Carbon Monoxide Dehydrogenase Enzyme Research Articles

Kinetics and Mechanism of Alkyl Transfer from Organocobalt(III) to Nickel(I): Implications for the Synthesis of Acetyl Coenzyme A by CO Dehydrogenase

Reaction of CH3Co(dmgBF2)2L (dmgBF2 = (difluoroboryl)dimethylglyoximato); L = py, PEt3) with 2 equiv of [Ni(tmc)]OTf (tmc = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane; OTf- = CF3SO3-) gave Co(dmgBF2)2py-, [Ni(tmc)]OTf2, and [Ni(tmc)CH3]OTf in 80% yield. The overall transformation provides the first model for the transfer of a CH3 group from methylcobalamin to the Ni-containing enzyme carbon monoxide dehydrogenase during acetyl coenzyme A synthesis. RRSS−[Ni(tmc)CH3](BAr‘4) (BAr‘4- = B(3,5-(CF3)2C6H3)4-) has been characterized by X-ray diffraction. The products and 1CH3Co(dmgBF2)2L:2[Ni(tmc)]OTf stoichiometry of the reaction are consistent with a three-step mechanism initiated by electron transfer from [Ni(tmc)]OTf to CH3Co(dmgBF2)2L. The second step is rapid CH3−Co- bond homolysis yielding Co(dmgBF2)2L- and CH3•; then the CH3 radical is captured by the second equivalent of [Ni(tmc)]OTf, yielding [Ni(tmc)CH3]OTf. Radical clock experiments have corroborated the production of free radicals. Reaction of (5-hexenyl)Co(dmgBF2)2L with [Ni(tmc)]OTf, followed by hydrolysis of the organonickel products, gave methylcyclopentane, consistent with the formation and cyclization of the 1-hexenyl radical. The second-order rate constants measured by stopped-flow experiments parallel the relative radical stabilities: R = CH3 (2.43 × 103 M-1 s-1) < C2H5 (7.88 × 103 M-1 s-1) < CH(CH3)2 (19.2 × 103 M-1 s-1), L = py (2.43 × 103 M-1 s-1) < PEt3 (5.01 × 103 M-1 s-1). During the course of these studies the following molecules were also characterized by X-ray diffraction, CH3Co(dmgBF2)2L, L = PEt3, py, H2O.

DNA sequence of the cut A, B and C genes, encoding the molybdenum containing hydroxylase carbon monoxide dehydrogenase, from Pseudomonas thermocarboxydovorans strain C2

Pseudomonas thermocarboxydovorans strain C2 is capable of using carbon monoxide as the sole source of carbon and energy. The key enzyme for CO utilisation is the molybdenum containing iron-flavoprotein carbon monoxide dehydrogenase (CODH). This paper reports the DNA sequencing of a 4.7 kb region of the C2 genome which appears to encode the CODH enzyme. The genes for the three subunits of CODH, which we have named cut A, B and C, have been identified and they appear to form an operon. The predicted protein sequences of the three subunits have homology to the structurally related protein, xanthine dehydrogenase, from Drosophila melanogaster. By comparison with xanthine dehydogenase it can be predicted that the molybdenum cofactor binds to the large subunit of CODH, the small subunit of CODH contains the iron-sulphur centers and the medium subunit binds FAD/NAD +.

Characterization of the metal centers of the Ni/Fe-S component of the carbon-monoxide dehydrogenase enzyme complex from Methanosarcina thermophila

Methanosarcina thermophila contains a multienzyme complex called the carbon-monoxide dehydrogenase complex, which has been resolved into a nickel/iron-sulfur and a corrinoid/iron-sulfur component. This complex plays a central role in acetoclastic methanogenesis. The Ni/Fe-S component catalyzes CO oxidation and has been proposed to be involved in cleavage of acetyl-CoA into its methyl, carbonyl, and CoA moieties. In the work reported here, three metal centers in the Ni/Fe-S component were characterized by electron paramagnetic resonance (EPR) spectroscopy and spectroelectrochemistry and pre-steady state kinetics. Center A contains nickel and iron and forms an EPR active adduct with CO, which is called the NiFeC species. The EPR spectrum of the NiFeC species has g values of 2.059, 2.051, and 2.029 and is observable at temperatures as high as 150 K. This signal had previously been observed only in the carbon-monoxide dehydrogenase complex of M. thermophila and the acetyl-CoA synthase from acetate-producing bacteria. Incubation of the CO-reduced Ni/Fe-S component with acetyl-CoA resulted in an increase in intensity of the NiFeC signal, which supports a role for the component in the cleavage of acetyl-CoA. Generation of the NiFeC EPR signal occurs with a rate constant of 0.4 s-1, a result that demonstrates the kinetic competence of this species in the acetyl-CoA cleavage reaction but rules it out as the site of oxidation of CO to CO2. Center B is likely to be a [4Fe-4S]2+/1+ center with g values of 2.04, 1.93, and 1.89 (gav = 1.95) and a standard reduction potential (E'0) of -444 mV. At potentials less than -500 mV, another EPR signal develops that appears to originate from another state of Center B. Center C is a fast relaxing center with g values of 2.02, 1.88, and 1.71 (gav = 1.87) and an E'0 of -154 mV.

