Methyl coenzyme M reductase

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Methyl coenzyme M reductase

Existing structural data : 3SQG , 1MRO

Secondary to quaternary structure C 2 -symmetric α 2 β 2 γ 2 complex
Cofactor F430
Identifier
Gene name (s) McrA, McrB, McrG
Enzyme classification
EC, category 2.8.4.1 ,  transferase
Response type Transfer of hydrogen to methyl
Substrate Methyl coenzyme M, coenzyme B
Products Methane, CoB-SS-CoM
Occurrence
Parent taxon Archaea

The enzyme methyl-coenzyme-M-reductase catalyzes the last step of the biological methane formation . In the catalytic reaction , the methyl thioether methyl coenzyme M is converted with the thiol coenzyme B to methane and the corresponding heterodisulfide:

Me-S-CoM + CoB-SH → CH 4 + CoB-SS-CoM ΔG ° '= −30 kJ mol −1

Occurrence and function

Methyl coenzyme M reductase occurs in all methanogenic archaea , regardless of whether the substrate is CO 2 , formate , carbon monoxide , acetate or a methyl group ( methanol , dimethyl sulfide or methylamine ). In anerobic methanotrophic archaea ( ANME archaea), methyl-coenzyme-M-reductase is used for methane activation . Methane is converted into methyl coenzyme M in the process.

Function as a phylogenetic marker

Because the methyl coenzyme M reductase is found in all methanogenic and methanotrophic archaea, the mcrA gene can be used as a phylogenetic marker for these organisms.

structure

Methyl coenzyme M reductase consists of three different protein chains , which as a C 2 -symmetric α 2 β 2 γ 2 - complex composed. Two molecules of the nickel hydrocorphinate F 430 form the active sites. Methyl-coenzyme-M-reductase could be crystallized by methanogens as well as methanotrophic organisms and the corresponding X-ray structures are published.

Activation of methyl coenzyme M reductase

The enzyme is only catalytically active if the nickel ion in cofactor F430 is in the Ni (I) oxidation state . In the more stable oxidation state Ni (II), the enzyme is inactive and must be converted into the active Ni (I) form by means of an ATP- dependent enzyme complex.

reaction

The enzymatic reaction is a conversion of an alkyl thioether (methyl coenzyme M) with a thiol (coenzyme B) to an alkane (methane) and a disulfide (CoB-SS-CoM). Such a chemical reaction has never been possible in the laboratory be performed. The elucidation of the reaction mechanism is therefore of particular interest to chemists .

mechanism

The reaction mechanism of methyl coenzyme M reductase is still unclear.

Intermediates

With the natural substrates it could be shown that intermediate products are formed, but it has never been possible to spectroscopically characterize an intermediate product that occurs via the natural catalytic pathway. Studies with inhibitors and analogous substrates show that the enzyme has the ability to form Ni-H, Ni-C and Ni-S bonds , all of which could be proven by ESR spectroscopy .

S N 2 mechanism

An S N 2 mechanism would be analogous to vitamin B12 as a supernucleophile. In such a mechanism, Ni (I) (analogous to Co (I)) would nucleophilically attack the methyl group of methyl-coenzyme-M and lead to methyl-Ni (III) (analogous to methyl-Co (III)). Methyl Ni (III) would then be reduced and protonated to methane. This mechanism is able to explain the inversion on carbon, which could be shown with the help of chrial ethyl coenzyme M. Experimentally determined kinetic isotope effects seem to rule out an S N 2 mechanism.

Radical mechanism

A radical mechanism is compatible with the kinetic isotope effects . However, it is unclear how an inversion with chrial ethyl coenzyme M can be measured, since primary radicals invert quickly. For the reverse reaction (methane oxidation) such a mechanism would represent a CH activation on methane by means of a thiyl radical , which would be highly endergonic and has never been shown.

Alternative mechanisms

A Oxidative addition has been considered as the first step of methane oxidation into consideration. Another possibility is a protonation of coenzyme F430 as the first intermediate product.

