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Diol dehydratase, dependent on coenzyme B12 (B12 -dDDH), displays a peculiar feature of being inactivated by its native substrate glycerol (GOL). Surprisingly, the isofunctional enzyme, B12 -independent glycerol dehydratase (B12 -iGDH), does not undergo suicide inactivation by GOL. Herein we present a series of QM/MM and MD calculations aimed at understanding the mechanisms of substrate-induced suicide inactivation in B12 -dDDH and that of resistance of B12 -iGDH to inactivation. We show that the first step in the enzymatic transformation of GOL, hydrogen abstraction, can occur from both ends of the substrate (either C1 or C3 of GOL). Whereas C1 abstraction in both enzymes leads to product formation, C3 abstraction in B12 -dDDH results in the formation of a low energy radical intermediate, which is effectively trapped within a deep well on the potential energy surface. The long lifetime of this radical intermediate likely enables its side reactions, leading to inactivation. In B12 -iGDH, by comparison, C3 abstraction is an endothermic step; consequently, the resultant radical intermediate is not of low energy, and the reverse process of reforming the reactant is possible.

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 (Eo') 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 (Eo' = -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.

Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F430. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 A distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)-sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.

Methyl-coenzyme M reductase (MCR) catalyzes both synthesis and anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of Cofactor F430. The Ni ion, in its low-valent Ni(I) state lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from Coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. Based on crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears too long for such a reaction. Spectroscopic, kinetic, structural and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both forward and reverse MCR reactions emanate through long-range electron transfer from Ni(I)-sulfonate complexes with methyl-SCoM or CoMSSCoB, respectively.

A sophisticated intracellular trafficking pathway in humans is used to tailor vitamin B(12) into its active cofactor forms, and to deliver it to two known B(12-)dependent enzymes. Herein, we report an unexpected strategy for cellular retention of B(12), an essential and reactive cofactor. If methylmalonyl-CoA mutase is unavailable to accept the coenzyme B(12) product of adenosyltransferase, the latter catalyzes homolytic scission of the cobalt−carbon bond in an unconventional reversal of the nucleophilic displacement reaction that was used to make it. The resulting homolysis product binds more tightly to adenosyltransferase than does coenzyme B(12), facilitating cofactor retention. We have trapped, and characterized spectroscopically, an intermediate in which the cobalt−carbon bond is weakened prior to being broken. The physiological relevance of this sacrificial catalytic activity for cofactor retention is supported by the significantly lower coenzyme B(12) concentration in patients with dysfunctional methylmalonyl-CoA mutase but normal adenosyltransferase activity.

The B12 responding btuB riboswitch is a short, non-coding RNA sequence involved in the gene-regulation of an outer membrane B12-transport protein in E. coli. This RNA is characterized by its selective high-affinity binding to coenzyme B12 and by the structural rearrangement it undergoes upon this interaction. Due to their involvement in (mostly) bacterial gene regulation, the btuB riboswitch as well as the further about twenty known classes of riboswitches received much attention in recent years. In case of the btuB riboswitch, the light sensitivity of its ligand, coenzyme B12, poses one of the greater challenges for its investigation. Vitamin B12 derivatives carrying a cyanide-bridged platinum(II) moiety offer an ideal strategy for the design of light stable coenzyme B12 analogs. Developed by Alberto and coworkers in 2005 these conjugates provide the possibility to coordinate an additional nucleobase making them potential coenzyme B12 mimics. However, although these derivatives show a high structural similarity to coenzyme B12, their functionality might differ and offers the opportunity to develop new classes of antibiotic agents. Especially the platinum(II)-complex could interact with RNA in an unexpected way, which is the main question addressed in the work presented here. We characterized the binding of three vitamin B12-platinum(II) complexes to two different RNAs: the B12-specific btuB riboswitch and the short RNA D1-45, which is a non-B12-binder. cisPt(II)VitB12+ (1) and enPt(II)VitB12+ (2) carry both a labile chloride ligand at the platinum(II) moiety whereas dienPt(II)VitB122+ (3), that carries no labile chloride ligand anymore, can be considered chemically inert under the applied conditions. Complexes 1 and 2 covalently bind to both RNAs as monitored by band-shift assays. In the case of the short D1-45 the shifted bands are well separated and were further analyzed by MALDI-MS proving the covalent interaction. Complex 3 is unable to covalently bind any of the two RNAs, which proves the general stability of the Pt(II) complex. However, the presence of this moiety has a dramatic influence on the binding property towards the B12-sensing riboswitch, as was observed in in-line probing assays by comparison to the natural ligand coenzyme B12.

Reduction of the disulfide of coenzyme M and coenzyme B (CoMS–SCoB) by heterodisulfide reductases (HdrED and HdrABC) is the final step in all methanogenic pathways. Flavin-based electron bifurcation (FBEB) by soluble HdrABC homologs play additional roles in driving essential endergonic reactions at the expense of the exergonic reduction of CoMS–SCoM. In the first step of the CO2 reduction pathway, HdrABC complexed with hydrogenase or formate dehydrogenase generates reduced ferredoxin (Fdx2-) for the endergonic reduction of CO2 coupled to the exergonic reduction of CoMS–SCoB dependent on FBEB of electrons from H2 or formate. Roles for HdrABC:hydrogenase complexes are also proposed for pathways wherein the methyl group of methanol is reduced to methane with electrons from H2. The HdrABC complexes catalyze FBEB-dependent oxidation of H2 for the endergonic reduction of Fdx driven by the exergonic reduction of CoMS–SCoB. The Fdx2- supplies electrons for reduction of the methyl group to methane. In H2- independent pathways, three-fourths of the methyl groups are oxidized producing Fdx2- and reduced coenzyme F420 (F420H2). The F420H2 donates electrons for reduction of the remaining methyl groups to methane requiring transfer of electrons from Fdx2- to F420. HdrA1B1C1 is proposed to catalyze FBEB-dependent oxidation of Fdx2- for the endergonic reduction of F420 driven by the exergonic reduction of CoMS–SCoB. In H2- independent acetotrophic pathways, the methyl group of acetate is reduced to methane with electrons derived from oxidation of the carbonyl group mediated by Fdx. Electron transport involves a membrane-bound complex (Rnf) that oxidizes Fdx2- and generates a Na+ gradient driving ATP synthesis. It is postulated that F420 is reduced by Rnf requiring HdrA2B2C2 catalyzing FBEB-dependent oxidation of F420H2 for the endergonic reduction of Fdx driven by the exergonic reduction of CoMS–SCoB. The Fdx2- is recycled by Rnf and HdrA2B2C2 thereby conserving energy. The HdrA2B2C2 is also proposed to play a role in Fe(III)-dependent reverse methanogenesis. A flavin-based electron confurcating (FBEC) HdrABC complex is proposed for nitrate-dependent reverse methanogenesis in which the oxidation of CoM-SH/CoB-SH and Fdx2- is coupled to reduction of F420. The F420H2 donates electrons to a membrane complex that generates a proton gradient driving ATP synthesis.