Low spin quantitation of NiFeC EPR signal from carbon monoxide dehydrogenase is not due to damage incurred during protein purification

Evidence is presented that the O 2-sensitive, nickel- and iron-containing enzyme carbon monoxide dehydrogenase from Clostridium thermoaceticum was purified without significantly inactivating either its CO oxidation or CO/acetyl-CoA exchange activities. All CO oxidation activity from the crude extract was recovered in the purified enzyme (and side fractions). The exchange activity could not be quantified similarly, because the crude extract and early purification step fractions exhibited little or no exchange activity. Later purification fractions exhibited much more exchange activity, suggesting that an inhibitor was present in the impure fractions. The NiFeC EPR signal intensity was used as an indicator of the enzyme's capacity to catalyze exchange. This signal was extremely sensitive to oxygen; exposure to as little as 0.5 equiv/mol enzyme dimer resulted in substantial loss of intensity. The NiFeC intensities at each step in the purification were virtually invariant, indicating that the enzyme had not been exposed to oxygen and had not been inactivated towards catalyzing exchange. The ability to purify carbon monoxide dehydrogenase (CODH) without inactivating nearly any of the molecules suggests that it is quite stable under anaerobic conditions. The purified enzyme, which could not have lost functional metal ions during purification, contained 1.9 Ni and 11.3 Fe, similar to previous reports. The NiFeC EPR signal intensity from each purification fraction (0.2 spins/mol enzyme dimer) was as low as from previous preparations, indicating that its low spin quantitation is not the result of damage incurred during purification. If the low intensity arises from heterogeneity as proposed earlier, the heterogeneity must originate prior to purification.

Life with CO or CO 2 and H 2 as a source of carbon and energy

An account is presented of the recent discovery of a pathway of growth by bacteria in which CO or CO2 and H2 are sources of carbon and energy. The Calvin cycle and subsequently other cycles were discovered in the 1950s, and in each the initial reaction of CO2 involved adding CO2 to an organic compound formed during the cyclic pathway (for example, CO2 and ribulose diphosphate). Studies were initiated in the 1950s with the thermophylic anaerobic organism Clostridium thermoaceticum, which Barker and Kamen had found fixed CO2 in both carbons of acetate during fermentation of glucose. The pathway of acetyl-CoA biosynthesis differs from all others in that two CO2 are combined with coenzyme A (CoASH) forming acetyl CoA, which then serves as the source of carbon for growth. This mechanism is designated the acetyl CoA pathway and some have called it the Wood pathway. A unique feature is the role of the enzyme carbon monoxide dehydrogenase (CODH), which catalyzes the conversion of CoASH, CO, and a methyl group to acetyl CoA, the final step of the pathway. The pathway involves the reduction of CO2 to formate, which then combines with tetrahydrofolate (THF) to form formyl THF. It in turn is reduced to CH3-THF. The methyl is then transferred to the cobalt on a corrinoid-containing enzyme. From there the methyl is transferred to CODH, and CO and CoASH bind with the enzyme at separate sites. Acetyl CoA is then synthesized. CODH would more properly be called carbon monoxide dehydrogenase-acetyl CoA synthase as it catalyzes oxidation of CO to CO2 and the synthesis of acetyl CoA. The solution of the mechanism of this pathway required more than 30 years, in part because the intermediate compounds are bound to enzymes, the enzymes are extremely sensitive to O2 and must be isolated under strictly anerobic conditions, and the role of a corrinoid and CODH was unprecedented. It is now apparent that this pathway occurs (perhaps with some modification) in many bacteria including the methane and sulfur bacteria. In some humans this pathway is catalyzed by the bacteria of the gut and acetate is produced rather than methane; it is calculated that 2.3 x 10(6) metric tons of acetate are formed daily from CO2. A similar synthesis occurs in the hind gut of termites. It is becoming apparent that the acetyl CoA pathway plays a significant role in the carbon cycle.(ABSTRACT TRUNCATED AT 400 WORDS)

Identification of a Ni- and Fe-containing cluster in Rhodospirillum rubrum carbon monoxide dehydrogenase

Methyl viologen-oxidized carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum exhibits complex EPR. Comparison to EPR of oxidized apo-CODH (CODH from which Ni is lacking) leads to the identification of signals whose intensity is correlated with the presence of Ni. 61Ni labeling observably broadens the sharpest feature of these signals, as does 57Fe. R. rubrum CODH thus contains a cluster containing both Ni and Fe. The EPR associated with this cluster is unlike any EPR previously attributed to Ni-containing prosthetic groups in other CODH enzymes or Ni-containing hydrogenases. The CO-analogue, CN-, perturbs the EPR signals that are attributed to the Ni-Fe species.

Reduction of co-ordinated carbon dioxide to carbon monoxide via protonation by thiols and other Brønsted acids promoted by Ni-systems: a contribution to the understanding of the mode of action of the enzyme carbon monoxide dehydrogenase

Carbon dioxide co-ordinated to Ni0 is easily reduced to bound carbon monoxide by R–SH (R = H, alkyl, benzyl, phenyl, and substituted phenyl) and other Bronsted acids, providing a reasonable model for the Ni-containing enzyme carbon monoxide dehydrogenase.

Methods for Isolation of Auxotrophic Mutants of Methanobacterium ivanovii and Initial Characterization of Acetate Auxotrophs

To develop a biochemical genetic approach to understanding cell carbon synthesis or metabolic pathways in methanogens, Methanobacterium ivanovii was selected as a model organism for genetic manipulation studies. The organism displayed a colony size of 3 to 6 mm in less than 2 weeks and had a plating efficiency of about 90%, which made it suitable for replica plating. Mutagenesis and selection techniques were developed for selection of acetate auxotrophs. Chemical mutagenesis with ethyl methanesulfonate, followed by enrichment with bacitracin as a selective agent, resulted in stable acetate auxotrophs. M. ivanovii was very sensitive to UV, but UV-induced acetate auxotrophs were unstable and reverted within two to four transfers. The acetate auxotrophs were analyzed in relation to wild type for carbon monoxide dehydrogenase enzyme activity.