Component C of the methylreductase system of Methanobacterium

The crystal structure of methanogen McrD, a methyl-coenzyme M reductase-associated protein

Methyl-coenzyme M reductase (MCR) is a multi-subunit (α2β2γ2) enzyme responsible for methane formation via its unique F430 cofactor. The genes responsible for producing MCR (mcrA, mcrB and mcrG) are typically colocated with two other highly conserved genes mcrC and mcrD. We present here the high-resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin-like domain assembled into an α + β barrel-like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.

Model Organisms To Study Methanogenesis, a Uniquely Archaeal Metabolism

Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.

A Cobalamin-Dependent Radical SAM Enzyme Catalyzes the Unique Cα -Methylation of Glutamine in Methyl-Coenzyme M Reductase

Methyl‐coenzyme M reductase, which is responsible for the production of the greenhouse gas methane during biological methane formation, carries several unique posttranslational amino acid modifications, including a 2‐(S)‐methylglutamine. The enzyme responsible for the C_α‐methylation of this glutamine is not known. Herein, we identify and characterize a cobalamin‐dependent radical SAM enzyme as the glutamine C‐methyltransferase. The recombinant protein from Methanoculleus thermophilus binds cobalamin in a base‐off, His‐off conformation and contains a single [4Fe‐4S] cluster. The cobalamin cofactor cycles between the methyl‐cob(III)alamin, cob(II)alamin and cob(I)alamin states during catalysis and produces methylated substrate, 5′‐deoxyadenosine and S‐adenosyl‐l‐homocysteine in a 1 : 1 : 1 ratio. The newly identified glutamine C‐methyltransferase belongs to the class B radical SAM methyltransferases known to catalyze challenging methylation reactions of sp³‐hybridized carbon atoms.

The Wolfe cycle of carbon dioxide reduction to methane revisited and the Ralph Stoner Wolfe legacy at 100 years

Methanogens are a component of anaerobic microbial consortia decomposing biomass to CO₂ and CH₄ that is an essential link in the global carbon cycle. One of two major pathways of methanogenesis involves reduction of the methyl group of acetate to CH₄ with electrons from oxidation of the carbonyl group while the other involves reduction of CO₂ to CH₄ with electrons from H₂ or formate. Pioneering investigations of the CO₂ reduction pathway by Ralph S. Wolfe in the 70s and 80s contributed findings impacting the broader fields of biochemistry and microbiology that directed discovery of the domain Archaea and expanded research on anaerobic microbes for decades that continues to the present. This review presents an historical overview of the CO₂ reduction pathway (Wolfe cycle) with recent developments, and an account of Wolfe's larger and enduring impact on the broad field of biology 100 years after his birth.

Catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase

Methane is among the most potent of the greenhouse gases, which plays a key role in global climate change. As an excellent carbon and energy source, methane can be utilized by anaerobic methane oxidizing archaea and aerobic methane oxidizing bacteria. The previous work shows that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. However, the catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase is still unknown. Therefore, molecular dynamics (MD) simulation was used to investigate the dynamics differences of catalytic mechanism between methane coenzyme M reductase (MCR) and alkyl-coenzyme M reductase (ACR). At first, the binding pocket of ACR is larger than that of MCR. Then, the complex of butane and ACR is more stable than that of methane and ACR. Protein conformation cloud suggests that the position of methane is dynamics and methane escapes from the binding pocket of ACR during most of the simulation time, while butane tightly binds in the pocket of ACR. The hydrophobic interactions between butane and ACR are more and stronger than those between methane and ACR. At the same time, the binding free energy between butane and ACR is significantly lower than that between methane and ACR. The dynamics correlation network indicates that the transformation of information flow for ACR-butane is smoother than that for ACR-methane. The shortest pathway for ACR-butane is from Gln144, Ala141, Hie135, Ile133, Ala160, Arg206, Asp97, Met94, Tyr347 to Phe345 with synergistic effect for two butane molecules. This study can insight into the catalytic mechanism for butane/ACR complex.

Examining pathways of iron and sulfur acquisition, trafficking, deployment, and storage in mineral-grown methanogen cells