The purpose of this study was to compare the intestinal permeation of vitamin B12 and various derivatives thereof. Permeation behavior and cytotoxicity of four derivatives (coenzyme B12, hydroxocobalamin, methylcobalamin and 4-ethylphenylcobalamin) in comparison to vitamin B12 were evaluated in two different in vitro models, Caco-2 cells and freshly excised rat intestinal mucosa. Resazurin assay was used to evaluate cytotoxicity of the test substances. All test compounds were used at a concentration of 200 μg/ml. Permeation experiments were carried out for 3h and test compounds were quantified via reversed phase high performance liquid chromatography (HPLC). Cytotoxicity studies showed all test compounds are not toxic to cells. HPLC analyses of test compounds revealed the following rank order of increasing hydrophobicity: hydroxocobalamin

Methanogens are anaerobic archaea that grow by producing methane, a gas that is both an efficient renewable fuel and a potent greenhouse gas. We observed that overexpression of the cytoplasmic heterodisulfide reductase enzyme HdrABC increased the rate of methane production from methanol by 30% without affecting the growth rate relative to the parent strain. Hdr enzymes are essential in all known methane-producing archaea. They function as the terminal oxidases in the methanogen electron transport system by reducing the coenzyme M (2-mercaptoethane sulfonate) and coenzyme B (7-mercaptoheptanoylthreonine sulfonate) heterodisulfide, CoM-S-S-CoB, to regenerate the thiol-coenzymes for reuse. In Methanosarcina acetivorans , HdrABC expression caused an increased rate of methanogenesis and a decrease in metabolic efficiency on methylotrophic substrates. When acetate was the sole carbon and energy source, neither deletion nor overexpression of HdrABC had an effect on growth or methane production rates. These results suggest that in cells grown on methylated substrates, the cell compensates for energy losses due to expression of HdrABC with an increased rate of substrate turnover and that HdrABC lacks the appropriate electron donor in acetate-grown cells.

Methanogens are ancient obligate anaerobes, originating in an early Earth period before oxygen accumulated in the atmosphere and oceans. Unlike aerobic cells, all methanogens that persist in highly sulfidic, anaerobic niches are able to grow with sulfide as the sole sulfur source. These organisms have retained a unique apparatus for the assimilation and distribution of sulfur from the ambient environment. Recent work has revealed the presence of a unique set of at least six highly conserved genes likely responsible for sulfide uptake and synthesis of persulfide groups, cysteine, homocysteine, coenzyme M, coenzyme B, and cysteinyl-tRNACys. Phylogenetic studies show that these ancient sulfur assimilatory proteins share an evolutionary history with methanogenesis enzymes, suggesting that they played a key role in supporting the development of this metabolism. Little is yet known about most methanogen pathways that mobilize sulfur to form thiolated tRNA, iron-sulfur clusters, molybdopterin, and other important cofactors. However, for at least some of these pathways, it appears that the sulfur can be assimilated directly as sulfide, which is present at high intracellular levels without causing toxic effects. The many unique aspects of sulfur assimilation and trafficking in contemporary methanogens appear to be relics of ancient metabolic processes that were prevalent on the early anaerobic Earth.

Methanogens are masters of CO2 reduction. They conserve energy by coupling H2 oxidation to the reduction of CO2 to CH4, the primary constituent of natural gas. They also generate methane by the reduction of acetic acid, methanol, methane thiol, and methylamines. Methanogens produce 109 tons of methane per year and are the major source of the earth’s atmospheric methane. Reverse methanogenesis or anaerobic methane oxidation, which is catalyzed by methanotrophic archaea living in consortia among bacteria that can act as an electron acceptor, is responsible for annual oxidation of 108 tons of methane to CO2. This chapter briefly describes the overall process of methanogenesis and then describes the enzymatic mechanism of the nickel enzyme, methyl-CoM reductase (MCR), the key enzyme in methane synthesis and oxidation. MCR catalyzes the formation of methane and the heterodisulfide (CoBSSCoM) from methyl-coenzyme M (methyl-CoM) and coenzyme B (HSCoB). Uncovering the mechanistic and molecular details of MCR catalysis is critical since methane is an abundant and important fuel and is the second (to CO2) most prevalent greenhouse gas.

Methyl-coenzyme M reductase (MCR) catalyzes the reversible reduction of methyl-coenzyme M (CH 3 -S-CoM) and coenzyme B (HS-CoB) to methane and heterodisulfide CoM-S-S-CoB (HDS). MCR contains the hydroporphinoid nickel complex coenzyme F 430 in its active site, and the Ni center has to be in its Ni(I) valence state for the enzyme to be active. Until now, no in vitro method that fully converted the inactive MCR silent -Ni(II) form to the active MCR red1 -Ni(I) form has been described. With the potential use of recombinant MCR in the production of biofuels and the need to better understand this enzyme and its activation process, we studied its activation under nonturnover conditions and achieved full MCR activation in the presence of dithiothreitol and protein components A2, an ATP carrier, and A3a. It was found that the presence of HDS promotes the inactivation of MCR red1 , which makes it essential that the activation process is isolated from the methane formation assay, which tends to result in minimal activation rates. Component A3a is a multienzyme complex that includes the mcrC gene product, an Fe-protein homolog, an iron-sulfur flavoprotein, and protein components involved in electron bifurcation. A hypothetical model for the cellular activation process of MCR is presented.

Adenosylcobalamin, a coenzyme form of vitamin B 12 , is an organometallic compound that participates in about ten enzymatic reactions. These enzymes catalyze chemically challenging reactions by using a highly reactive primary carbon radical that is derived from homolysis of the coenzyme Co–C bond. Among them, diol dehydratases and ethanolamine ammonia-lyase have been most extensively studied to establish the general mechanism of adenosylcobalamin-assisted enzymatic catalysis and radical-catalyzed reactions. Another important point is that adenosylcobalamin-dependent radical enzymes are prone to mechanism-based irreversible inactivation during catalysis and have their own chaperones for the maintenance of catalytic activities. This review will highlight biochemical, structural, and computational studies with special emphases on radical catalysis and reactivating chaperones of these enzymes.

Heterodisulfide reductase (Hdr), is an iron-sulfur protein which in anaerobic methanogenic archaea catalyzes the reduction of the disulphide bond between coenzyme M and coenzyme B and is coupled to methane formation. In aerobic acidophilic chemolithotrophic bacteria (e.g., biomining bacteria) the function of this enzyme is unclear. Inspection of the genomic sequences of Acidithiobacillus ferrooxidans DSM 16786 and Acidithiobacillus thiooxidans DSM 17318 and reverse transcriptase-PCR results revealed a cluster of six co-transcribed genes, hdrC1, hdrB1, hdrA, orf1, hdrC2 and hdrB2, encoding proteins with high similarity to catalytic Hdr subunits. Additionally, microarray expression profiling and quantitative RT-PCR experiments demonstrated that the hdr genes of A.ferrooxidans and A. thiooxidans were highly expressed when bacteria are grown in the presence of sulfur and tetrathionate. Moreover, hdr genes in A. ferrooxidans were greatly up-regulated when this microorganism was grown in sulfur compared to ferrous medium. These results strongly support a role for Hdr in oxidative metabolism of reduced sulfur compounds in aerobic chemolithotrophic bacteria.

