Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase

Biester, Alison; Dementin, Sébastien; Drennan, Catherine L.

doi:10.1016/j.jinorgbio.2022.111774

Cited by 16 publications

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“…The closure of an entrance tunnel toward cluster C was also found for the M. thermoacetica CODH/ACS complex by comparing its xenonbinding sites with those of the monofunctional CODH of Desulfovibrio vulgaris. 52 Furthermore, the tunnels in the CODH-III/ACS complex were found to be narrower than their counterparts in CODH-II and -IV. Here, the widest tunnel had a bottleneck with a radius of 1.38 Å or of 1.44 Å for CODH-II or -IV, respectively.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

On the Kinetics of CO₂ Reduction by Ni, Fe-CO Dehydrogenases

et al. 2022

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Ni,Fe-CO dehydrogenases (CODHases) catalyze reversibly the reduction of CO 2 to CO, making them valuable catalysts for the generation of renewable fuels. The individual states of the active site cluster C during catalysis have been extensively studied by spectroscopic and crystallographic methods but less so by enzyme kinetics. Here, we report the kinetic characterization of three CODHases with distinct physiological roles with two reductants and at different temperatures. For all CODHases, a two-site ping-pong model fits to the data for both reductants. However, we cannot eliminate the possibility of alternative models by using the data. Our kinetic characterization provided insights into the rate-determining steps in catalysis and allowed modeling the influence of the reduction potential of the electron-transferring clusters on catalysis. Furthermore, we investigated potential clues for the different activities of the CODHases and found a point mutation that doubled the activity of the CODH-III/acetyl-CoA synthase complex. However, the main reason for the different activities seems to be the architecture of the substrate tunnels. These findings open up fresh perspectives for understanding and engineering efficient CO 2 reduction catalysts.

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Section: ■ Results and Discussionmentioning

confidence: 99%

On the Kinetics of CO₂ Reduction by Ni, Fe-CO Dehydrogenases

et al. 2022

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“…Structure of the ACS/CODH from M. thermoacetica (PDB ID 2Z8Y), indicating the position of the clusters A–D, and marking the long hydrophobic channel that connects them. Reprinted (adapted or reprinted in part) with permission from ref . Copyright 2022 Elsevier.…”

Section: Co Dehydrogenasementioning

confidence: 99%

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

et al. 2022

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Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in “green” energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

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“…The other branch of the gas channel observed in DvCODH is absent in MtCODH/ ACS; this channel appears to be blocked by bulky aromatic residues. 37,38 In the bifunctional CaCODH/ACS, cavity calculations suggest that the opposite is true, that the channel leading toward the CODH homodimer interface is blocked, 33,38 whereas the channel leading away from the CODH homodimer interface is present. The use of different channels in these two bifunctional CODH/ACS enzymes is likely related to their different quaternary structures.…”

Section: Have Revealed Gas Channels In Codhsmentioning

confidence: 99%

“…In the monofunctional Dv CODH and the bifunctional CODH/ACS from M. thermoacetica ( Mt CODH/ACS), the gas channels have been experimentally visualized through xenon crystallographic studies. In these studies, crystals were pressurized with xenon, and when the crystal structure was determined, the xenon sites were used to determine the path of gas channels through the enzymes. , The Dv CODH gas channel originates near the C-cluster and splits into two branches, with one branch leading toward the homodimer interface and the other leading away. Cavity calculations indicate that the gas channels of other monofunctional CODHs, including Rr CODH, Ch CODH type II, and Ch CODH type IV, are likely similar to those of Dv CODH (Figure ).…”

Section: Crystallographic Studies With Xenon Gas Have Revealed Gas Ch...mentioning

confidence: 99%

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Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni–Fe–S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases

2022

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Ni−Fe−S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO 2 by using their catalytic Ni−Fe−S C-cluster and their Fe−S B-and Dclusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO 2 as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood−Ljungdahl pathway, where acetyl-CoA is assembled from two CO 2 -derived one-carbon units. A Ni−Fe− S A-cluster is key to this chemistry. Whereas acetogens use the A-and C-clusters of CODH/ACS to produce acetate from CO 2 , methanogens use A-and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO 2 and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.

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Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase

Cited by 16 publications

References 54 publications

On the Kinetics of CO₂ Reduction by Ni, Fe-CO Dehydrogenases

On the Kinetics of CO₂ Reduction by Ni, Fe-CO Dehydrogenases

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni–Fe–S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases

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Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase

Cited by 16 publications

References 54 publications

On the Kinetics of CO2 Reduction by Ni, Fe-CO Dehydrogenases

On the Kinetics of CO2 Reduction by Ni, Fe-CO Dehydrogenases

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni–Fe–S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases

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On the Kinetics of CO₂ Reduction by Ni, Fe-CO Dehydrogenases

On the Kinetics of CO₂ Reduction by Ni, Fe-CO Dehydrogenases