Methanogens have a high demand for iron (Fe) and sulfur (S); however, little is known of how they acquire, deploy, and store these elements and how this, in turn, affects their physiology. Methanogens were recently shown to reduce pyrite (FeS₂) generating aqueous iron-sulfide (FeS_(aq)) clusters that are likely assimilated as a source of Fe and S. Here, we compare the phenotype of Methanococcus voltae when grown with FeS₂ or ferrous iron (Fe(II)) and sulfide (HS^-). FeS₂-grown cells are 33% smaller yet have 193% more Fe than Fe(II)/HS^--grown cells. Whole cell EPR revealed similar distributions of paramagnetic Fe, although FeS₂-grown cells showed a broad spectral feature attributed to intracellular thioferrate-like nanoparticles. Differential proteomic analyses showed similar expression of core methanogenesis enzymes, indicating that Fe and S source does not substantively alter the energy metabolism of cells. However, a homolog of the Fe(II) transporter FeoB and its putative transcriptional regulator DtxR were up-expressed in FeS₂-grown cells, suggesting that cells sense Fe(II) limitation. Two homologs of IssA, a protein putatively involved in coordinating thioferrate nanoparticles, were also up-expressed in FeS₂-grown cells. We interpret these data to indicate that, in FeS₂-grown cells, DtxR cannot sense Fe(II) and therefore cannot down-regulate FeoB. We suggest this is due to the transport of Fe(II) complexed with sulfide (FeS_(aq)) leading to excess Fe that is sequestered by IssA as a thioferrate-like species. This model provides a framework for the design of targeted experiments aimed at further characterizing Fe acquisition and homeostasis in M. voltae and other methanogens. IMPORTANCE FeS₂ is the most abundant sulfide mineral in the Earth's crust and is common in environments inhabited by methanogenic archaea. FeS₂ can be reduced by methanogens, yielding aqueous FeS_(aq) clusters that are thought to be a source of Fe and S. Here, we show that growth of Methanococcus voltae on FeS₂ results in smaller cell size and higher Fe content per cell, with Fe likely stored intracellularly as thioferrate-like nanoparticles. Fe(II) transporters and storage proteins were up-regulated in FeS₂-grown cells. These responses are interpreted to result from cells incorrectly sensing Fe(II) limitation due to assimilation of Fe(II) as FeS_(aq). These findings have implications for our understanding of how Fe/S availability influences methanogen physiology and the biogeochemical cycling of these elements.

Investigation of central energy metabolism-related protein complexes of ANME-2d methanotrophic archaea by complexome profiling

The anaerobic oxidation of methane is important for mitigating emissions of this potent greenhouse gas to the atmosphere and is mediated by anaerobic methanotrophic archaea. In a 'Candidatus Methanoperedens BLZ2' enrichment culture used in this study, methane is oxidized to CO₂ with nitrate being the terminal electron acceptor of an anaerobic respiratory chain. Energy conservation mechanisms of anaerobic methanotrophs have mostly been studied at metagenomic level and hardly any protein data is available at this point. To close this gap, we used complexome profiling to investigate the presence and subunit composition of protein complexes involved in energy conservation processes. All enzyme complexes and their subunit composition involved in reverse methanogenesis were identified. The membrane-bound enzymes of the respiratory chain, such as F₄₂₀H₂:quinone oxidoreductase, membrane-bound heterodisulfide reductase, nitrate reductases and Rieske cytochrome bc₁ complex were all detected. Additional or putative subunits such as an octaheme subunit as part of the Rieske cytochrome bc₁ complex were discovered that will be interesting targets for future studies. Furthermore, several soluble proteins were identified, which are potentially involved in oxidation of reduced ferredoxin produced during reverse methanogenesis leading to formation of small organic molecules. Taken together these findings provide an updated, refined picture of the energy metabolism of the environmentally important group of anaerobic methanotrophic archaea.

Origin of the Enhanced Binding Capability toward Axial Nitrogen Bases of Ni(II) Porphyrins Bearing Electron-Withdrawing Substituents: An Electronic Structure and Bond Energy Analysis

Axial coordination to metalloporphyrins is important in many biological and catalytic processes. Experiments found the axial coordination of nitrogenous bases to nickel(II) porphyrins to be strongly favored by electron-withdrawing substituents such as perfluorophenyls at the meso carbon positions. Careful analysis of the electronic structure reveals that the natural explanation in terms of density change of the nickel(II) porphyrin system (in particular the metal), does not apply. Electron density changes, by the assumed inductive or polarizing effects on the metal or on the porphyrin ring system, are slight. The effect is caused by a remarkable through-space electric field effect on the metalloporphyrin system, originating from the charge distribution inside the perfluorphenyl groups (mostly the C-F dipoles).

Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin

Methyl coenzyme M reductase (MCR) catalyzes the last step in the biological production of methane by methanogenic archaea, as well as the first step in the anaerobic oxidation of methane to methanol by methanotrophic archaea. MCR contains a number of unique post-translational modifications in its α subunit, including thioglycine, 1-N-methylhistidine, S-methylcysteine, 5-C-(S)-methylarginine, and 2-C-(S)-methylglutamine. Recently, genes responsible for the thioglycine and methylarginine modifications have been identified in bioinformatics studies and in vivo complementation of select mutants; however, none of these reactions has been verified in vitro Herein, we purified and biochemically characterized the radical S-adenosylmethionine (SAM) protein MaMmp10, the product of the methanogenesis marker protein 10 gene in the methane-producing archaea Methanosarcina acetivorans Using an array of approaches, including kinetic assays, LC-MS-based quantification, and MALDI TOF-TOF MS analyses, we found that MaMmp10 catalyzes the methylation of the equivalent of Arg²⁸⁵ in a peptide substrate surrogate, but only in the presence of cobalamin. We noted that the methyl group derives from SAM, with cobalamin acting as an intermediate carrier, and that MaMmp10 contains a C-terminal cobalamin-binding domain. Given that Mmp10 has not been annotated as a cobalamin-binding protein, these findings suggest that cobalamin-dependent radical SAM proteins are more prevalent than previously thought.

Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. The active enzyme harbors the nickel(I) hydrocorphin coenzyme F-430 as a prosthetic group and catalyzes the reversible reduction of methyl-coenzyme M (CH₃–S-CoM) with coenzyme B (HS-CoM) to methane and CoM-S–S-CoB. MCR is also involved in anaerobic methane oxidation in reverse of methanogenesis and most probably in the anaerobic oxidation of ethane, propane, and butane. The challenging question is how the unreactive CH₃–S thioether bond in methyl-coenzyme M and the even more unreactive C–H bond in methane and the other hydrocarbons are anaerobically cleaved. A key to the answer is the negative redox potential (E_o′) of the Ni(II)F-430/Ni(I)F-430 couple below −600 mV and the radical nature of Ni(I)F-430. However, the negative one-electron redox potential is also the Achilles heel of MCR; it makes the nickel enzyme one of the most O₂-sensitive enzymes known to date. Even under physiological conditions, the Ni(I) in MCR is oxidized to the Ni(II) or Ni(III) states, e.g., when in the cells the redox potential (E′) of the CoM-S–S-CoB/HS-CoM and HS-CoB couple (E_o′ = −140 mV) gets too high. Methanogens therefore harbor an enzyme system for the reactivation of inactivated MCR in an ATP-dependent reduction reaction. Purification of active MCR in the Ni(I) oxidation state is very challenging and has been achieved in only a few laboratories. This perspective reviews the function, structure, and properties of MCR, what is known and not known about the catalytic mechanism, how the inactive enzyme is reactivated, and what remains to be discovered.

The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order

Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(Ni(I))·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s(-1) at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(Ni(II))·CoB7S(-)·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.

Methyl-coenzyme M reductase from Methanothermobacter marburgensis

Methyl-coenzyme M reductase catalyzes the reversible synthesis of methane from methyl-coenzyme M in methanogenic and ANME-1 and ANME-2 Archaea. The purification procedure for methyl-coenzyme M reductase from Methanothermobacter marburgensis is described. The procedure is an accumulation of almost 30 years of research on MCR starting with the first purification described by Ellefson and Wolfe (Ellefson, W.L., and Wolfe, R.S. (1981). Component C of the methylreductase system of Methanobacterium. J. Biol. Chem.256, 4259-4262). To provide a context for this procedure, some background information is provided, including a description of whole cell experiments that provided much of our knowledge of the behavior and properties of methyl-coenzyme M reductase.

Structural insight into methyl-coenzyme M reductase chemistry using coenzyme B analogues

Methyl-coenzyme M reductase (MCR) catalyzes the final and rate-limiting step in methane biogenesis: the reduction of methyl-coenzyme M (methyl-SCoM) by coenzyme B (CoBSH) to methane and a heterodisulfide (CoBS-SCoM). Crystallographic studies show that the active site is deeply buried within the enzyme and contains a highly reduced nickel-tetrapyrrole, coenzyme F(430). Methyl-SCoM must enter the active site prior to CoBSH, as species derived from methyl-SCoM are always observed bound to the F(430) nickel in the deepest part of the 30 A long substrate channel that leads from the protein surface to the active site. The seven-carbon mercaptoalkanoyl chain of CoBSH binds within a 16 A predominantly hydrophobic part of the channel close to F(430), with the CoBSH thiolate lying closest to the nickel at a distance of 8.8 A. It has previously been suggested that binding of CoBSH initiates catalysis by inducing a conformational change that moves methyl-SCoM closer to the nickel promoting cleavage of the C-S bond of methyl-SCoM. In order to better understand the structural role of CoBSH early in the MCR mechanism, we have determined crystal structures of MCR in complex with four different CoBSH analogues: pentanoyl, hexanoyl, octanoyl, and nonanoyl derivatives of CoBSH (CoB(5)SH, CoB(6)SH, CoB(8)SH, and CoB(9)SH, respectively). The data presented here reveal that the shorter CoB(5)SH mercaptoalkanoyl chain overlays with that of CoBSH but terminates two units short of the CoBSH thiolate position. In contrast, the mercaptoalkanoyl chain of CoB(6)SH adopts a different conformation, such that its thiolate is coincident with the position of the CoBSH thiolate. This is consistent with the observation that CoB(6)SH is a slow substrate. A labile water in the substrate channel was found to be a sensitive indicator for the presence of CoBSH and HSCoM. The longer CoB(8)SH and CoB(9)SH analogues can be accommodated in the active site through exclusion of this water. These analogues react with Ni(III)-methyl, a proposed MCR catalytic intermediate of methanogenesis. The CoB(8)SH thiolate is 2.6 A closer to the nickel than that of CoBSH, but the additional carbon of CoB(9)SH only decreases the nickel thiolate distance a further 0.3 A. Although the analogues do not induce any structural changes in the substrate channel, the thiolates appear to preferentially bind at two distinct positions in the channel, one being the previously observed CoBSH thiolate position and the other being at a hydrophobic annulus of residues that lines the channel proximal to the nickel.