The biotechnological production of the methyl methacrylate precursor 2-hydroxyisobutyric acid (2-HIBA) via bacterial poly-3-hydroxybutyrate (PHB) overflow metabolism requires suitable ( R )-3-hydroxybutyryl coenzyme A (CoA)-specific coenzyme B 12 -dependent mutases (RCM). Here, we characterized a predicted mutase from Bacillus massiliosenegalensis JC6 as a mesophilic RCM closely related to the thermophilic enzyme previously identified in Kyrpidia tusciae DSM 2912 (M.-T. Weichler et al., Appl Environ Microbiol 81:4564–4572, 2015, https://doi.org/10.1128/AEM.00716-15 ). Using both RCM variants, 2-HIBA production from methanol was studied in fed-batch bioreactor experiments with recombinant Methylobacterium extorquens AM1. After complete nitrogen consumption, the concomitant formation of PHB and 2-HIBA was achieved, indicating that both sets of RCM genes were successfully expressed. However, although identical vector systems and incubation conditions were chosen, the metabolic activity of the variant bearing the RCM genes from strain DSM 2912 was severely inhibited, likely due to the negative effects caused by heterologous expression. In contrast, the biomass yield of the variant expressing the JC6 genes was close to the wild-type performance, and 2-HIBA titers of 2.1 g liter −1 could be demonstrated. In this case, up to 24% of the substrate channeled into overflow metabolism was converted to the mutase product, and maximal combined 2-HIBA plus PHB yields from methanol of 0.11 g g −1 were achieved. Reverse transcription-quantitative PCR analysis revealed that metabolic genes, such as methanol dehydrogenase and acetoacetyl-CoA reductase genes, are strongly downregulated after exponential growth, which currently prevents a prolonged overflow phase, thus preventing higher product yields with strain AM1. IMPORTANCE In this study, we genetically modified a methylotrophic bacterium in order to channel intermediates of its overflow metabolism to the C 4 carboxylic acid 2-hydroxyisobutyric acid, a precursor of acrylic glass. This has implications for biotechnology, as it shows that reduced C 1 substrates, such as methanol and formic acid, can be alternative feedstocks for producing today's commodities. We found that product titers and yields depend more on host physiology than on the activity of the introduced heterologous function modifying the overflow metabolism. In addition, we show that the fitness of recombinant strains substantially varies when they express orthologous genes from different origins. Further studies are needed to extend the overflow production phase in methylotrophic microorganisms for the implementation of biotechnological processes.

Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting., IMPORTANCE Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO2-reducing methanogens to include diverse prokaryotes from the domains Bacteria and Archaea. The unprecedented coenzyme F420-dependent electron bifurcation, an emerging fundamental principle of energy conservation, predicts a role for HdrA2B2C2 in diverse metabolisms, including anaerobic CH4-oxidizing pathways. The results document an electron transport role for HdrA2B2C2 in acetate-utilizing methanogens responsible for at least two-thirds of the methane produced in Earth’s biosphere. The previously unavailable heterologous production of individual subunits and the reconstitution of HdrA2B2C2 with activity have provided an understanding of intersubunit electron transfer in the HdrABC class and a platform for investigating the principles of electron bifurcation.

The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes two important transformations in the global carbon cycle: methane formation and its reverse, the anaerobic oxidation of methane. MCR uses the methyl thioether methyl-coenzyme M (CH3-S-CH2CH2-SO3(-), Me-S-CoM) and the thiol coenzyme B (CoB-SH) as substrates and converts them reversibly to methane and the corresponding heterodisulfide (CoB-S-S-CoM). The catalytic mechanism is still unknown. Here, we present isotope effects for this reaction in both directions, catalyzed by the enzyme isolated from Methanothermobacter marburgensis . For methane formation, a carbon isotope effect ((12)CH3-S-CoM/(13)CH3-S-CoM) of 1.04 ± 0.01 was measured, showing that breaking of the C-S bond in the substrate Me-S-CoM is the rate-limiting step. A secondary isotope effect of 1.19 ± 0.01 per D in the methyl group of CD3-S-CoM indicates a geometric change of the methyl group from tetrahedral to trigonal planar upon going to the transition state of the rate-limiting step. This finding is consistent with an almost free methyl radical in the highest transition state. Methane activation proceeds with a primary isotope effect of 2.44 ± 0.22 for the C-H vs C-D bond breakage and a secondary isotope effect corresponding to 1.17 ± 0.05 per D. These values are consistent with isotope effects reported for oxidative cleavage/reductive coupling occurring at transition metal centers during C-H activation but are also in the range expected for the radical substitution mechanism proposed by Siegbahn et al. The isotope effects presented here constitute boundary conditions for any suggested or calculated mechanism.

JBIC Journal of Biological Inorganic Chemistry, 8 (5), ISSN:0949-8257, ISSN:1432-1327

JBIC Journal of Biological Inorganic Chemistry, 13 (8), ISSN:0949-8257, ISSN:1432-1327

Find your path: Methyl-coenzyme M reductase (MCR, turquoise) reversibly catalyzes the reduction of methyl-coenzyme M (methyl-S-CoM) with coenzyme B (CoB-SH) to form methane and the heterodisulfide. Recently, spectroscopic methods were used to detect trapped intermediates in a stopped-flow system, and CoM-S-NiII was identified after half a turnover of the MCR reaction (F430 =nickel porphinoid). This finding supports a methyl-radical catalytic mechanism.

Crenarchaeotal genomes encode the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle for carbon dioxide fixation. Of the 13 enzymes putatively comprising the cycle, several of them, including methylmalonyl-coenzyme A (CoA) epimerase (MCE) and methylmalonyl-CoA mutase (MCM), which convert ( S )-methylmalonyl-CoA to succinyl-CoA, have not been confirmed and characterized biochemically. In the genome of Metallosphaera sedula (optimal temperature [ T opt ], 73°C), the gene encoding MCE (Msed_0639) is adjacent to that encoding the catalytic subunit of MCM-α (Msed_0638), while the gene for the coenzyme B 12 -binding subunit of MCM (MCM-β) is located remotely (Msed_2055). The expression of all three genes was significantly upregulated under autotrophic compared to heterotrophic growth conditions, implying a role in CO 2 fixation. Recombinant forms of MCE and MCM were produced in Escherichia coli ; soluble, active MCM was produced only if MCM-α and MCM-β were coexpressed. MCE is a homodimer and MCM is a heterotetramer (α 2 β 2 ) with specific activities of 218 and 2.2 μmol/min/mg, respectively, at 75°C. The heterotetrameric MCM differs from the homo- or heterodimeric orthologs in other organisms. MCE was activated by divalent cations (Ni 2+ , Co 2+ , and Mg 2+ ), and the predicted metal binding/active sites were identified through sequence alignments with less-thermophilic MCEs. The conserved coenzyme B 12 -binding motif ( DXHXXG -SXL-GG) was identified in M. sedula MCM-β. The two enzymes together catalyzed the two-step conversion of ( S )-methylmalonyl-CoA to succinyl-CoA, consistent with their proposed role in the 3-HP/4-HB cycle. Based on the highly conserved occurrence of single copies of MCE and MCM in Sulfolobaceae genomes, the M. sedula enzymes are likely to be representatives of these enzymes in the 3-HP/4-HB cycle in crenarchaeal thermoacidophiles.

