Crystallographic Characterization of the Carbonylated A-Cluster in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase

Cohen, Steven E.; Can, Mehmet; Wittenborn, E.C.; Hendrickson, Rachel A; Ragsdale, Stephen W.; Drennan, Catherine L.

doi:10.1021/acscatal.0c03033

Cited by 27 publications

(39 citation statements)

References 35 publications

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“…Similar values can be seen in the calculations (Table 3) although these distances are slightly longer for the formate and hydroxyl ligands. At the same time, it can be found that the Ni p -Fe1 distance is very small (2.243 Å) in the PDB ID: 6YTT crystal structure [46] where there is no ligand on Ni p and in turn very long in the crystal structure PDB ID: 6X5K [36] with the carbonyl ligand. This is not the case in the EXAFS results for the CO ligand, where this distance is equal to 2.80 Å [56] (Table 2).…”

Section: Structural Propertiesmentioning

confidence: 96%

“…It also would be prone to oxidation and would be unstable in biological environment. A red1 was observed experimentally, it can be formed as the product of Fe 4 S 2+ 4 Ni + p CO photolysis and it binds back CO very quickly [36]. The direct presence of Fe 4 S + 4 Ni + p in the catalytic reaction has not been proven.…”

Section: Energetics Of Methylation and Carbonylation Reactionmentioning

confidence: 99%

“…The iron-sulfur cubane (Fe 4 S 4 ) is connected through a cysteine sulfur with the proximal nickel ion (Ni p ), which in turn is linked by two cysteine sulfur atoms to the distal nickel atom (Ni d ). The ACS enzyme has been extensively studied using experimental [12,[32][33][34][35][36][37][38][39][40][41][42][43][44][45][46] and theoretical [47][48][49][50][51][52][53][54][55] methods. Different oxidation states are postulated for Ni p from Ni(0) to Ni(III) while the distal nickel is always in Ni(II) oxidation state.…”

Section: Introductionmentioning

confidence: 99%

“…Several forms of the A-cluster relevant to the catalytic reaction were characterized structurally or spectroscopically [8,36,37,46,[56][57][58][59][60][61][62][63][64][65]. They can be described by the oxidation state, electronic configuration, spin, and ligands attached to Ni p , as shown in Table 1.…”

Section: Introductionmentioning

confidence: 99%

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Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism

Jaworska

Lodowski

2022

Catalysts

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DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.

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Section: Structural Propertiesmentioning

confidence: 96%

Section: Energetics Of Methylation and Carbonylation Reactionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism

Jaworska

Lodowski

2022

Catalysts

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“…Interestingly, the architecture of Dv HCP and Dd HCP is similar to that of the subunit of Ni, Fe‐containing carbon monoxide dehydrogenases (Ni, Fe‐CODHs) [31–38], despite the low sequence identity (15–18%) of HCPs with Ni, Fe‐CODHs. Therefore, comparisons of the three‐dimensional structures of HCPs and Ni, Fe‐CODHs are necessary to elucidate their structural evolution and functional diversities [39].…”

Section: Introductionmentioning

confidence: 99%

Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe‐4S] cluster at the N‐terminal protrusion

2021

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Hybrid cluster protein (HCP) is a unique Fe‐S‐O‐type metallocluster‐containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X‐ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Surprisingly, Ec HCP was found to harbor a [4Fe‐4S] cluster rather than a [2Fe‐2S] cluster at the N‐terminal Cys‐rich region, similar to class I HCPs. It was also found that the Cys‐rich motif forms a unique protrusion and that the surrounding charge distributions on the surface of class II Ec HCP are distinct from those of class I HCPs. The functional significance of the Cys‐rich region was investigated using an Ec HCP variant (chimeric HCP) containing a class I HCP Cys‐rich motif from Desulfovibrio desulfuricans. The biochemical analyses showed that the chimeric HCP lacks the hybrid cluster and the electron‐accepting function from HCR despite the formation of the chimeric HCP‐HCR complex. Furthermore, HCP‐HCR molecular docking analysis suggested that the protrusion area serves as an HCR‐binding region. Therefore, the protrusion of the unique Cys‐rich motif and the surrounding area of class II HCP are likely important for maturation of Ec HCP and orienting HCR onto the surface of HCP to facilitate electron transfer in the HCP‐HCR complex.

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The Moon‐Forming Impact and the Autotrophic Origin of Life

Mrnjavac,

Wimmer,

Brabender

et al. 2023

ChemPlusChem

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The Moon‐forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon‐forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2. According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2, forging a direct line of continuity between Earth's initial CO2‐rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.

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Crystallographic Characterization of the Carbonylated A-Cluster in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase

Cited by 27 publications

References 35 publications

Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism

Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism

Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe‐4S] cluster at the N‐terminal protrusion

The Moon‐Forming Impact and the Autotrophic Origin of Life

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