A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations

We propose a new DFT-based mechanism for methane production using the full F430 cofactor of MCR (methyl-coenzyme M reductase) along with a coordinated O=CH2CH2C(H)NH2C(H)O (surrogate for glutamine) as a model of the active site for conversion of CH3SCoM(-) (CH3SCH2CH2SO3(-)) + HSCoB to methane plus the corresponding heterodisulfide. The cycle begins with the protonation of F430, either on Ni or on the C-ring nitrogen of the tetrapyrrole ring, both of which are nearly equally favorable. The C-ring protonated form is predicted to oxidatively add CH3SCoM(-) to give a 4-coordinate Ni center where the Ni moves out of the plane of the four ring nitrogens. The movement of Ni (and the attached CH3 and SCH2CH2SO3(2-) ligands) toward the SCoB(-) (deprotonated HSCoB) cofactor allows a 2c-3e interaction to form between the two sulfur atoms. The release of the heterodisulfide yields a Ni(III) center with a methyl group attached. The concerted elimination of methane, where the methyl group coordinated to Ni abstracts the proton from the C-ring nitrogen, has a very small calculated activation barrier (5.4 kcal/mol). The NPA charge on Ni for the various reaction steps indicates that the oxidation state changes occur largely on the attached ligands.

On the mechanism of methyl-coenzyme M reductase

Methyl-coenzyme M reductase (MCR) catalyzes the reaction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterodisulfide CoM-S-S-CoB. This unique reaction proceeds under strictly anaerobic conditions in the presence of coenzyme F430, a Ni-porphinoid. MCR is a large (alphabetagamma)2 heterohexameric protein complex containing two 50 A long active sites channels. Coenzyme F430 is embedded at the channel bottom and the substrates CH3-SCoM and HS-CoB bind in front of F430 into a solvent free and hydrophobic channel segment. Two principally different catalytic mechanisms are currently discussed. Mechanism I is based on a nucleophilic attack of Ni(I) onto the methyl group of CH3-SCoM yielding methyl-Ni(III) and mechanism II on an attack of Ni(I) onto the thioether sulfur of CH3-SCoM generating a Ni(II)-SCoM intermediate. Both mechanisms are discussed in the light of a large number of data collected about MCR over the last twenty years.

Catalysis by methyl-coenzyme M reductase: a theoretical study for heterodisulfide product formation

Hybrid density functional theory has been used to investigate the catalytic mechanism of methyl-coenzyme M reductase (MCR), an essential enzyme in methanogenesis. In a previous study of methane formation, a scheme was suggested involving oxidation of Ni(I) in the starting square-planar coordination to the high-spin Ni(II) form in the CoM-S-Ni(II)F(430) octahedral intermediate. The methyl radical, concomitantly released by methyl-coenzyme M (CoM), is rapidly quenched by hydrogen atom transfer from the coenzyme B (CoB) thiol group, yielding methane as the first product of the reaction. The present investigation primarily concerns the second and final step of the reaction: oxidation of CoB and CoM to the CoB-S-S-CoM heterodisulfide product and reduction of nickel back to the Ni(I) square-planar form. The activation energy for the second step is found to be around 10 kcal/mol, implying that the first step of methane formation with an activation energy of 20 kcal/mol should be rate-limiting. An oxygen of the Gln147 residue, occupying the rear axial position in the oxidized Ni(II) state, is shown to stabilize the intermediate by 6 kcal/mol, thereby slightly decreasing the barrier for the preceding rate-limiting transition state. The mechanism suggested is discussed in the context of available experimental data. An analysis of the flexibility of the F(430) cofactor during the reaction cycle is also given.

The unique biochemistry of methanogenesis

Methanogenic archaea have an unusual type of metabolism because they use H2 + CO2, formate, methylated C1 compounds, or acetate as energy and carbon sources for growth. The methanogens produce methane as the major end product of their metabolism in a unique energy-generating process. The organisms received much attention because they catalyze the terminal step in the anaerobic breakdown of organic matter under sulfate-limiting conditions and are essential for both the recycling of carbon compounds and the maintenance of the global carbon flux on Earth. Furthermore, methane is an important greenhouse gas that directly contributes to climate changes and global warming. Hence, the understanding of the biochemical processes leading to methane formation are of major interest. This review focuses on the metabolic pathways of methanogenesis that are rather unique and involve a number of unusual enzymes and coenzymes. It will be shown how the previously mentioned substrates are converted to CH4 via the CO2-reducing, methylotrophic, or aceticlastic pathway. All catabolic processes finally lead to the formation of a mixed disulfide from coenzyme M and coenzyme B that functions as an electron acceptor of certain anaerobic respiratory chains. Molecular hydrogen, reduced coenzyme F420, or reduced ferredoxin are used as electron donors. The redox reactions as catalyzed by the membrane-bound electron transport chains are coupled to proton translocation across the cytoplasmic membrane. The resulting electrochemical proton gradient is the driving force for ATP synthesis as catalyzed by an A1A0-type ATP synthase. Other energy-transducing enzymes involved in methanogenesis are the membrane-integral methyltransferase and the formylmethanofuran dehydrogenase complex. The former enzyme is a unique, reversible sodium ion pump that couples methyl-group transfer with the transport of Na+ across the membrane. The formylmethanofuran dehydrogenase is a reversible ion pump that catalyzes formylation and deformylation of methanofuran. Furthermore, the review addresses questions related to the biochemical and genetic characteristics of the energy-transducing enzymes and to the mechanisms of ion translocation.