Coenzyme B12 dependent diol dehydratase undergoes mechanism-based inactivation by glycerol, accompanying the irreversible cleavage of the coenzyme Co–C bond. Bachovchin et al. [Biochemistry16, 1082–1092 (1977)] reported that glycerol bound in the GS conformation, in which the pro-S-CH2OH group is oriented to the hydrogen-abstracting site, primarily contributes to the inactivation reaction. To understand the mechanism of inactivation by glycerol, we analyzed the X-ray structure of diol dehydratase complexed with cyanocobalamin and glycerol. Glycerol is bound to the active site preferentially in the same conformation as that of (S)-1,2-propanediol, i.e. in the GS conformation, with its 3-OH group hydrogen bonded to Serα301, but not to nearby Glnα336. kinact of the Sα301A, Qα336A and Sα301A/Qα336A mutants with glycerol was much smaller than that of the wild-type enzyme. kcat/kinact showed that the Sα301A and Qα336A mutants are substantially more resistant to glycerol inactivation than the wild-type enzyme, suggesting that Serα301 and Glnα336 are directly or indirectly involved in the inactivation. The degree of preference for (S)-1,2-propanediol decreased on these mutations. The substrate activities towards longer chain 1,2-diols significantly increased on the Sα301A/Qα336A double mutation, probably because these amino acid substitutions yield more space for accommodating a longer alkyl group on C3 of 1,2-diols. Database Structural data are available in the Protein Data Bank under the accession number 3AUJ. Structured digital abstract • Diol dehydrase gamma subunit, Diol dehydrase beta subunit and Diol dehydrase alpha subunit physically interact by X-ray crystallography (View interaction)

The pathways of glutamate catabolism in the anaerobic bacterium Fusobacterium varium, grown on complex, undefined medium and chemically defined, minimal medium, were investigated using specifically labelled (13)C-glutamate. The metabolic end-products acetate and butyrate were isolated from culture fluids and derivatized for analysis by nuclear magnetic resonance and mass spectrometry. On complex medium, labels from L-[1-(13)C]glutamate and L-[4-(13)C]glutamate were incorporated into C1 of acetate and equally into C1/C3 of butyrate, while label derived from L-[5-(13)C]glutamate was not incorporated. The isotopic incorporation results and the detection of glutamate mutase and 3-methylaspartate ammonia lyase in cell extracts are most consistent with the methylaspartate pathway, the best known route of glutamate catabolism in Clostridium species. When F. varium was grown on defined medium, label from L-[4-(13)C]glutamate was incorporated mainly into C4 of butyrate, demonstrating a major role for the hydroxyglutarate pathway. Upon addition of coenzyme B(12) or cobalt ion to the defined medium in replicate experiments, isotope was located equally at C1/C3 of butyrate in accord with the methylaspartate pathway. Racemization of D-glutamate and subsequent degradation of L-glutamate via the methylaspartate pathway are supported by incorporation of label into C2 of acetate and equally into C2/C4 of butyrate from D-[3-(13)C]glutamate and the detection of a cofactor-independent glutamate racemase in cell extracts. Together the results demonstrate a major role for the methylaspartate pathway of glutamate catabolism in F. varium and substantial participation of the hydroxyglutarate pathway when coenzyme B(12) is not available.

ATP:Cobalamin adenosyltransferases catalyze the transfer a 5'-deoxyadenosyl moiety from ATP to cob(I)alamin in the synthesis of the Co-C bond of coenzyme B(12). There are three types of adenosyltransferases, CobA, PduO and EutT. Among these adenosyltransferases, the PduO-type adenosyltransferases is the most widely distributed enzyme. Structural comparisons between apo BcPduO and BcPduO in complex with MgATP revealed that the N-terminal strands of both structures were ordered, which is in contrast with the most previously available PduO-type adenosyltransferase structures. Furthermore, unlike other reported structures, apo BcPduO was bound to additional dioxane molecules causing a side chain conformational change at the Tyr30 residue, which is an important residue that mediates hydrogen bonding with ATP molecules upon binding of cobalamin to the active site. This study provides more structural information into the role of active site residues on substrate binding.

Dunaliella salina is one natural food that is good enough for the larvae of sea urchins and also can be used as food Brachionus plicatilis and Artemia in aquaculture feed Artemia. Blotong is precipitated in the process of purification juice before cooking and crystallized into sugar. Purification is a process to separate the juice from dirt or fibers. Sugarcane is used as fertilizer by using oven dried first. Vitamin B is needed some algae to build 12 proteins and essential as a coenzyme necessary for DNA synthesis in the formation of new cells. Vitamin B is a 12 coenzyme B -dependent methionine synthase and vitamin B -dependent ribonucleotide reductase. Vitamin B 12 12 12 dependent methionine synthase function for synthesis methionin (essential amino acids), whereas vitamin B 12 dependent ribonucleotide reductase functions to DNA synthesis. This study aims to determine the effect of vitamin B in dry blotong media on the growth of D. salina 12 population and to determine the optimal dosage of vitamin B in dry blotong media which can produce the highest 12 population growth of D. salina. This research used Completely Randomized Design (CRD) with seven treatments and three replications. The study used namely: Fertilizer blotong dried with the addition of vitamin B 10 g / L (A), dose of 12 12 ug / L (B), the dose of 14 ug / L (C), a dose of 16 ug / L (D), dose 18 ug / L (E), a dose of 20 ug / L (F) and control treatment of dry sugarcane fertilizer without adding vitamin B12 or dose 0 g / L (G). The main parameter used is the population of D. salina, while supporting the water quality parameters (salinity, pH and water temperature). Data were analyzed with ANOVA (analysis of variants) and to know the differences among the treatments performed Duncan's Multiple Range Test. The results showed that the addition of vitamin B in dry blotong media had no effect on the growth of population D. salina (p> 0.05).

Adenosylcobalamin-dependent diol dehydratase (DD) undergoes suicide inactivation by glycerol, one of its physiological substrates, resulting in the irreversible cleavage of the coenzyme Co–C bond. The damaged cofactor remains tightly bound to the active site. The DD-reactivating factor reactivates the inactivated holoenzyme in the presence of ATP and Mg2+ by mediating the exchange of the tightly bound damaged cofactor for free intact coenzyme. In this study, we demonstrated that this reactivating factor mediates the cobalamin exchange not stoichiometrically but catalytically in the presence of ATP and Mg2+. Therefore, we concluded that the reactivating factor is a sort of enzyme. It can be designated DD reactivase. The reactivase showed broad specificity for nucleoside triphosphates in the activation of the enzyme·cyanocobalamin complex. This result is consistent with the lack of specific interaction with the adenine ring of ADP in the crystal structure of the reactivase. The specificities of the reactivase for divalent metal ions were also not strict. DD formed 1 : 1 and 1 : 2 complexes with the reactivase in the presence of ADP and Mg2+. Upon complex formation, one β subunit was released from the (αβ)2 tetramer of the reactivase. This result, together with the similarity in amino acid sequences and folds between the DD β subunit and the reactivase β subunit, suggests that subunit displacement or swapping takes place upon formation of the enzyme·reactivase complex. This would result in the dissociation of the damaged cofactor from the inactivated holoenzyme, as suggested by the crystal structures of the reactivase and DD. Structured digital abstract • MINT-7997177: Reactivase alpha (uniprotkb: O68195), Reactivase beta (uniprotkb: O68196), Diol Dehydratase gamma (uniprotkb: Q59472), Diol Dehydratase beta (uniprotkb: Q59471) and Diol Dehydratase alpha (uniprotkb: Q59470) physically interact (MI:0915) by comigration in non denaturing gel electrophoresis (MI:0404) • MINT-7997157: Diol Dehydratase alpha (uniprotkb: Q59470), Diol Dehydratase beta (uniprotkb: Q59471), Diol Dehydratase gamma (uniprotkb: Q59472), Reactivase beta (uniprotkb: O68196) and Reactivase alpha (uniprotkb: O68195) physically interact (MI:0915) by molecular sieving (MI:0071)