Individual evidence

  1. ↑ InterPro entry
  2. ↑ B. Jaun, RK Thauer: Methyl-Coenzyme M Reductase and its Nickel Corphin Coenzyme F430 in Methanogenic Archaea. In: Astrid Sigel, Helmut Sigel, Roland KO Sigel: Nickel and Its Surprising Impact in Nature: Metal Ions in Life Sciences. Volume 2, John Wiley & Sons 2007, ISBN 978-0470028124 , 323-356.
  3. ^ A b Rudolf K. Thauer: Biochemistry of methanogenesis: a tribute to Marjory Stephenson : 1998 Marjory Stephenson Prize Lecture. In: Microbiology. 144, No. 9, 1998, pp. 2377-2406, doi : 10.1099 / 00221287-144-9-2377 , PMID 9782487 .
  4. ↑ Steven J. Hallam, Nik Putnam, Christina M. Preston, John C. Detter, Daniel Rokhsar, Paul M. Richardson, Edward F. DeLong: Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics. In: Science. 305, No. 5689, 2004, pp. 1457-1462, doi : 10.1126 / science.1100025 , PMID 15353801 .
  5. ↑ Silvan Scheller, Meike Goenrich, Reinhard Boecher, Rudolf K. Thauer, Bernhard Jaun: The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. In: Nature. 465, No. 7298, 2010, pp. 606-608, doi : 10.1038 / nature09015 .
  6. ↑ Michael W. Friedrich: Methyl ‐ Coenzyme M Reductase Genes: Unique Functional Makers for Methanogenic and Anaerobic Methane ‐ Oxidizing Archaea. In: Methods in Enzymology. Volume 397,2005, ISSN  0076-6879 , pp. 428-442.
  7. ↑ Ulrich Ermler, Wolfgang Grabarse, Seigo Shima, Marcel Goubeaud, Rudolf K. Thauer: Crystal Structure of Methyl-Coenzyme M Reductase: The Key Enzyme of Biological Methane Formation. In: Science. 278, No. 5342, 1997, pp. 1457-1462, doi : 10.1126 / science.278.5342.1457 , PMID 9367957 .
  8. ↑ Seigo Shima, Martin Krueger, Tobias Weinert, Ulrike Demmer, Jörg Kahnt, Rudolf K. Thauer, Ulrich Ermler: Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. In: Nature. 481, No. 7379, 2012, pp. 98-101, doi : 10.1038 / nature10663 .
  9. ↑ S. Rospert, R. Böcher, SPJ Albracht, RK Thauer: methyl coenzyme M reductase preparations with high specific activity from H2-preincubated cells of methanobacterium thermoautotrophicum. In: FEBS Letters. 291, No. 2, 1991, pp. 371-375, doi : 10.1016 / 0014-5793 (91) 81323-Z .
  10. ↑ Divya Prakash, Yonnie Wu, Sang-Jin Suh, Evert C. Duin: Elucidating the Process of Activation of Methyl-Coenzyme M Reductase. In: Journal of Bacteriology. 196, No. 13, 2014, pp. 2491-2498, doi : 10.1128 / JB.01658-14 , PMID 24769699 .
  11. ↑ a b c d Silvan Scheller, Meike Goenrich, Rudolf K. Thauer, Bernhard Jaun: Methyl-Coenzyme M Reductase from Methanogenic Archaea: Isotope Effects on the Formation and Anaerobic Oxidation of Methane. In: Journal of the American Chemical Society. 135, No. 40, 2013, pp. 14975–14984, doi : 10.1021 / ja406485z .
  12. ↑ a b Silvan Scheller, Meike Goenrich, Stefan Mayr, Rudolf K. Thauer, Bernhard Jaun: Intermediate products in the catalytic cycle of methyl-coenzyme-M-reductase: the pattern of isotope exchange is consistent with the formation of a σ-alkane-nickel complex . In: Angewandte Chemie. 122, No. 44, 2010, pp. 8289-8292, doi : 10.1002 / anie.201003214 .