Novel thiols of prokaryotes

Glutathione metabolism is associated with oxygenic cyanobacteria and the oxygen-utilizing purple bacteria, but is absent in many other prokaryotes. This review focuses on novel thiols found in those bacteria lacking glutathione. Included are glutathione amide and its perthiol, produced by phototrophic purple sulfur bacteria and apparently involved in their sulfide metabolism. Among archaebacteria, coenzyme M (2-mercaptoethanesulfonic acid) and coenzyme B (7-mercaptoheptanoylthreonine phosphate) play central roles in the anaerobic production of CH4 and associated energy conversion by methanogens, whereas the major thiol in the aerobic phototrophic halobacteria is gamma-glutamylcysteine. The highly aerobic actinomycetes produce mycothiol, a conjugate of N-acetylcysteine with a pseudodisaccharide of glucosamine and myo-inositol, AcCys-GlcNalpha(1 --> 1)Ins, which appears to play an antioxidant role similar to glutathione. Ergothioneine, also produced by actinomycetes, remains a mystery despite many years of study. Available data on the biosynthesis and metabolism of these and other novel thiols is summarized and key areas for additional study are identified.

Structure and function of enzymes involved in the methanogenic pathway utilizing carbon dioxide and molecular hydrogen

Methane is an end product of anaerobic degradation of organic compounds in fresh water environments such as lake sediments and the intestinal tract of animals. Methanogenic archaea produce methane from carbon dioxide and molecular hydrogen, acetate and C1 compounds such as methanol in an energy gaining process. The methanogenic pathway utilizing carbon dioxide and molecular hydrogen involves ten methanogen specific enzymes, which catalyze unique reactions using novel coenzymes. These enzymes have been purified and biochemically characterized. The genes encoding the enzymes have been cloned and sequenced. Recently, crystal structures of five methanogenic enzymes: formylmethanofuran : tetrahydromethanopterin formyltransferase, methenyltetrahydromethanopterin cyclohydrolase, methylenetetrahydromethanopterin reductase, F420H2:NADP oxidoreductase and methyl-coenzyme M reductase were reported. In this review, we describe the pathway utilizing carbon dioxide and molecular hydrogen and the catalytic mechanisms of the enzymes based on their crystal structures.

Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation

The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea. In this reaction methyl-coenzyme M and coenzyme B are converted to methane and the heterodisulfide of coenzyme M and coenzyme B. The crystal structures of methyl-coenzyme M reductase from Methanosarcina barkeri (growth temperature optimum, 37 degrees C) and Methanopyrus kandleri (growth temperature optimum, 98 degrees C) were determined and compared with the known structure of MCR from Methanobacterium thermoautotrophicum (growth temperature optimum, 65 degrees C). The active sites of MCR from M. barkeri and M. kandleri were almost identical to that of M. thermoautotrophicum and predominantly occupied by coenzyme M and coenzyme B. The electron density at 1.6 A resolution of the M. barkeri enzyme revealed that four of the five modified amino acid residues of MCR from M. thermoautotrophicum, namely a thiopeptide, an S-methylcysteine, a 1-N-methylhistidine and a 5-methylarginine were also present. Analysis of the environment of the unusual amino acid residues near the active site indicates that some of the modifications may be required for the enzyme to be catalytically effective. In M. thermoautotrophicum and M. kandleri high temperature adaptation is coupled with increasing intracellular concentrations of lyotropic salts. This was reflected in a higher fraction of glutamate residues at the protein surface of the thermophilic enzymes adapted to high intracellular salt concentrations.

Four-Coordinate, Low-Spin (S = 0) and Six-Coordinate, High-Spin (S = 1) Nickel(II) Complexes of Tetraphenylporphyrins with beta-Pyrrole Electron-Withdrawing Substituents: Porphyrin-Core Expansion and Conformation