The genomes of Listeria spp. encode all but one of 25 enzymes required for the biosynthesis of adenosylcobalamin (AdoCbl; coenzyme B(12) ). Notably, all Listeria genomes lack CobT, the nicotinamide mononucleotide:5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (EC 2.4.2.21) enzyme that synthesizes the unique α-linked nucleotide N(1) -(5-phospho-α-D-ribosyl)-DMB (α-ribazole-5'-P, α-RP), a precursor of AdoCbl. We have uncovered a new pathway for the synthesis of α-RP in Listeria innocua that circumvents the lack of CobT. The cblT and cblS genes (locus tags lin1153 and lin1110) of L. innocua encode an α-ribazole (α-R) transporter and an α-R kinase respectively. Results from in vivo experiments indicate that L. innocua depends on CblT and CblS activities to salvage exogenous α-R, allowing conversion of the incomplete corrinoid cobinamide (Cbi) into AdoCbl. Expression of the L. innocua cblT and cblS genes restored AdoCbl synthesis from Cbi and α-R in a Salmonella enterica cobT strain. LinCblT transported α-R across the cell membrane, but not α-RP or DMB. UV-visible spectroscopy and mass spectrometry data identified α-RP as the product of the ATP-dependent α-R kinase activity of LinCblS. Bioinformatics analyses suggest that α-R salvaging occurs in important Gram-positive human pathogens.

The X-ray analyses of coenzyme B(12)-dependent diol dehydratase revealed two kinds of electron densities that correspond to metal ions in the active site. One is directly coordinated by substrate [Shibata, N., et al. (1999) Structure 7, 997-1008] and the other located near the adenine ring of the coenzyme adenosyl group [Masuda, J., et al. (2000) Structure 8, 775-788]. Both have been assigned as potassium ions, although the coordination distances of the former are slightly shorter than expected. We examined the possibility that the enzyme is a metalloenzyme. Apodiol dehydratase was strongly inhibited by incubation with EDTA and EGTA in the absence of substrate. The metal analysis revealed that the enzyme contains approximately 2 mol of tightly bound calcium per mole of enzyme. The calcium-deprived, EDTA-free apoenzyme was obtained by the EDTA treatment, followed by ultrafiltration. The activity of the calcium-deprived apoenzyme was dependent on Ca(2+) when assayed with 1 mM substrate. The K(m) for Ca(2+) evaluated in reconstitution experiments was 0.88 muM. These results indicate that the calcium is essential for catalysis. Ca(2+) showed a significant stabilizing effect on the calcium-deprived apoenzyme as well. It was thus concluded that the substrate-coordinated metal ion is not potassium but calcium. The potassium ion bound near the adenine ring would be the essential one for the diol dehydratase catalysis. Therefore, this enzyme can be considered to be a metal-activated metalloenzyme.

SummarySmall molecules play crucial roles in every major cellular process. Despite this, detecting their levels within cells remains a significant challenge. Here, we describe intracellular sensors of coenzyme B12 that make use of the exquisite molecular detection capabilities of a naturally occurring riboswitch. These probes sensitively detect their target using colorimetric, fluorescent, or luminescent reporters. To assess their utility in the study of biological systems, the sensors were applied to examine the synthesis and the import of coenzyme B12. The sensors were able to monitor the effects of genetic deletions, recombinant expression of foreign genes, and varied growth conditions on both of these processes. These results indicate that riboswitch-based sensors can provide valuable information on intracellular small molecule concentrations that can be employed in the study of related cellular processes.

Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B(12), AdoCbl) or by single-electron reduction of S-adenosylmethionine (AdoMet) complexed to an iron-sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans.

The methods of homologous high-level expression and simple large-scale purification for coenzyme B(12)-dependent ethanolamine ammonia-lyase of Escherichia coli were developed. The eutB and eutC genes in the eut operon encoded the large and small subunits of the enzyme, respectively. The enzyme existed as the heterododecamer alpha(6)beta(6). Upon active-site titration with adeninylpentylcobalamin, a strong competitive inhibitor for coenzyme B(12), the binding of 1 mol of the inhibitor per mol of the alphabeta unit caused complete inhibition of enzyme, in consistent with its subunit structure. EPR spectra indicated the formation of substrate-derived radicals during catalysis and the binding of cobalamin in the base-on mode, i.e. with 5,6-dimethylbenzimidazole coordinating to the cobalt atom. The purified wild-type enzyme underwent aggregation and inactivation at high concentrations. Limited proteolysis with trypsin indicated that the N-terminal region is not essential for catalysis. His-tagged truncated enzymes were similar to the wild-type enzyme in catalytic properties, but more resistant to p-chloromercuribenzoate than the wild-type enzyme. A truncated enzyme was highly soluble even in the absence of detergent and resistant to aggregation and oxidative inactivation at high concentrations, indicating that a short N-terminal sequence is sufficient to change the solubility and stability of the enzyme.

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that use free radicals to catalyse unusual and chemically difficult rearrangements involving 1,2-migrations of hydrogen atoms. A key mechanistic feature of these enzymes is the transfer of the migrating hydrogen atom between substrate, coenzyme and product. The present review summarizes recent experiments from my laboratory that have used rapid chemical quench techniques to identify intermediates in the reaction and probe the mechanism of hydrogen transfer through a variety of pre-steady-state kinetic isotope effect measurements.

The genes encoding glycerol dehydratase were cloned and characterized by genomic DNA from Klebsiella pneumoniae XJPD-Li, and the assigned accession number EF634063 was available from the GenBank database. The DNA sequence analysis showed that the clone included three ORFs ( dha B, dha C and dha E, encoding α, β and γ subunit of glycerol dehydratase, respectively). Among three subunits of glycerol dehydratase, amino acid residues H 13 , S 193 , N 359 , E 407 , and M 515 of α subunit, N 47 , L 150 , V 189 of β subunit are different with what had been reported. Subsequently, the expression vector was constructed and transformed into E. coli BL21, and the colony carried genes of glycerol dehydratase were selected. SDS-PAGE examination showed that the three subunits were well expressed. The specific activity of recombined glycerol dehydratase reached to 0.299 U mg −1 , which was about 3 times comparing with that of the wild strain. The research also displayed that both glycerol and O 2 could inactive the glycerol dehydratase expressed in E. coli quickly in 10 min. The inactivated glycerol dehydratase could be effectively reactivated under the system as follows: the concentration of ATP, Mg 2+ and coenzyme B 12 were 50 mM, 10 mM and 3 μM, respectively, when the ratio (W/W) of glycerol dehydratase to reactivation factor was 4:1. The O 2 -inactivated and glycerol-inactivated dehydratase could be reactivated to 97.3% and 98.9% of initial activity in 10 min in above-mentioned conditions, respectively. The reactivation factor together with ATP was considered as the “ON/OFF” reactivating condition.

