Abstract
The anaerobic oxidation of methane (AOM) with sulphate, an area currently generating great interest in microbiology, is accomplished by consortia of methanotrophic archaea (ANME) and sulphate-reducing bacteria1,2. The enzyme activating methane in methanotrophic archaea has tentatively been identified as a homologue of methyl-coenzyme M reductase (MCR) that catalyses the methane-forming step in methanogenic archaea3,4. Here we report an X-ray structure of the 280 kDa heterohexameric ANME-1 MCR complex. It was crystallized uniquely from a protein ensemble purified from consortia of microorganisms collected with a submersible from a Black Sea mat catalysing AOM with sulphate4. Crystals grown from the heterogeneous sample diffract to 2.1 Å resolution and consist of a single ANME-1 MCR population, demonstrating the strong selective power of crystallization. The structure revealed ANME-1 MCR in complex with coenzyme M and coenzyme B, indicating the same substrates for MCR from methanotrophic and methanogenic archaea. Differences between the highly similar structures of ANME-1 MCR and methanogenic MCR include a F430 modification, a cysteine-rich patch and an altered post-translational amino acid modification pattern, which may tune the enzymes for their functions in different biological contexts.
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Acknowledgements
This work was supported by the Max Planck Society, the Fonds der Chemischen Industrie, the Deutsche Forschungsgemeinschaft (SPP 1319, ER 222/5-1, KR 3311/6-2) and the projects MUMM, and BEBOP (Biogeochemistry and Microbiology of Bioherms Prospering in the Black Sea funded by the University of Hamburg). S.S. was financed by the PRESTO program, Japan Science and Technology Agency (JST). We are indebted to W. Michaelis and R. Seifert for access to samples. We thank the crews of RV Poseidon with JAGO for help during field work, M. Brefort and L. Känel for the electron spin resonance measurement and Edman sequencing, respectively. We are grateful to H. Michel for continuous support, the staff of the PXII beamline at the Swiss-Light-Source, Villigen for assistance during data collection, and K. Davies for critical reading of the manuscript.
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S.S., R.K.T. and U.E. designed the experiments, interpreted the data and wrote the paper. The mat sample from the Black Sea was collected and maintained by M.K. The enzyme was purified and characterized by M.K. and S.S. Crystallization was performed by S.S. and U.D.; U.E. collected the X-ray data. T.W. refined the structure and found that the primary structure conformed with that of the D1JBK2-4 sequences in the metagenome. J.K. performed the mass-spectrometric analyses.
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Atomic coordinates and structure factors of ANME-1 MCR have been deposited in the Protein Data Bank with the code 3SQG.
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Shima, S., Krueger, M., Weinert, T. et al. Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 481, 98–101 (2012). https://doi.org/10.1038/nature10663
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DOI: https://doi.org/10.1038/nature10663
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