To examine the porphyrin-core expansion and the conformational variations induced by a change in the coordination sphere of nickel(II) from four-coordinate, low-spin (S = 0) to six-coordinate, high-spin (S = 1), several nickel(II) derivatives of tetraphenylporphyrins, substituted in their beta-pyrrole positions with electron-withdrawing groups, were isolated and studied by X-ray crystallography. The four-coordinate nickel(II) complex studied, Ni(TPP(Br)(4)(CN)(4)) (1), is a derivative of the antipodal beta-pyrrole brominated and cyanated macrocycle, 2,3,12,13-tetrabromo-7,8,17,18-tetracyano-5,10,15,20-tetraphenylporphyrin. One of the six-coordinate species is the bis-pyridine nickel(II) adduct, Ni(TPP(Br)(4)(CN)(4))(py)(2) (2), of this antipodal beta-pyrrole brominated and cyanated ring, whereas the second six-coordinate complex is the bis-1-methylimidazole nickel(II) adduct, Ni(TPP(CN)(4))(1-MeIm)(2) (3), of the antipodal tetracyanated macrocycle, 7,8,17,18-tetracyano-5,10,15,20-tetraphenylporphyrin. This study confirms that, upon conversion of a four-coordinate, low-spin nickel(II) derivative of a beta-pyrrole-substituted tetraphenylporphyrin into a six-coordinate, high-spin complex, a radial expansion of the porphyrin core also takes place. This radial expansion flattens the porphyrin core, inducing more planarity in the conformations of the six-coordinate nickel(II) porphyrin species. The X-ray structure of 1 reveals an average Ni-N(p) bond distance of 1.920(2) Å, similar to that present in tetragonal Ni(OEP) [(Ni-N(p))(av) = 1.929(3) Å], the ruffled low-spin nickel(II) (S = 0) porphyrin derivative, and many other low-spin nickel(II) complexes of distorted porphyrins. The conformation of the macrocycle present in 1 is severely saddle-shaped with a small ruffling and a minor doming. The structures of 2 and 3 indicate a clear expansion of the porphyrin cores with two sets of (Ni-N(p))(av) bond lengths of 2.040(2) and 2.073(2) Å in 2 and 2.037(2) and 2.068(2) Å in 3, which differ significantly from the average Ni-N(p) distance occurring in 1. Relative to the conformation of the porphyrin ring present in 1, the high-spin complex 2 is less saddle-shaped, but more ruffled. In 3, in which only two opposite pyrrole rings of the porphyrin are substituted by cyano groups, the macrocycle adopts a slightly waved conformation. Crystal data: Ni(TPP(Br)(4)(CN)(4)).2.5(1,2-Cl(2)C(2)H(4)), [1.2.5(1,2-Cl(2)C(2)H(4))], triclinic, space group P&onemacr;, a = 13.741(1) Å, b = 14.029(2) Å, c = 15.201(2) Å, alpha = 89.037(9) degrees, beta = 70.829(8) degrees, gamma = 67.607(8) degrees, V = 2539.4(5) Å(3), T = 20 degrees C, Z = 2, R(F)() = 0.047 and R(wF) = 0.067 based on 5341 reflections with I > 3sigma(I); Ni(TPP(Br)(4)(CN)(4))(py)(2).2.5(1,2-Cl(2)C(2)H(4)), [2.2.5(1,2-Cl(2)C(2)H(4))], triclinic, space group P&onemacr;, a = 11.9472(9) Å, b = 14.3651(7) Å, c = 19.556(1) Å, alpha = 87.049(5) degrees, beta = 73.181(6) degrees, gamma = 70.613(5) degrees, V = 3026.8(4) Å(3), T = 173 K, Z = 2, R(F)() = 0.036, R(wF) = 0.041 based on 6846 reflections with I > 3sigma(I); Ni(TPP(CN)(4))(1-MeIm)(2).2CH(2)Cl(2), [3.2(CH(2)Cl(2))], monoclinic, space group C2/c, a = 26.804(8) Å, b = 10.948(3) Å, c = 19.453(5) Å, beta = 113.13(2) degrees, V = 5251.5 Å(3), T = 20 degrees C, Z = 4, R(F)() = 0.047, R(wF) = 0.067 based on 4384 reflections with I > 3sigma(I).

Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation

Methyl-coenzyme M reductase (MCR), the enzyme responsible for the microbial formation of methane, is a 300-kilodalton protein organized as a hexamer in an alpha2beta2gamma2 arrangement. The crystal structure of the enzyme from Methanobacterium thermoautotrophicum, determined at 1.45 angstrom resolution for the inactive enzyme state MCRox1-silent, reveals that two molecules of the nickel porphinoid coenzyme F430 are embedded between the subunits alpha, alpha', beta, and gamma and alpha', alpha, beta', and gamma', forming two identical active sites. Each site is accessible for the substrate methyl-coenzyme M through a narrow channel locked after binding of the second substrate coenzyme B. Together with a second structurally characterized enzyme state (MCRsilent) containing the heterodisulfide of coenzymes M and B, a reaction mechanism is proposed that uses a radical intermediate and a nickel organic compound.

Metabolism of methanogens

Methanogenic archaea convert a few simple compounds such as H2 + CO2, formate, methanol, methylamines, and acetate to methane. Methanogenesis from all these substrates requires a number of unique coenzymes, some of which are exclusively found in methanogens. H2-dependent CO2 reduction proceeds via carrier-bound C1 intermediates which become stepwise reduced to methane. Methane formation from methanol and methylamines involves the disproportionation of the methyl groups. Part of the methyl groups are oxidized to CO2, and the reducing equivalents thereby gained are subsequently used to reduce other methyl groups to methane. This process involves the same C1 intermediates that are formed during methanogenesis from CO2. Conversion of acetate to methane and carbon dioxide is preceded by its activation to acetyl-CoA. Cleavage of the latter compound yields a coenzyme-bound methyl moiety and an enzyme-bound carbonyl group. The reducing equivalents gained by oxidation of the carbonyl group to carbon dioxide are subsequently used to reduce the methyl moiety to methane. All these processes lead to the generation of transmembrane ion gradients which fuel ATP synthesis via one or two types of ATP synthases. The synthesis of cellular building blocks starts with the central anabolic intermediate acetyl-CoA which, in autotrophic methanogens, is synthesized from two molecules of CO2 in a linear pathway.