3-Hydroxypropionic acid (3-HP) is an important platform chemical from which several commodity and specialty chemicals can be generated. The present investigation focuses on the construction and evaluation of a recombinant strain Escherichia coli SH254 that produces 3-HP from glycerol. The strain was developed by cloning two genes, dhaB of Klebsiella pneumoniae DSM 2026 encoding glycerol dehydratase and aldH of E. coli K-12 MG1655 encoding aldehyde dehydrogenase, respectively. In vitro assays of crude enzyme extract of glycerol dehydratase (DhaB) showed 37.0 U mg −1 protein on glycerol with coenzyme B 12 , and partially purified aldehyde dehydrogenase (AldH) exhibited 22.8 U mg −1 protein on 3-hydroxypropionaldehyde (3-HPA) with NAD + as a cofactor. When cultivated aerobically on a glycerol medium containing yeast extract, the recombinant E. coli SH254 produced 3-HP at a maximum of 6.5 mmol l −1 (0.58 g l −1 ). The highest specific rate and yield of 3-HP production were estimated as 6.6 mmol g −1 cdw h −1 and 0.48 mol mol −1 glycerol, respectively. Although not optimized extensively, this study is encouraging for further development of a bioprocess to produce 3-HP from glycerol.

The X-ray structure of the diol dehydratase–adeninylpentylcobalamin complex revealed that the adenine moiety of adenosylcobalamin is anchored in the adenine-binding pocket of the enzyme by hydrogen bonding of N3 with the side chain OH group of Serα224, and of 6-NH2, N1 and N7 with main chain amide groups of other residues. A salt bridge is formed between the e-NH2 group of Lysβ135 and the phosphate group of cobalamin. To assess the importance of adenine anchoring and ion pairing, Serα224 and Lysβ135 mutants of diol dehydratase were prepared, and their catalytic properties investigated. The Sα224A, Sα224N and Kβ135E mutants were 19–2% as active as the wild-type enzyme, whereas the Kβ135A, Kβ135Q and Kβ135R mutants retained 58–76% of the wild-type activity. The presence of a positive charge at the β135 residue increased the affinity for cobalamins but was not essential for catalysis, and the introduction of a negative charge there prevented the enzyme–cobalamin interaction. The Sα224A and Sα224N mutants showed a kcat/kinact value that was less than 2% that of the wild-type, whereas for Lysβ135 mutants this value was in the range 25–75%, except for the Kβ135E mutant (7%). Unlike the wild-type holoenzyme, the Sα224N and Sα224A holoenzymes showed very low susceptibility to oxygen in the absence of substrate. These findings suggest that Serα224 is important for cobalt–carbon bond activation and for preventing the enzyme from being inactivated. Upon inactivation of the Sα224A holoenzyme during catalysis, cob(II)alamin accumulated, and a trace of doublet signal due to an organic radical disappeared in EPR. 5′-Deoxyadenosine was formed from the adenosyl group, and the apoenzyme itself was not damaged. This inactivation was thus considered to be a mechanism-based one.

Adenosylcobalamin (AdoCbl)-dependent glutamate mutase from Clostridium tetanomorphum comprises two weakly-associating subunits, MutS and MutE, which combine with AdoCbl to form the active holo-enzyme. Three coenzyme analogs, methylcobinamide (MeCbi), adenosylcobinamide (AdoCbi) and adeosylcobinamide-GDP (AdoCbi-GDP), were synthesized at milligram scale. Equilibrium dialysis was used to measure the binding of coenzyme B(12) analogs to glutamate mutase. Our results show that, unlike AdoCbl-dependent methylmalonyl CoA mutase, the ratio k(cat)/K(m) decreased approximately 10(4)-fold in both cases when AdoCbi or AdoCbi-GDP was used as the cofactor. The coenzyme analog-binding studies show that, in the absence of the ribonucleotide tail of AdoCbl, the enzyme's active site cannot correctly accommodate the coenzyme analog AdoCbi. The results presented here shed some light on the cobalt-carbon cleavage mechanism of B(12).

Coenzyme B(12)-dependent glycerol dehydratase is a radical enzyme that catalyses the conversion of glycerol into 3-hydroxypropanal and propane-1,2-diol into propanal via enzyme-bound intermediate radicals. The substrate analogue but-3-ene-1,2-diol was studied in the expectation that it would lead to the 4,4-dihydroxylbut-2-en-1-yl radical, which is stabilised (allylic) and not reactive enough to retrieve a hydrogen atom from 5'-deoxyadenosine, thereby interrupting the catalytic cycle. Racemic and enantiomerically pure but-3-ene-1,2-diols and their [1,1-(2)H(2)], [2-(2)H] and [4,4-(2)H(2)] isotopomers were synthesised and characterised by NMR spectroscopy. (S)-[4-(14)C]but-3-ene-1,2-diol was also prepared. Kinetic measurements showed but-3-ene-1,2-diol to be a competitive inhibitor of glycerol dehydratase (K(i)=0.21 mM, k(i)=5.0x10(-2) s(-1)). With [4-(14)C]but-3-ene-1,2-diol it was demonstrated that species derived from the diol become tightly bound to the enzyme's active site, but not covalently bound, because the radioactivity could be removed upon denaturation of the enzyme. EPR measurements with propane-1,2-diol as substrate generated sharp signals after 10 s that disappeared after about 1 min. In contrast, EPR resonances appeared and disappeared more slowly when but-3-ene-1,2-diol was incubated with the enzyme. Among the deuterated isotopomers, only [1,1-(2)H(2)]but-3-ene-1,2-diol showed a significantly different EPR spectrum from that of the unlabelled diol; this indicated that coupling between the unpaired electron and a deuterium at C-1 was stronger than with deuterium at C-2 or C-4. The experiments suggest the formation of the 1,2-dihydroxybut-3-en-1-yl radical, which decomposes to unidentified product(s).

Methanogenic archaea utilize a specific pathway in their metabolism, converting C1 substrates (i.e., CO2) or acetate to methane and thereby providing energy for the cell. Methyl-coenzyme M reductase (MCR) catalyzes the key step in the process, namely methyl-coenzyme M (CH3-S-CoM) plus coenzyme B (HS-CoB) to methane and CoM-S-S-CoB. The active site of MCR contains the nickel porphinoid F430. We report here on the coordinated ligands of the two paramagnetic MCR red2 states, induced when HS-CoM (a reversible competitive inhibitor) and the second substrate HS-CoB or its analogue CH3-S-CoB are added to the enzyme in the active MCR red1 state (Ni(I)F430). Continuous wave and pulse EPR spectroscopy are used to show that the MCR red2a state exhibits a very large proton hyperfine interaction with principal values A((1)H) = [-43,-42,-5] MHz and thus represents formally a Ni(III)F430 hydride complex formed by oxidative addition to Ni(I). In view of the known ability of nickel hydrides to activate methane, and the growing body of evidence for the involvement of MCR in "reverse" methanogenesis (anaerobic oxidation of methane), we believe that the nickel hydride complex reported here could play a key role in helping to understand both the mechanism of "reverse" and "forward" methanogenesis.

The reactions of diol dehydratase with 3-unsaturated 1,2-diols and thioglycerol were investigated. Holodiol dehydratase underwent rapid and irreversible inactivation by either 3-butene-1,2-diol, 3-butyne-1,2-diol or thioglycerol without catalytic turnovers. In the inactivation, the Co-C bond of adenosylcobalamin underwent irreversible cleavage forming unidentified radicals and cob(II)alamin that resisted oxidation even in the presence of oxygen. Two moles of 5'-deoxyadenosine per mol of enzyme was formed as an inactivation product from the coenzyme adenosyl group. Inactivated holoenzymes underwent reactivation by diol dehydratase-reactivating factor in the presence of ATP, Mg(2+) and adenosylcobalamin. It was thus concluded that these substrate analogues served as mechanism-based inactivators or pseudosubstrates, and that the coenzyme was damaged in the inactivation, whereas apoenzyme was not damaged. In the inactivation by 3-unsaturated 1,2-diols, product radicals stabilized by neighbouring unsaturated bonds might be unable to back-abstract the hydrogen atom from 5'-deoxyadenosine and then converted to unidentified products. In the inactivation by thioglycerol, a product radical may be lost by the elimination of sulphydryl group producing acrolein and unidentified sulphur compound(s). H(2)S or sulphide ion was not formed. The loss or stabilization of product radicals would result in the inactivation of holoenzyme, because the regeneration of the coenzyme becomes impossible.

