Publications

• Methane formation by reaction of a methyl thioether with a photo-excited nickel thiolate--a process mimicking methanogenesis in archaea.

  Signor L., Knuppe C., Hug R., Schweizer B., Pfaltz A., Jaun B.

  The formation of a sulfuranyl radical intermediate followed by methyl transfer to the nickel(I) center of coenzyme F430 and generation of the disulfide has been proposed as a possible mechanism for the formation of methane catalyzed by methyl coenzyme M reductase in methanogenic archaea. In order ... >> More

  The formation of a sulfuranyl radical intermediate followed by methyl transfer to the nickel(I) center of coenzyme F430 and generation of the disulfide has been proposed as a possible mechanism for the formation of methane catalyzed by methyl coenzyme M reductase in methanogenic archaea. In order to test this hypothesis, a sterically shielded, bifunctional model substrate that contained a methyl thioether and a sulfhydryl functional group, which could form a five-membered cyclic sulfuranyl radical according to the postulated mechanism, was synthesized. The corresponding thiolate reacted with Ni(II) salts to give a diamagnetic, square-planar Ni(II) dithiolate complex, which was characterized by X-ray diffraction. Upon irradiation of this complex with light of lambda > 300 nm, methane and the cyclic disulfide were formed, whereas irradiation of the thiolate in the absence of nickel gave only traces of methane and no cyclic disulfide. The observed products are consistent with the postulated mechanism via a sulfuranyl radical, and the role of light is interpreted as the formation of a Ni(I)/thiyl radical pair upon excitation of a charge-transfer band of the Ni(II) dithiolate. In the presence of a large excess of thiolate, the diamagnetic complex was transformed into a paramagnetic, five- or six-coordinate complex that proved to be more active in the generation of both methane and the cyclic disulfide, than the square-planar diamagnetic dithiolate. << Less

  Chemistry 6:3508-3516(2000) [PubMed] [EuropePMC]

• Intermediates in the catalytic cycle of methyl coenzyme M reductase: isotope exchange is consistent with formation of a sigma-alkane-nickel complex.

  Scheller S., Goenrich M., Mayr S., Thauer R.K., Jaun B.

  Angew Chem Int Ed Engl 49:8112-8115(2010) [PubMed] [EuropePMC]

• Geometric and electronic structures of the Ni(I) and methyl-Ni(III) intermediates of methyl-coenzyme M reductase.

  Sarangi R., Dey M., Ragsdale S.W.

  Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni-F(430) cofactor, which can exist in different oxidation states. The catalytic mechanism of methane form ... >> More

  Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni-F(430) cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the Ni(I) active state (MCR(red1)) on Me-SCoM to form a Ni(III)-methyl intermediate, while computational studies indicate that the first step involves the attack of Ni(I) on the sulfur of Me-SCoM, forming a CH(3)(*) radical and a Ni(II)-thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the Ni(I) (MCR(red1)), Ni(II) (MCR(red1-silent)), and Ni(III)-methyl (MCR(Me)) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCR(red1). Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni-C bond ( approximately 2.04 A) in the Ni(III)-methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni-C bond length suggests a homolytic cleavage of the Ni(III)-methyl bond in the subsequent catalytic step. The XAS data provide insight into the role of the unique F(430) cofactor in tuning the stability of the different redox states of MCR. << Less

  Biochemistry 48:3146-3156(2009) [PubMed] [EuropePMC]

• Post-translational modifications in the active site region of methyl-coenzyme M reductase from methanogenic and methanotrophic archaea.

  Kahnt J., Buchenau B., Mahlert F., Kruger M., Shima S., Thauer R.K.

  Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. Isoenzyme I from Methanothermobacter marburgensiswas shown to contain a thioxo peptide bond and four methylated amino acids in the active site region. We report here that MCRs from all methanogens investi ... >> More

  Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. Isoenzyme I from Methanothermobacter marburgensiswas shown to contain a thioxo peptide bond and four methylated amino acids in the active site region. We report here that MCRs from all methanogens investigated contain the thioxo peptide bond, but that the enzymes differ in their post-translational methylations. The MS analysis included MCR I and MCR II from Methanothermobacter marburgensis, MCR I from Methanocaldococcus jannaschii and Methanoculleus thermophilus, and MCR from Methanococcus voltae, Methanopyrus kandleri and Methanosarcina barkeri. Two MCRs isolated from Black Sea mats containing mainly methanotrophic archaea of the ANME-1 cluster were also analyzed. << Less

  FEBS J 274:4913-4921(2007) [PubMed] [EuropePMC]

• Characterization of alkyl-nickel adducts generated by reaction of methyl-coenzyme m reductase with brominated acids.

  Dey M., Kunz R.C., Lyons D.M., Ragsdale S.W.

  Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the final step in the biological synthesis of methane. Using coenzyme B (CoBSH) as the two-electron donor, MCR reduces methyl-coenzyme M (methyl-SCoM) to methane and the mixed disulfide, CoB-S-S-CoM. MCR contains coenzyme F430, ... >> More

  Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the final step in the biological synthesis of methane. Using coenzyme B (CoBSH) as the two-electron donor, MCR reduces methyl-coenzyme M (methyl-SCoM) to methane and the mixed disulfide, CoB-S-S-CoM. MCR contains coenzyme F430, an essential redox-active nickel tetrahydrocorphin, at its active site. The active form of MCR (MCRred1) contains Ni(I)-F430. When 3-bromopropane sulfonate (BPS) is incubated with MCRred1, an alkyl-Ni(III) species is formed that elicits the MCRPS EPR signal. Here we used EPR and UV-visible spectroscopy and transient kinetics to study the reaction between MCR from Methanothermobacter marburgensis and a series of brominated carboxylic acids, with carbon chain lengths of 4-16. All of these compounds give rise to an alkyl-Ni intermediate with an EPR signal similar to that of the MCRPS species. Reaction of the alkyl-Ni(III) adduct, formed from brominated acids with eight or fewer total carbons, with HSCoM as nucleophile at pH 10.0 results in the formation of a thioether coupled to regeneration of the active MCRred1 state. When reacted with 4-bromobutyrate, MCRred1 forms the alkyl-Ni(III) MCRXA state and then, surprisingly, undergoes "self-reactivation" to regenerate the Ni(I) MCRred1 state and a bromocarboxy ester. The results demonstrate an unexpected reactivity and flexibility of the MCR active site in accommodating a broad range of substrates, which act as molecular rulers for the substrate channel in MCR. << Less

  Biochemistry 46:11969-11978(2007) [PubMed] [EuropePMC]

• Binding of coenzyme B induces a major conformational change in the active site of methyl-coenzyme M reductase.

  Ebner S., Jaun B., Goenrich M., Thauer R.K., Harmer J.

  Methyl-coenzyme M reductase (MCR) is the key enzyme in methane formation by methanogenic Archaea. It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B. The catalytic mechanism of MCR and the role of its prosthetic gr ... >> More

  Methyl-coenzyme M reductase (MCR) is the key enzyme in methane formation by methanogenic Archaea. It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B. The catalytic mechanism of MCR and the role of its prosthetic group, the nickel hydrocorphin coenzyme F(430), is still disputed, and no intermediates have been observed so far by fast spectroscopic techniques when the enzyme was incubated with the natural substrates. In the presence of the competitive inhibitor coenzyme M instead of methyl-coenzyme M, addition of coenzyme B to the active Ni(I) state MCR(red1) induces two new species called MCR(red2a) and MCR(red2r) which have been characterized by pulse EPR spectroscopy. Here we show that the two MCR(red2) signals can also be induced by the S-methyl- and the S-trifluoromethyl analogs of coenzyme B. (19)F-ENDOR data for MCR(red2a) and MCR(red2r) induced by S-CF(3)-coenzyme B show that, upon binding of the coenzyme B analog, the end of the 7-thioheptanoyl chain of coenzyme B moves closer to the nickel center of F(430) by more than 2 A as compared to its position in both, the Ni(I) MCR(red1) form and the X-ray structure of the inactive Ni(II) MCR(ox1-silent) form. The finding that the protein is able to undergo a conformational change upon binding of the second substrate helps to explain the dramatic change in the coordination environment induced in the transition from MCR(red1) to MCR(red2) forms and opens the possibility that nickel coordination geometries other than square planar, tetragonal pyramidal, or elongated octahedral might occur in intermediates of the catalytic cycle. << Less

  J Am Chem Soc 132:567-575(2010) [PubMed] [EuropePMC]

• Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase.

  Hinderberger D., Ebner S., Mayr S., Jaun B., Reiher M., Goenrich M., Thauer R.K., Harmer J.

  Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S-S-CoB. MCR harbors the nickel porphyrinoid coenzyme F430 as a prosthetic ... >> More

  Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S-S-CoB. MCR harbors the nickel porphyrinoid coenzyme F430 as a prosthetic group, which has to be in the Ni(I) oxidation state for the enzyme to be active. To date no intermediates in the catalytic cycle of MCRred1 (red for reduced Ni) have been identified. Here, we report a detailed characterization of MCRred1m ("m" for methyl-coenzyme M), which is the complex of MCRred1a ("a" for absence of substrate) with CH3-S-CoM. Using continuous-wave and pulse electron paramagnetic resonance spectroscopy in combination with selective isotope labeling (13C and 2H) of CH3-S-CoM, it is shown that CH3-S-CoM binds in the active site of MCR such that its thioether sulfur is weakly coordinated to the Ni(I) of F430. The complex is stable until the addition of the second substrate, HS-CoB. Results from EPR spectroscopy, along with quantum mechanical calculations, are used to characterize the electronic and geometric structure of this complex, which can be regarded as the first intermediate in the catalytic mechanism. << Less

  J Biol Inorg Chem 13:1275-1289(2008) [PubMed] [EuropePMC]

• Properties of the two isoenzymes of methyl-coenzyme M reductase in Methanobacterium thermoautotrophicum.