Association of the mcrD gene product with methyl coenzyme M reductase in Methanococcus vannielii

The mcrD gene, subcloned from the methyl coenzyme M reductase (MR) encoding mcrBDCGA operon in Methanococcus vannielii, has been expressed at a high level in Escherichia coli. Rabbit antibodies, raised against the product of this gene (rgpmcrD, recombinant gene product of mcrD) purified from E. coli, have been used to quantitate gpmcrD in M. vannielii and to follow its fate during MR purification. The molar ratio of gpmcrD to MR was found to be approx. 1:15 in cells of M. vannielii taken from batch cultures at all stages of growth. Sedimentation of lysates of M. vannielii cells through sucrose gradients and analyses of the fractions obtained by Western blotting and immunoprecipitation have demonstrated the presence of a macromolecular complex containing both gpmcrD and MR. Addition of mcrD antibodies or removal of gpmcrD from lysates of M. vannielii cells by immunoprecipitation decreased the rates of methanogenesis in vitro by approx. 20%. Addition of purified rgpmcrD to these lysates did not stimulate methanogenesis.

Identification of the mcrC gene product in Methanococcus vannielii

The polypeptide encoded by the mcrC gene has been identified in Methanococcus vannielii by immunoblotting using rabbit antibodies raised against the product of a lacZ-mcrC gene fusion synthesized and purified from Escherichia coli. The mcrC gene product (gpmcrC) was located in both the supernatant and pellet fractions after centrifugation of Mc. vannielii cell extracts for 2 h at 100,000 x g. When anaerobic reducing conditions were maintained during purification, gpmcrC co-sedimented through sucrose gradients to the same position as molecules of the methyl coenzyme M reductase holoenzyme (approx. 300 kDa). This co-sedimentation was lost under aerobic, nonreducing conditions.

Energetics of methanogenesis studied in vesicular systems

Methanogenesis is restricted to a group of prokaryotic microorganisms which thrive in strictly anaerobic habitats where they play an indispensable role in the anaerobic food chain. Methanogenic bacteria possess a number of unique cofactors and coenzymes that play an important role in their specialized metabolism. Methanogenesis from a number of simple substrates such as H2 + CO2, formate, methanol, methylamines, and acetate is associated with the generation of transmembrane electrochemical gradients of protons and sodium ions which serve as driving force for a number of processes such as the synthesis of ATP via an ATP synthase, reverse electron transfer, and solute uptake. Several unique reactions of the methanogenic pathways have been identified that are involved in energy transduction. Their role and importance for the methanogenic metabolism are described.

Evidence for the involvement of corrinoids and factor F430 in the reductive dechlorination of 1,2-dichloroethane by Methanosarcina barkeri

Cobalamin and the native and diepimeric forms of factor F430 catalyzed the reductive dechlorination of 1,2-dichloroethane (1,2-DCA) to ethylene or chloroethane (CA) in a buffer with Ti(III) citrate as the electron donor. Ethylene was the major product in the cobalamin-catalyzed transformation, and the ratio of ethylene to CA formed was 25:1. Native F430 and 12,13-di-epi-F430 produced ethylene and CA in ratios of about 2:1 and 1:1, respectively. Cobalamin dechlorinated 1,2-DCA much faster than did factor F430. Dechlorination rates by all three catalysts showed a distinct pH dependence, correlated in a linear manner with the catalyst concentration and doubled with a temperature increase of 10 degrees C. Crude and boiled cell extracts of Methanosarcina barkeri also dechlorinated 1,2-DCA to ethylene and CA with Ti(III) citrate as the reductant. The catalytic components in boiled extracts were heat and oxygen stable and had low molecular masses. Fractionation of boiled extracts by a hydrophobic interaction column revealed that part of the dechlorinating components had a hydrophilic and part had a hydrophobic character. These chemical properties of the dechlorinating components and spectral analysis of boiled extracts indicated that corrinoids or factor F430 was responsible for the dechlorinations. The ratios of 3:1 to 7:1 of ethylene and CA formed by cell extracts suggested that both cofactors were concomitantly active.

Methyl-coenzyme M reductase of Methanobacterium thermoautotrophicum delta H catalyzes the reductive dechlorination of 1,2-dichloroethane to ethylene and chloroethane

Reductive dechlorination of 1,2-dichloroethane (1,2-DCA) to ethylene and chloroethane (CA) by crude cell extracts of Methanobacterium thermoautotrophicum delta H with H2 as the electron donor was stimulated by Mg-ATP. The heterodisulfide of coenzyme M (CoM) and 7-mercaptoheptanoylthreonine phosphate together with Mg-ATP partially inhibited ethylene production but stimulated CA production compared Mg-ATP alone. The pH optimum for the dechlorination was 6.8 (at 60 degrees C). Michaelis-Menten kinetics for initial product formation rates with different 1,2-DCA concentrations indicated the enzymatic character of the dechlorination. Apparent Kms for 1,2-DCA of 89 and 119 microM and Vmaxs of 34 and 20 pmol/min/mg of protein were estimated for ethylene and CA production, respectively. 3-Bromopropanesulfonate, a specific inhibitor for methyl-CoM reductase, completely inhibited dechlorination of 1,2-DCA. Purified methyl-CoM reductase, together with flavin adenine dinucleotide and a crude component A fraction which reduced the nickel of factor F430 in methyl-CoM reductase, converted 1,2-DCA to ethylene and CA with H2 as the electron donor. In this system, methyl-CoM reductase was also able to transform its own inhibitor 2-bromoethanesulfonate to ethylene.

