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Molecular mechanism of energy conservation in polysulfide respiration

Abstract

Bacterial polysulfide reductase (PsrABC) is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. We determined the structure of polysulfide reductase from Thermus thermophilus at 2.4-Å resolution, revealing how the PsrA subunit recognizes and reduces its unique polyanionic substrate. The integral membrane subunit PsrC was characterized using the natural substrate menaquinone-7 and inhibitors, providing a comprehensive representation of a quinone binding site and revealing the presence of a water-filled cavity connecting the quinone binding site on the periplasmic side to the cytoplasm. These results suggest that polysulfide reductase could be a key energy-conserving enzyme of the T. thermophilus respiratory chain, using polysulfide as the terminal electron acceptor and pumping protons across the membrane via a previously unknown mechanism.

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Figure 1: Overall structure of Psr.
Figure 2: Stereoviews of the active site.
Figure 3: Structure of the integral membrane subunit.
Figure 4: Quinone binding site in hb1.

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Acknowledgements

This study was supported by the Australian Research Council (ARC; DP0666970 to M.J.), the European Membrane Protein Consortium (EU-PF6 E-MEP to S.I.) and Grants-in-Aid from the Ministry of Education, Science, Sports and Culture of Japan (No. 18370055 and No. 19042008 to K.Y.). M.J. was a recipient of the European Molecular Biology Organization (EMBO) Long-term Fellowship. Data collection was done at the European Synchrotron Radiation Facility (ESRF) and GM/CA-CAT at Advanced Photon Source (APS). We acknowledge the support of S. Corcoran, N. Venugopolan and M. Becker at GM/CA-CAT, and beamline scientists at ID23-1, ESRF, for scientific support and assistance with data collection. GM/CA-CAT beamline (ID23) is supported by the US National Cancer Institute and the US National Institute of General Medical Science. Visits to APS were supported by the Australian Nuclear Science Technology Organization (ANSTO). Part of the work was performed at the Membrane Protein Laboratory at Diamond Light Source, UK, which is funded by Wellcome Trust grant 079209/Z/06/Z. We thank U. Kappler, M. Maher, M. Rapp, B. Byrne and L. Carpenter for critical assessment of the manuscript.

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K.Y. and M.J. designed the research; K.Y. and T.Y. oversaw experimental design of biochemical studies, largely performed by S.A.; M.T. performed protein expression and optimization; T.S. generated antibodies for protein detection; P.C. assisted with data collection and interpretation; M.J. performed Psr purification, crystallization, data collection and structure determination; M.J. and S.I. performed initial phasing and structure interpretation. M.J. and S.I. prepared the manuscript, and all authors discussed the results and commented on the manuscript.

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Correspondence to Mika Jormakka or So Iwata.

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Jormakka, M., Yokoyama, K., Yano, T. et al. Molecular mechanism of energy conservation in polysulfide respiration. Nat Struct Mol Biol 15, 730–737 (2008). https://doi.org/10.1038/nsmb.1434

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