Binding of Coenzyme B Induces a Major Conformational Change in the Active Site of Methyl-Coenzyme M Reductase

Density functional calculations have been used to compare the geometric, electronic, and functional properties of the three important tetrapyrrole systems in biology, heme, coenzyme B 12, and coenzyme F430, formed from iron porphyrin ( Por ), cobalt corrin ( Cor ), and nickel hydrocorphin ( Hcor ). The results show that the flexibility of the ring systems follows the trend Hcor > Cor > Por and that the size of the central cavity follows the trend Cor < Por < Hcor . Therefore, low-spin Co I, Co II, and Co III fit well into the Cor ring, whereas Por seems to be more ideal for the higher spin states of iron, and the cavity in Hcor is tailored for the larger Ni ion, especially in the high-spin Ni II state. This is confirmed by the thermodynamic stabilities of the various combinations of metals and ring systems. Reduction potentials indicate that the +I and +III states are less stable for Ni than for the other metal ions. Moreover, Ni – C bonds are appreciably less stable than Co - C bonds. However, it is still possible that a Ni – CH 3 bond is formed in F 430 by a heterolytic methyl transfer reaction, provided that the donor is appropriate, e.g. if coenzyme M is protonated. This can be facilitated by the adjacent SO 3− group in this coenzyme and by the axial glutamine ligand, which stabilizes the Ni III state. Our results also show that a Ni III– CH 3 complex is readily hydrolysed to form a methane molecule and that the Ni III hydrolysis product can oxidize coenzyme B and M to a heterodisulphide in the reaction mechanism of methyl coenzyme M reductase.

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A Nickel Hydride Complex in the Active Site of Methyl-Coenzyme M Reductase: Implications for the Catalytic Cycle

Journal of the American Chemical Society ◽

10.1021/ja710949e ◽

2008 ◽

Vol 130 (33) ◽

pp. 10907-10920 ◽

Cited By ~ 42

Author(s):

Jeffrey Harmer ◽

Cinzia Finazzo ◽

Rafal Piskorski ◽

Sieglinde Ebner ◽

Evert C. Duin ◽

...

Keyword(s):

Active Site ◽

Catalytic Cycle ◽

Coenzyme M ◽

Hydride Complex ◽

Nickel Hydride ◽

Methyl Coenzyme M Reductase

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Mechanistic Studies of Methane Biogenesis by Methyl-Coenzyme M Reductase: Evidence that Coenzyme B Participates in Cleaving the C−S Bond of Methyl-Coenzyme M†

Biochemistry ◽

10.1021/bi011196y ◽

2001 ◽

Vol 40 (43) ◽

pp. 12875-12885 ◽

Cited By ~ 37

Author(s):

Yih-Chern Horng ◽

Donald F. Becker ◽

Stephen W. Ragsdale

Keyword(s):

Mechanistic Studies ◽

Coenzyme M ◽

Coenzyme B ◽

Methyl Coenzyme M Reductase

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Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales

Journal of Bacteriology ◽

10.1128/jb.00197-17 ◽

2017 ◽

Vol 199 (16) ◽

Cited By ~ 17

Author(s):

Tristan Wagner ◽

Carl-Eric Wegner ◽

Jörg Kahnt ◽

Ulrich Ermler ◽

Seigo Shima

Keyword(s):

Active Site ◽

Phylogenetic Analyses ◽

Methanogenic Archaea ◽

Methane Formation ◽

Type I ◽

Type Ii ◽

Coenzyme M ◽

Content Type ◽

Type Iii ◽

Methyl Coenzyme M Reductase

ABSTRACT The phylogenetically diverse family of methanogenic archaea universally use methyl coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteriales and Methanococcales contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from Methanobacteriales and Methanococcales into three distinct types: (i) MCRs from Methanobacteriales, (ii) MCRs from Methanobacteriales and Methanococcales, and (iii) MCRs from Methanococcales. The first and second types contain MCR isoenzymes I and II from Methanothermobacter marburgensis, respectively; therefore, they were designated MCR type I and type II and accordingly; the third one was designated MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from Methanotorris formicicus and Methanothermococcus thermolithotrophicus. As predicted, the three MCR types revealed highly similar overall structures and virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active-site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II, and III share most of the posttranslational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of M. formicicus a 6-hydroxy-tryptophan, which thus far has been found only in the α-amanitin toxin peptide but not in proteins. IMPORTANCE Methyl coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCRs suggested several distinct sequence clusters; those from Methanobacteriales and Methanococcales were subdivided into three types: MCR type I from Methanobacteriales, MCR type II from Methanobacteriales and Methanococcales, and the newly designated MCR type III exclusively from Methanococcales. We determined the first X-ray structures for an MCR type III. Detailed analyses revealed substantial differences between the three types only in the peripheral region. The subtle modifications identified and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from Methanotorris formicicus contains 6-hydroxy-tryptophan, a new posttranslational modification that thus far has been found only in the α-amanitin toxin.

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The Biosynthesis of Methylated Amino Acids in the Active Site Region of Methyl-coenzyme M Reductase

Journal of Biological Chemistry ◽

10.1074/jbc.275.6.3755 ◽

2000 ◽

Vol 275 (6) ◽

pp. 3755-3760 ◽

Cited By ~ 65

Author(s):

Thorsten Selmer ◽

Jörg Kahnt ◽

Marcel Goubeaud ◽

Seigo Shima ◽

Wolfgang Grabarse ◽

...

Keyword(s):

Amino Acids ◽

Active Site ◽

Coenzyme M ◽

Methyl Coenzyme M Reductase ◽

Active Site Region

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Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase

10.1101/211441 ◽

2017 ◽

Cited By ~ 3

Author(s):

Zhe Lyu ◽

Chau-wen Chou ◽

Hao Shi ◽

Ricky Patel ◽

Evert C. Duin ◽

...

Keyword(s):

Active Site ◽

Methane Formation ◽

Wild Type ◽

Coenzyme M ◽

Methane Cycle ◽

Gene Encoding ◽

Post Translational Modifications ◽

Whole Cells ◽

Type Gene ◽

Methyl Coenzyme M Reductase

AbstractCatalyzing the key step for anaerobic methane production and oxidation, methyl-coenzyme M reductase or Mcr plays a key role in the global methane cycle. The McrA subunit possesses up to five post-translational modifications (PTM) at its active site. Bioinformatic analyses had previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To examine its role, MMP1554, the gene encoding Mmp10 inMethanococcus maripaludis, was deleted with a new genetic tool, resulting in the specific loss of the 5-(S)-methylarginine PTM of residue 275 in the McrA subunit and a 40~60 % reduction in the maximal rates of methane formation by whole cells. Methylation was restored by complementations with the wild-type gene. However, the rates of methane formation of the complemented strains were not always restored to the wild type level. This study demonstrates the importance of Mmp10 and the methyl-Arg PTM on Mcr activity.

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