Differential expression of the two methyl-coenzyme M reductases in Methanobacterium thermoautotrophicum as determined immunochemically via isoenzyme-specific antisera

Methanobacterium thermoautotrophicum contains two isoenzymes of methyl-coenzyme M reductase (MCR), MCR I and MCR II, which catalyze the methane-forming step and which together represent more than 10% of the cellular protein. We describe here the preparation of isoenzyme-specific antisera against the two MCR isoenzymes and their use in the quantitative immunochemical determination of the two isoenzymes in the methanogen. The relative and absolute cellular concentration of the two proteins is shown to be strongly affected by growth conditions such as the temperature, pH, and substrate concentration. Conditions were found yielding cells which contained essentially only MCR I or MCR II. Using antisera against MCR I and MCR II, MCR from other methanogens were immunochemically compared. Evidence is presented that Methanobacterium wolfei also contains two isoenzymes of MCR.

Ni(II) and Ni(I) forms of pentaalkylamide derivatives of cofactor F430 of Methanobacterium thermoautotrophicum

A series of pentaalkylamide forms of F430 and of its 12,13-diepimer have been generated and characterized. Carbodiimide-assisted N-hydroxysulfosuccinimide activation of all five peripheral carboxylates of the F430 macrocycle allows nucleophilic attack by a number of primary amines (RNH2, R- = CH3-, CH3CH2-, CF3CH2-, CH3(CH2)3-) generating the pentaalkylamide derivatives. The identity of each derivative has been verified by fast-atom bombardment mass spectrometry (FAB-MS). The solubility of these derivatives in aprotic organic solvents varies as the amine alkyl substituent (R-) is changed. Electrochemical measurements have shown that the Ni(II/I) reduction potentials in N,N-dimethylformamide (DMF) are approximately -1 V (Ag/AgCl). Reduction by sodium amalgam in THF generates the Ni(I) form of the F430 diepimer pentabutylamide. The visible and EPR spectra of this Ni(I) species are very similar to the corresponding spectra of Ni(I) F430M (Jaun, B. and Pfaltz, A. (1986) J. Chem. Soc. Chem. Commun. 1327-1329.).

Two genetically distinct methyl-coenzyme M reductases in Methanobacterium thermoautotrophicum strain Marburg and delta H

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaebacteria. The reductase has been characterized in detail from Methanobacterium thermoautotrophicum strain Marburg and delta H, which grow on H2 and CO2 as energy source. During purification of the enzyme we have now discovered a second methyl-coenzyme M reductase (MCR II) in the two strains, which elutes at lower salt concentration from anion-exchange columns than the enzyme (MCR I) previously characterized. MCR II is similar to MCR I in that it is also composed of three different subunits alpha, beta, and gamma but distinct from MCR I in that the gamma subunit is 5 kDa smaller, as revealed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The N-terminal amino acid sequences of the alpha, beta, and gamma subunits of MCR II and MCR I were found to be different in several amino acid positions. The respective sequences showed, however, strong similarities indicating that MCR II was not derived from MCR I by limited proteolysis. The relative amounts of MCR I and MCR II present in the cells were affected by the growth conditions. When the cultures were supplied with sufficient H2 and and CO2 and the cells grew exponentially, essentially only MCR II was found. When growth was limited by the gas supply, MCR I predominated.

Purification and characterization of the reduced-nicotinamide-dependent 2,2'-dithiodiethanesulfonate reductase from Methanobacterium thermoautotrophicum delta H

A novel reduced nicotinamide-dependent disulfide reductase, the 2,2'-dithiodiethanesulfonate [(S-CoM)2] reductase (CoMDSR) of Methanobacterium thermoautotrophicum was purified 405-fold to electrophoretic homogeneity. Both NADPH and NADH functioned as electron donors, although rates with NADPH were three times higher. Reduced factor F420, the deazaflavin electron carrier characteristic of methanogenic bacteria, was not a substrate for the enzyme. The enzyme was most active with (S-CoM)2 but could also reduce L-cystine at 23% the (S-CoM)2 rate. Results of sodium dodecyl sulfate polyacrylamide gel electrophoresis indicated that the enzyme was monomeric with an Mr of about 64,000; spectral analysis showed that it was a flavoprotein with an estimated composition of one molecule of flavin per polypeptide. Maximal activity occurred at 64 degrees C, and the pH optimum was 8.5. The apparent Km for both NADPH and (S-CoM)2 was 80 microM. The enzyme was completely inactivated by oxygen in crude cell extracts but was oxygen stable in the homogeneous state. The low activity of the CoMDSR in cell extracts as well as its relatively low rate of reducing CoM-S-S-HTP (the heterodisulfide of the two thiol cofactors involved in the last step of methanogenesis) make it unlikely that it plays a role in the methylreductase system. It may be involved in the redox balance of the cell, such as the NADPH-dependent bis-gamma-glutamylcystine reductase with which it shows physical similarity in another archaebacterium, Halobacterium halobium (A. R. Sundquist and R. C. Fahey, J. Bacteriol. 170:3459-3467, 1988). The CoMDSR might also be involved in regenerating the coenzyme M trapped as its homodisulfide, a nonutilizable form of the cofactor.