  13. ↑ Jeffrey Harmer et al: A Nickel Hydride Complex in the Active Site of Methyl-Coenzyme M Reductase: Implications for the Catalytic Cycle. In: Journal of the American Chemical Society. 130, No. 33, 2008, pp. 10907-10920, doi : 10.1021 / ja710949e .
  14. ↑ B. Jaun, RK Thauer, Met. Ions Life Sci. 2009, 6, 115;
  15. ^ R. Sarangi, M. Dey, SW Ragsdale, Biochemistry 2009, 48, 3146
  16. ↑ Na Yang, Markus Reiher, Mi Wang, Jeffrey Harmer, Evert C. Duin: Formation of a Nickel − Methyl Species in Methyl-Coenzyme M Reductase, an Enzyme Catalyzing Methane Formation. In: Journal of the American Chemical Society. 129, No. 36, 2007, pp. 11028-11029, doi : 10.1021 / ja0734501 .
  17. ↑ Dariush Hinderberger, Rafal P. Piskorski, Meike Goenrich, Rudolf K. Thauer, Arthur Schweiger, Jeffrey Harmer, Bernhard Jaun: A Nickel – Alkyl Bond in an Inactivated State of the Enzyme Catalyzing Methane Formation. In: Angewandte Chemie International Edition. 45, No. 22, 2006, pp. 3602-3607, doi : 10.1002 / anie.200600366 .
  18. ↑ Jeffrey Harmer et al: Spin Density and Coenzyme M Coordination Geometry of the ox1 Form of Methyl-Coenzyme M Reductase: A Pulse EPR Study. In: Journal of the American Chemical Society. 127, No. 50, 2005, pp. 17744-17755, doi : 10.1021 / ja053794w .
  19. ↑ David Dophin: Preparation of the reduced forms of vitamin B12 and of some analogs of the vitamin B12 coenzyme Containing a cobalt-carbon bond. In: D. Dolphin: Donald B. McCormick and Lemuel D. Wright (Eds.): Methods in Enzymology. Volume 18, Part C, 1971, ISSN  0076-6879 , pp. 34-52.
  20. ↑ Bernhard Jaun: Coenzyme F430 from Methanogenic Bacteria: Oxidation of F430 Pentamethyl Ester to the Ni (III) Form. In: Helvetica Chimica Acta. 73, No. 8, 1990, pp. 2209-2217, doi : 10.1002 / hlca.19900730818 .
  21. ↑ Xianghui Li, Joshua Telser, Ryan C. Kunz, Brian M. Hoffman, Gary Gerfen, Stephen W. Ragsdale: Observation of Organometallic and Radical Intermediates Formed during the Reaction of Methyl-Coenzyme M Reductase with Bromoethanesulfonate. In: Biochemistry. 49, No. 32, 2010, pp. 6866-6876, doi : 10.1021 / bi100650m .
  22. ↑ a b Yonghyun Ahn, Joseph A. Krzycki, Heinz G. Floss: Steric course of the reduction of ethyl coenzyme M to ethane catalyzed by methyl coenzyme M reductase from Methanosarcina barkeri. In: Journal of the American Chemical Society. 113, No. 12, 1991, pp. 4700-4701, doi : 10.1021 / ja00012a059 .
  23. ↑ Vladimir Pelmenschikov, Margareta RA Blomberg, Per EM Siegbahn, Robert H. Crabtree: A Mechanism from Quantum Chemical Studies for Methane Formation in Methanogenesis. In: Journal of the American Chemical Society. 124, No. 15, 2002, pp. 4039-4049, doi : 10.1021 / ja011664r .
  24. ↑ Shi-Lu Chen, Margareta RA Blomberg, Per EM Siegbahn: An investigation of possible competing mechanisms for Ni-containing methyl-coenzyme M reductase. In: Physical Chemistry Chemical Physics. 16, No. 27, 2014, pp. 14029-14035, doi : 10.1039 / C4CP01483A .
  25. ^ Evert C. Duin, Michael L. McKee: A New Mechanism for Methane Production from Methyl-Coenzyme M Reductase As Derived from Density Functional Calculations. In: The Journal of Physical Chemistry B. 112, No. 8, 2008, pp. 2466-2482, doi : 10.1021 / jp709860c .