Homolytic cobalt–carbon bond cleavages of methylcobalamin (coenzyme B12) and a B12 analogue, [(DH)2(CH3)Co(py)] ((DH)2 = bis(dimethylglyoximate), py = pyridine) by UVA irradiation induced effective DNA strand scission by generated methyl radical under anaerobic conditions. The efficiency of DNA strand scission is drastically changed depending on the type of generated radicals. For example, the photoexcitation of 5′-deoxyladenosylcobalamin (one of coenzyme B12) under anaerobic condition results in less effective DNA cleavage. No DNA cleavage has occurred under photoirradiation of (DH)2(PhCH2)Co(py), because the reactivity of benzyl radical formed by Co–C bond cleavage is much lower than that of methyl radical. The photoreactivity of coenzyme B12 and organocobaloximes toward DNA nucleotides was also examined in order to compare the reactivity with those of DNA cleavage. In contrast to the efficient DNA strand scission by photoirradiation of methylcobalamin and (DH)2(CH3)Co(py) in the absence of oxygen, the photoirradiation in the presence of oxygen under otherwise the same experimental conditions resulted in no DNA cleavage. This indicates that the DNA cleavage by alkyl radicals is suppressed by molecular oxygen, because alky radicals are converted to the much less reactive alkylperoxyl radicals.

Complete B 12 derivatives are natural "molecular switches" as a result of the coordinative switch ("base on" or "base off") of the natural nucleotide base. Certain predesigned B 12 -nucleotide conjugates were shown recently to behave as "retro riboswitches", in which the nucleotide environment modified the equilibrium between these two isomeric B 12 structures. In contrast, the "reverse" situation has been discovered in natural B 12 riboswitches, in which the binding of coenzyme B 12 induces a conformational switch in the RNA species. The first (predesigned) B 12 -retro-riboswitches were DNA conjugates of methylcobalamin. We describe herein two representative B 12 -retro-riboswitches, in which an appended (RNA) nucleotide is used to destabilize the base-on form and induce the base-on to base-off switch. Through use of heterogeneous solid-phase synthetic methods, Co β -cyanoco-balamin-(3"→2')-2"-methoxyguaninyl-3"-ate was prepared first as the crucial covalent RNA conjugate of vitamin B 12 . This cyanocorrinoid opened the door to two organometallic B 12 -nucleo-tide conjugates, which were made by electrosynthetic means: the cyanocorrinoid was cleanly methylated or adeno-sylated at the cobalt center to furnish covalent RNA conjugates of the organometallic B 12 cofactors methylcobalamin and coenzyme B 12 , respectively. At room temperature, aqueous solutions of both of these organometallic RNA-B 12 conjugates exhibited properties indicative of significant weakening of the axial (Co-N) bond (of their base-on forms) and of an enhanced formation of the base-off species. The base-on to base-off switch was studied by UV/Vis and NMR spectroscopic studies, which showed that the switch was very temperature-dependent and was accentuated with increasing temperatures. Thermodynamic data of the two organometallic RNA-B 12 conjugates revealed an important contribution of entropic effects to the observed base-on to base-off switch. The two organometallic RNA-B 12 conjugates thus acted as B 12 -retro-riboswitches and allowed the observation of a temperature-dependent reverse switch in the B 12 cofactor moiety, induced by the appended nucleotide moiety. This behavior may be of interest in the "RNA-world" hypothesis, in which (simple) B 12 derivatives are thought to act as possible catalytic enhancers ("cofactors") in RNA-based "B 12 ribozymes".

Kinetic isotope effects (KIEs) provide a powerful tool to interrogate transition states of both enzymic and non-enzymic reactions, provided that one can measure the intrinsic KIE on the chemical step of interest, that is, the isotope effect undiminished by other isotope-insensitive steps that may contribute to the overall rate of reaction. For small molecules reacting in solution the KIE measured usually represents the intrinsic value; however, for enzymes this is seldom the case. Here we report the first measurement of the intrinsic KIE in an adenosylcobalamin enzyme (AdoCbl, coenzyme B12) for hydrogen atom transfer from substrate to coenzyme, which is a key step in the mechanism of this class of enzymes. For the B12 enzyme glutamate mutase the intrinsic deuterium KIE for hydrogen transfer from the substrate, (2S,3S)-3-methylaspartate, to 5’-deoxyadensosine is 4.1. This value is well within the semiclassical limit for a deuterium isotope effect and is much smaller than the anomalously large KIEs previously measured in other B12 enzymes and non-enzymatic model reactions, which were attributed to extensive hydrogen tunneling. Glutamate mutase one is of a group of AdoCbl-dependent enzymes that catalyze unusual isomerization reactions that formally involve a 1,2 hydrogen atom migration and proceed through a mechanism involving carbon-based free radical intermediates (Scheme 1). Radicals are generated by homolysis of the reactive cobalt–carbon bond of the coenzyme to form cob(II)alamin, a cobalt(II) intermediate, and the 5’-deoxyadenosyl radical. The adenosyl radical then abstracts the migrating hydrogen from the substrate to form 5’-deoxyadenosine and the substrate radical. The substrate radical next undergoes rearrangement to give the product radical, which is then quenched by hydrogen transfer from 5’deoxyadenosine to give the product and regenerate the 5’deoxyadenosyl radical. Finally, recombination of the adenosyl radical and cob(II)alamin to reform the coenzyme completes the catalytic cycle. Our interest in the mechanisms by which enzymes generate free radicals, as exemplified by dependent glutamate mutase, led us to undertake an extensive set of KIE measurements to examine how hydrogen abstraction from the substrate and coenzyme homolysis are coupled together. KIE measurements using deuteriumand tritium-labeled substrates and coenzyme have proved especially informative probes of the key steps of Co C bond homolysis and hydrogen atom abstraction from substrate. Pre-steady-state measurements on a number of enzymes have shown that hydrogen abstraction is kinetically coupled to Co C bond homolysis, as evidenced by the appearance of a kinetic isotope effect on cobalt–carbon bond homolysis when the enzymes are reacted with deuterated substrates. This observation implies that the 5’-dA radical is a highenergy intermediate that only has a fleeting existence. Furthermore, the KIEs reported for several AdoCbl enzymes are extremely large (ranging from 10 to 50), which has generally been attributed to hydrogen tunneling. In particular, extensive hydrogen tunneling in methylmalonyl-CoA mutase has been deduced from the temperature dependence of the deuterium isotope effect on hydrogen transfer and Co C bond homolysis. The KIEs discussed above were all measured indirectly by UV/Vis stopped-flow spectroscopy, using the spectroscopic changes associated with Co C bond homolysis as a convenient reporter of the kinetics. Although we originally reported a very large primary deuterium isotope effect, suggestive of tunneling, for the formation of cob(II)alamin and 5’-dA upon reaction of hologlutamate mutase with deuterated substrates (kH/kD= 28 with glutamate and 35 with methylaspartate), [11]

