Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically

Nature volume 481, pages 98–101 (2012)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Global architecture and active site of ANME-1 MCR.
Figure 2: Specific differences between ANME-1 and methanogenic MCRs.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

References

  1. Reeburgh, W. S. Oceanic methane biogeochemistry. Chem. Rev. 107, 486–513 (2007)

    Article  CAS  Google Scholar 

  2. Hallam, S. J. et al. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305, 1457–1462 (2004)

    Article  ADS  CAS  Google Scholar 

  3. Scheller, S., Goenrich, M., Boecher, R., Thauer, R. K. & Jaun, B. The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. Nature 465, 606–608 (2010)

    Article  ADS  CAS  Google Scholar 

  4. Krüger, M. et al. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426, 878–881 (2003)

    Article  ADS  Google Scholar 

  5. Meyerdierks, A. et al. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ. Microbiol. 12, 422–439 (2010)

    Article  CAS  Google Scholar 

  6. Knittel, K. & Boetius, A. Anaerobic oxidation of methane: progress with an unknown process. Annu. Rev. Microbiol. 63, 311–334 (2009)

    Article  CAS  Google Scholar 

  7. Losekann, T. et al. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl. Environ. Microbiol. 73, 3348–3362 (2007)

    Article  Google Scholar 

  8. Thauer, R. K. Anaerobic oxidation of methane with sulfate: on the reversibility of the reactions that are catalyzed by enzymes also involved in methanogenesis from CO2 . Curr. Opin. Microbiol. 14, 292–299 (2011)

    Article  CAS  Google Scholar 

  9. Thauer, R. K. & Shima, S. Methane as fuel for anaerobic microorganisms. Ann. NY Acad. Sci. 1125, 158–170 (2008)

    Article  ADS  CAS  Google Scholar 

  10. Nauhaus, K., Treude, T., Boetius, A. & Krüger, M. Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities. Environ. Microbiol. 7, 98–106 (2005)

    Article  CAS  Google Scholar 

  11. Heller, C., Hoppert, M. & Reitner, J. Immunological localization of coenzyme M reductase in anaerobic methane-oxidizing archaea of ANME 1 and ANME 2 type. Geomicrobiol. J. 25, 149–156 (2008)

    Article  CAS  Google Scholar 

  12. Mayr, S. et al. Structure of an F430 variant from archaea associated with anaerobic oxidation of methane. J. Am. Chem. Soc. 130, 10758–10767 (2008)

    Article  CAS  Google Scholar 

  13. Moran, J. J. et al. Methyl sulfides as intermediates in the anaerobic oxidation of methane. Environ. Microbiol. 10, 162–173 (2008)

    CAS  PubMed  Google Scholar 

  14. Kahnt, J. et al. Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea. FEBS J. 274, 4913–4921 (2007)

    Article  CAS  Google Scholar 

  15. Knittel, K., Losekann, T., Boetius, A., Kort, R. & Amann, R. Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microbiol. 71, 467–479 (2005)

    Article  CAS  Google Scholar 

  16. Grabarse, W. et al. On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding. J. Mol. Biol. 309, 315–330 (2001)

    Article  CAS  Google Scholar 

  17. Scheller, S., Goenrich, M., Mayr, S., Thauer, R. K. & Jaun, B. Intermediates in the catalytic cycle of methyl coenzyme M reductase: isotope exchange is consistent with formation of a σ-alkane–nickel complex. Angew. Chem. Int. Edn Engl. 49, 8112–8115 (2010)

    Article  CAS  Google Scholar 

  18. Dey, M., Li, X., Kunz, R. C. & Ragsdale, S. W. Detection of organometallic and radical intermediates in the catalytic mechanism of methyl-coenzyme M reductase using the natural substrate methyl-coenzyme M and a coenzyme B substrate analogue. Biochemistry 49, 10902–10911 (2010)

    Article  CAS  Google Scholar 

  19. Thauer, R. K. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. 1998 Marjory Stephenson Prize Lecture. Microbiology 144, 2377–2406 (1998)

    Article  CAS  Google Scholar 

  20. Satzger, H. et al. Photoswitchable elements within a peptide backbone-ultrafast spectroscopy of thioxylated amides. J. Phys. Chem. B 109, 4770–4775 (2005)

    Article  CAS  Google Scholar 

  21. Grove, T. L. et al. A radically different mechanism for S-adenosylmethionine-dependent methyltransferases. Science 332, 604–607 (2011)

    Article  ADS  CAS  Google Scholar 

  22. Krüger, M. et al. A novel, multi-layered methanotrophic microbial mat system growing on the sediment of the Black Sea. Environ. Microbiol. 10, 1934–1947 (2008)

    Article  Google Scholar 

  23. Michaelis, W. et al. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297, 1013–1015 (2002)

    Article  ADS  CAS  Google Scholar 

  24. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800 (1993)

    Article  CAS  Google Scholar 

  25. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  26. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  27. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    Article  CAS  Google Scholar 

  28. Afonine, P. V. et al. phenix. model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 43, 669–676 (2010)

    Article  CAS  Google Scholar 

  29. Grabarse, W., Mahlert, F., Shima, S., Thauer, R. K. & Ermler, U. Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation. J. Mol. Biol. 303, 329–344 (2000)

    Article  CAS  Google Scholar 

  30. Jensen, L. M., Sanishvili, R., Davidson, V. L. & Wilmot, C. M. In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex. Science 327, 1392–1394 (2010)

    Article  ADS  CAS  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. Max Planck Institute for Terrestrial Microbiology, Karl--Frisch-Strasse 10, D-35043 Marburg, Germany ,

    Seigo Shima, Jörg Kahnt & Rudolf K. Thauer

  2. PRESTO, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012 Japan ,

    Seigo Shima

  3. Federal Institute for Geosciences and Resources, Stilleweg 2, 30655 Hannover, Germany ,

    Martin Krueger

  4. Max Planck Institute for Biophysics, Max-von-Laue-Strasse 3, D-60438 Frankfurt, Germany ,

    Tobias Weinert, Ulrike Demmer & Ulrich Ermler

Authors
  1. Seigo Shima
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martin Krueger
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tobias Weinert
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ulrike Demmer
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jörg Kahnt
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Rudolf K. Thauer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ulrich Ermler
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

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.

Corresponding authors

Correspondence to Seigo Shima or Ulrich Ermler.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Atomic coordinates and structure factors of ANME-1 MCR have been deposited in the Protein Data Bank with the code 3SQG.

Supplementary information

Supplementary Information

The file contains Supplementary Tables 1-2, Supplementary Figures 1-5 with legends and additional references. (PDF 646 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature10663

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology