between H2 and the Huc [NiFe] active site during molecular dynamics simulations of HucSL in the presence of H2. Right, the location of H2 molecules in a representative subset of simulation frames when H2 molecules are in the closest proximity to the active site. h, Similar to g, but shows location of O2 relative to the Huc [NiFe] site in simulations of HucSL performed in the presence of O2. i, The proximity of HucL d-His166 to the proximal and medial [3Fe–4S] clusters and the location of the unknown ligand. Cryo-EM density potential maps in a,b,i are shown as a transparent blue surface at 5σ.</div>
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
OpenAccess logo Nature (2023)
Related entries: 7utd, 7uus, 8dqv

Cited: 17 times
EuropePMC logo PMID: 36890228

Abstract

Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival1. This globally significant process regulates the composition of the atmosphere, enhances soil biodiversity and drives primary production in extreme environments2,3. Atmospheric H2 oxidation is attributed to uncharacterized members of the [NiFe] hydrogenase superfamily4,5. However, it remains unresolved how these enzymes overcome the extraordinary catalytic challenge of oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2 and how the derived electrons are transferred to the respiratory chain1. Here we determined the cryo-electron microscopy structure of the Mycobacterium smegmatis hydrogenase Huc and investigated its mechanism. Huc is a highly efficient oxygen-insensitive enzyme that couples oxidation of atmospheric H2 to the hydrogenation of the respiratory electron carrier menaquinone. Huc uses narrow hydrophobic gas channels to selectively bind atmospheric H2 at the expense of O2, and 3 [3Fe-4S] clusters modulate the properties of the enzyme so that atmospheric H2 oxidation is energetically feasible. The Huc catalytic subunits form an octameric 833 kDa complex around a membrane-associated stalk, which transports and reduces menaquinone 94 Å from the membrane. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H2 oxidation, uncover a mode of energy coupling dependent on long-range quinone transport, and pave the way for the development of catalysts that oxidize H2 in ambient air.

Reviews - 7uur mentioned but not cited (1)

  1. Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion. Greening C, Kropp A, Vincent K, Grinter R. Biochem Soc Trans 51 1921-1933 (2023)

Articles - 7uur mentioned but not cited (1)

  1. Protein target highlights in CASP15: Analysis of models by structure providers. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Proteins 91 1571-1599 (2023)


Reviews citing this publication (5)

  1. Outer-sphere effects on the O2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases. Fasano A, Fourmond V, Léger C. Chem Sci 15 5418-5433 (2024)
  2. Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis. Ray AE, Tribbia DZ, Cowan DA, Ferrari BC. Microbiol Mol Biol Rev 87 e0004823 (2023)
  3. Health Benefits of Electrolyzed Hydrogen Water: Antioxidant and Anti-Inflammatory Effects in Living Organisms. Hu D, Kabayama S, Watanabe Y, Cui Y. Antioxidants (Basel) 13 313 (2024)
  4. Novel concepts and engineering strategies for heterologous expression of efficient hydrogenases in photosynthetic microorganisms. Schumann C, Fernández Méndez J, Berggren G, Lindblad P. Front Microbiol 14 1179607 (2023)
  5. The missing pieces in the catalytic cycle of [FeFe] hydrogenases. Lachmann MT, Duan Z, Rodríguez-Maciá P, Birrell JA. Chem Sci (2024)

Articles citing this publication (10)

  1. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15. Ozden B, Kryshtafovych A, Karaca E. Proteins 91 1636-1657 (2023)
  2. CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. Mulvaney T, Kretsch RC, Elliott L, Beton JG, Kryshtafovych A, Rigden DJ, Das R, Topf M. Proteins 91 1935-1951 (2023)
  3. CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction. Pang M, He W, Lu X, She Y, Xie L, Kong R, Chang S. BMC Bioinformatics 24 444 (2023)
  4. Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures. Leung PM, Grinter R, Tudor-Matthew E, Lingford JP, Jimenez L, Lee HC, Milton M, Hanchapola I, Tanuwidjaya E, Kropp A, Peach HA, Carere CR, Stott MB, Schittenhelm RB, Greening C. Nat Commun 15 3219 (2024)
  5. Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition. Baril X, Constant P. FEMS Microbiol Ecol 99 fiad159 (2023)
  6. Editorial Hidden hydrogen cycles in the ocean. Nat Microbiol 8 563-564 (2023)
  7. Marine sponge microbe provides insights into evolution and virulence of the tubercle bacillus. Pidot SJ, Klatt S, Ates LS, Frigui W, Sayes F, Majlessi L, Izumi H, Monk IR, Porter JL, Bennett-Wood V, Seemann T, Otter A, Taiaroa G, Cook GM, West N, Tobias NJ, Fuerst JA, Stutz MD, Pellegrini M, McConville M, Brosch R, Stinear TP. PLoS Pathog 20 e1012440 (2024)
  8. Structure of Aquifex aeolicus lumazine synthase by cryo-electron microscopy to 1.42 Å resolution. Savva CG, Sobhy MA, De Biasio A, Hamdan SM. IUCrJ 11 723-729 (2024)
  9. Structure of a fully assembled γδ T cell antigen receptor. Gully BS, Ferreira Fernandes J, Gunasinghe SD, Vuong MT, Lui Y, Rice MT, Rashleigh L, Lay CS, Littler DR, Sharma S, Santos AM, Venugopal H, Rossjohn J, Davis SJ. Nature 634 729-736 (2024)
  10. Unveiling the Low-Lying Spin States of [Fe3S4] Clusters via the Extended Broken-Symmetry Method. Chu S, Gao Q. Molecules 29 2152 (2024)


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