Adenosylcobalamin-dependent diol and glycerol dehydratases are isofunctional enzymes and undergo mechanism-based inactivation by a physiological substrate glycerol during catalysis. Inactivated holoenzymes are reactivated by their own reactivating factors that mediate the ATP-dependent exchange of an enzyme-bound, damaged cofactor for free adenosylcobalamin through intermediary formation of apoenzyme. The reactivation takes place in two steps: (a) ADP-dependent cobalamin release and (b) ATP-dependent dissociation of the resulting apoenzyme–reactivating factor complexes. The in vitro experiments with purified proteins indicated that diol dehydratase-reactivating factor (DDR) cross-reactivates the inactivated glycerol dehydratase, whereas glycerol dehydratase-reactivating factor (GDR) did not cross-reactivate the inactivated diol dehydratase. We investigated the molecular basis of their specificities in vitro by using purified preparations of cognate and noncognate enzymes and reactivating factors. DDR mediated the exchange of glycerol dehydratase-bound cyanocobalamin for free adeninylpentylcobalamin, whereas GDR cannot mediate the exchange of diol dehydratase-bound cyanocobalamin for free adeninylpentylcobalamin. As judged by denaturing PAGE, the glycerol dehydratase–DDR complex was cross-formed, although the diol dehydratase–GDR complex was not formed. There were no specificities of reactivating factors in the ATP-dependent dissociation of enzyme–reactivating factor complexes. Thus, it is very likely that the specificities of reactivating factors are determined by the capability of reactivating factors to form complexes with apoenzymes. A modeling study based on the crystal structures of enzymes and reactivating factors also suggested why DDR cross-forms a complex with glycerol dehydratase, and why GDR does not cross-form a complex with diol dehydratase.

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 F 430 , an essential redox-active nickel tetrahydrocorphin, at its active site. The active form of MCR (MCR red1 ) contains Ni(I)-F 430 . When 3-bromopropane sulfonate (BPS) is incubated with MCR red1 , an alkyl-Ni(III) species is formed that elicits the MCR PS 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 MCR red1 state. When reacted with 4-bromobutyrate, MCR red1 forms the alkyl-Ni(III) MCR XA state and then, surprisingly, undergoes "self-reactivation" to regenerate the Ni(I) MCR red1 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.

Glycerol dehydratase (EC 4.2.1.30), as one of the key enzymes in converting glycerol to the valuable intermediate 1,3-propanediol, is important for biochemical industry. The dhaB genes encoding coenzyme B(12)-dependent glycerol dehydratase in Klebsiella pneumoniae were cloned and expressed in Escherichia coli. An effective co-expression system of multiple subunits protein was constructed. Heterologous expression vectors were constructed using the splicing by overlap extension-PCR technique to co-express the three subunits of the glycerol dehydratase. After induction by isopropyl-beta-D-thiogalactopyranoside, SDS-PAGE analysis revealed that: (i) only the alpha subunit of glycerol dehydratase was expressed in direct expression system, (ii) the three subunits of glycerol dehydratase with predicted molecular massess of 64 (agr;), 22 (beta), and 16 kDa (gamma) were expressed simultaneously in co-expression system, and (iii) the fusion expression system expressed the fusion protein of 99 kDa. Enzyme assay showed that the activities of three heterologous expression products were 27.4, 2.3, and 0.2 U/mg. The highest enzyme activity was almost 17 times of that in K. pneumoniae. The recombinant enzyme was purified and biochemically characterized. The apparent Km values of the enzyme for coenzyme B(12) and 1, 2-propanediol were 8.5 nM and 1.2 mM, respectively. The enzyme showed maximum activity at pH 8.5 and 37 degrees C.

Arginine 100 plays an important role in substrate recognition in adenosylcobalamin-dependent glutamate mutase. We have examined how the mutation of this residue to lysine affects the partitioning of tritium, incorporated at the exchangeable position of the coenzyme, between substrate and product. We find that partitioning of tritium back to the substrate predominates in the mutant enzyme, regardless of whether the reaction is run in the forward or reverse direction. This contrasts with the behavior of the wild-type enzyme in which tritium partitions equally between substrate and product, independent of the direction of the reaction. From this we conclude that the mutation significantly impairs the ability of the enzyme to catalyze the rearrangement of substrate radical to product radical. The results illustrate the importance of electrostatic interactions in stabilizing free radical intermediates in this class of enzymes.

Kinetic isotope effects provide a powerful method to investigate the mechanisms of enzyme-catalyzed reactions, but often other slow steps in the reaction such as substrate binding or product release suppress the isotopically sensitive step. For reactions at methyl groups, this limitation may be overcomed by measuring the isotope effect by an intra-molecular competition experiment. This requires the synthesis of substrates containing regio-specifically mono- or di-deuterated methyl groups. To facilitate the mechanistic investigations of the adenosylcobalamin-dependent enzyme, glutamate mutase, we have developed a synthesis of mono- and di-deuterated (2S,3S)-3-methylaspartic acids. Key intermediates are the correspondingly labeled mesaconic acids and their dimethyl esters that potentially provide starting materials for a variety of isotopically labeled molecules.

The “complete” corrinoid 176-norpseudovitamin B12 was recently isolated as the cyano-Co(III)-form of the corrinoid cofactor of tetrachlorethene reductive dehalogenase of the anaerobe Sulfurospirillum (formerly Dehalospirillum) multivorans. 176-Norpseudovitamin B12 represents the first example of (the cyano-Co(III)-form of) a naturally occurring “complete” B12 cofactor lacking a characteristic peripheral methyl group of the cobamide ligand. Its discovery has generated interest in 176-nor-B12 derivatives, “complete” corrinoids lacking the methyl group attached to carbon 176. Here, we report the preparation of Coβ-5′-adenosyl-176-norcobinamide by in situ alkylation of Co(I)-176-norcobinamide, obtained from electrochemical reduction of Coα,Coβ-dicyano-176-norcobinamide. Since Coβ-5′-adenosylcobinamide is a biosynthetic intermediate of the complete cobamides, Coβ-5′-adenosyl-176-norcobinamide is a “rational” biosynthetic precursor for natural 176-nor-B12 derivatives. The spectroscopic data for adenosyl-176-norcobinamide establish the suggested structure of the title compound and give further evidence for the extensive flexibility and conformational dynamics of the organometallic 5′-deoxy-5′-adenosyl ligand.

Nylon-6 is a bulk polymer used for many applications. It consists of the non-natural building block 6-aminocaproic acid, the linear form of caprolactam. Via a retro-synthetic approach, two synthetic pathways were identified for the fermentative production of 6-aminocaproic acid. Both pathways require yet unreported novel biocatalytic steps. We demonstrated proof of these bioconversions by in vitro enzyme assays with a set of selected candidate proteins expressed in Escherichia coli. One of the biosynthetic pathways starts with 2-oxoglutarate and contains bioconversions of the ketoacid elongation pathway known from methanogenic archaea. This pathway was selected for implementation in E. coli and yielded 6-aminocaproic acid at levels up to 160 mg/L in lab-scale batch fermentations. The total amount of 6-aminocaproic acid and related intermediates generated by this pathway exceeded 2 g/L in lab-scale fed-batch fermentations, indicating its potential for further optimization toward large-scale sustainable production of nylon-6.