  Bonacker L.G., Baudner S., Morschel E., Bocher R., Thauer R.K.

  Methyl-coenzyme M reductase (MCR) catalyses the methane-forming step in the energy metabolism of methanogenic Archaea. It brings about the reduction of methyl-coenzyme M (CH3-S-CoM) by 7-mercaptoheptanoylthreonine phosphate (H-S-HTP). Methanobacterium thermoautotrophicum contains two isoenzymes of ... >> More

  Methyl-coenzyme M reductase (MCR) catalyses the methane-forming step in the energy metabolism of methanogenic Archaea. It brings about the reduction of methyl-coenzyme M (CH3-S-CoM) by 7-mercaptoheptanoylthreonine phosphate (H-S-HTP). Methanobacterium thermoautotrophicum contains two isoenzymes of MCR, designated MCR I and MCR II, which are expressed differentially under different conditions of growth. These two isoenzymes have been separated, purified and their catalytic and spectroscopic properties determined. Initial-velocity measurements of the two-substrate reaction showed that the kinetic mechanism for both isoenzymes involved ternary-complex formation. Double reciprocal plots of initial rates versus the concentration of either one of the two substrates at different constant concentrations of the other substrate were linear and intersected on the abcissa to the left of the 1/v axis. The two purified isoenzymes differed in their Km values for H-S-HTP and for CH3-S-CoM and in Vmax. MCR I displayed a Km for H-S-HTP of 0.1-0.3 mM, a Km for CH3-S-CoM of 0.6-0.8 mM and a Vmax of about 6 mumol.min-1 x mg-1 (most active preparation). MCR II showed a Km for H-S-HTP of 0.4-0.6 mM, a Km for CH3-S-CoM of 1.3-1.5 mM and a Vmax of about 21 mumol.min-1 x mg-1 (most active preparation). The pH optimum of MCR I was 7.0-7.5 and that of MCR II 7.5-8.0. Both isoenzymes exhibited very similar temperature activity optima and EPR properties. The location of MCR I and of MCR II within the cell, determined via immunogold labeling, was found to be essentially identical. The possible basis for the existence of MCR isoenzymes in M. thermoautotrophicum is discussed. << Less

  Eur J Biochem 217:587-595(1993) [PubMed] [EuropePMC]

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

  Ermler U., Grabarse W., Shima S., Goubeaud M., Thauer R.K.

  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 resol ... >> More

  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. << Less

  Science 278:1457-1462(1997) [PubMed] [EuropePMC]

• Spectroscopic and kinetic studies of the reaction of bromopropanesulfonate with methyl-coenzyme M reductase.

  Kunz R.C., Horng Y.C., Ragsdale S.W.

  Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis in which coenzyme B and methyl-coenzyme M are converted to methane and the heterodisulfide, CoMS-SCoB. MCR also appears to initiate anaerobic methane oxidation (reverse methanogenesis). At the active site of MCR is coenzy ... >> More

  Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis in which coenzyme B and methyl-coenzyme M are converted to methane and the heterodisulfide, CoMS-SCoB. MCR also appears to initiate anaerobic methane oxidation (reverse methanogenesis). At the active site of MCR is coenzyme F430, a nickel tetrapyrrole. This paper describes the reaction of the active MCR(red1) state with the potent inhibitor, 3-bromopropanesulfonate (BPS; I50 = 50 nM) by UV-visible and EPR spectroscopy and by steady-state and rapid kinetics. BPS was shown to be an alternative substrate of MCR in an ionic reaction that is coenzyme B-independent and leads to debromination of BPS and formation of a distinct state ("MCR(PS)") with an EPR signal that was assigned to a Ni(III)-propylsulfonate species (Hinderberger, D., Piskorski, R. P., Goenrich, M., Thauer, R. K., Schweiger, A., Harmer, J., and Jaun, B. (2006) Angew. Chem. Int. Ed. Engl. 45, 3602-3607). A similar EPR signal was generated by reacting MCR(red1) with several halogenated sulfonate and carboxylate substrates. In rapid chemical quench experiments, the propylsulfonate ligand was identified by NMR spectroscopy and high performance liquid chromatography as propanesulfonic acid after protonolysis of the MCR(PS) complex. Propanesulfonate formation was also observed in steady-state reactions in the presence of Ti(III) citrate. Reaction of the alkylnickel intermediate with thiols regenerates the active MCR(red1) state and eliminates the propylsulfonate group, presumably as the thioether. MCR(PS) is catalytically competent in both the generation of propanesulfonate and reformation of MCR(red1). These results provide evidence for the intermediacy of an alkylnickel species in the final step in anaerobic methane oxidation and in the initial step of methanogenesis. << Less

  J Biol Chem 281:34663-34676(2006) [PubMed] [EuropePMC]