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Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction

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Science  18 Aug 2017:
Vol. 357, Issue 6352, pp. 699-703
DOI: 10.1126/science.aan0425
  • Fig. 1 Reaction and structure of the heterodisulfide reductase [NiFe]–hydrogenase complex (HdrABC-MvhAGD) from M. thermolithotrophicus.

    (A) The catalytic reaction. The HdrABC-MvhAGD complex catalyzes the oxidation of two H2 (E0’ = −414 mV) and directs the two electrons of each H2 one by one toward CoM-S-S-CoB (E0’ = −140 mV) and the free electron-carrier ferredoxin (E0’ = ~−500 mV) via a flavin-based electron bifurcation process. (B) Overall structure. MvhA (green) and HdrB (purple), the sites of H2 oxidation and heterodisulfide reduction, are located at the periphery of the protein complex and are connected to the central HdrA (orange) by MvhG (cyan) and MvhD (yellow) as well as HdrC (light pink), which serve as electron-transfer units. Flavin, [4Fe-4S] clusters, and [NiFe] centers are depicted in ball and stick. (C) Architecture [top view of (B)] of HdrA with the following color code: N-terminal (blue), thioredoxin-reductase (orange), inserted ferredoxin (green), and C-terminal ferredoxin domains (red). (D) Distribution of the redox cofactors of one HdrABC-MvhAGD protomer. The colors are chosen as in (B).

  • Fig. 2 The noncubane [4Fe-4S] clusters bound to the HdrBC subcomplex.

    (A) Global view of the iron-sulfur clusters involved in heterodisulfide reduction. The proximal and distal noncubane [4Fe-4S] clusters are located at the bottom of the cleft formed by HdrB and the C-terminal arm of HdrC and supplied with electrons via a normal [4Fe-4S] cluster of HdrC. (B and C) Stereoview of the (B) proximal and (C) distal noncubane [4Fe-4S] clusters. The 2Fo-Fc electron density map is contoured at 8.0 σ (black mesh and light red surface). The Gly and cis-Pro residues at the equivalent positions of the CCG motifs are part of two loop segments involved in the noncubane [4Fe-4S] clusters and substrate binding. The unfavorable dihedral angle and the cis-peptide bond are allowed only for Gly and Pro, respectively, which might be crucial to adjust the conformation of this loop.

  • Fig. 3 The heterodisulfide reduction reaction.

    (A) Active-site structures of HdrBC with coenzyme M covalently bound to the proximal noncubane [4Fe-4S] cluster (left) and bromoethanesulfonate (right). The distance between Fe and S is 2.7 Å, and that between Fe and Br is 3.5 Å. The Br atom was detected using anomalous scattering, as shown as a magenta mesh and surface. (B) The structure of the active site of HdrB soaked with 66 mM heterodisulfide and incubated at 18°C for 2 min (left) and 3.5 min (right). The catalytic reaction was followed in cristallo, and its dynamics became visible by the decreasing occupancy of CoB-SH as a function of time. This time-dependent intermediate-trapping process was observed at only one HdrBC subcomplex of the HdrABC-MvhAGD heterododecamer. The other only contains coenzyme M covalently bound to the Fe. The 2Fo-Fc electron density map was contoured at 1.5 σ (black mesh and cyan surface). (C) Proposed catalytic mechanism of the heterodisulfide reduction. CoM-S-S-CoB is homolytically cleaved, and the sulfurs are bound to the Fe-S clusters, which thereby become oxidized. CoB-SH and CoM-SH are released after successive single-electron reduction.

  • Fig. 4 Proposed electron-transfer pathway.

    The different subunits have the same color code as in Fig. 1B. The solid arrows indicate the electron-transfer pathway composed of iron-sulfur clusters at distances less than 13.5 Å. The dashed arrows correspond to a hypothetical electron-transfer pathway with distances longer than 15 Å between the redox centers. The determined HdrABC-MvhAGD structure allows alternative scenarios for conformational changes to conduct the flavin-based electron bifurcation process (fig. S15).

Supplementary Materials

  • Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction

    Tristan Wagner, JuÌ^rgen Koch, Ulrich Ermler, Seigo Shima

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs S1 to S16
    • Table S1
    • References

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