Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations

Liao, Rong‐Zhen; Yu, Jianguo; Himo, Fahmi

doi:10.1016/j.jinorgbio.2011.03.020

Cited by 28 publications

(21 citation statements)

References 78 publications

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“…furiosus AOR described above, belonging to the AOR superfamily. In contrast, SaciAOR belongs to the aldehyde oxidase/xanthine dehydrogenase superfamily, which, however, seems to share some similarities in reaction mechanisms although exhibiting divergent folds (170,306).…”

Section: Gap Conversionmentioning

confidence: 99%

“…As a catalytic mechanism, a nucleophilic attack of a water molecule, activated by the tungsten atom, which changes its redox state from state IV to state VI, on the carbonyl group of the substrate is proposed. Electron transfer proceeds from the tungsten center via the pterin cofactor and the [4Fe:4S] cluster finally to the [4Fe:4S] cluster of ferredoxin (168,170). However, the GAPOR characterized for Sul.…”

Section: Glyceraldehyde 3-phosphate Oxidationmentioning

confidence: 99%

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Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Gap Conversionmentioning

confidence: 99%

Section: Glyceraldehyde 3-phosphate Oxidationmentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

View full text Add to dashboard Cite

show abstract

“…The mechanism and selectivity of three different tungstoenzymes have been subjected to QM and QM/MM calculations, namely, acetylene hydratase (Liao et al, 2010; Liao and Himo, 2011), formaldehyde oxidoreductase (Liao et al, 2011b; Liao, 2013) and benzoyl CoA reductase (Culka et al, 2017; Qian and Liao, 2018).…”

Section: Modeling Selectivities In Metalloenzymesmentioning

confidence: 99%

“…Liao et al has also investigated the mechanism of formaldehyde oxidoreductase (FOR) and the W vs. Mo selectivity for this enzyme (Liao et al, 2011b). QM calculations showed that this enzyme uses a W(VI) = O as the key oxidant and the formaldehyde coordinates to W(VI) directly via its oxygen atom.…”

Section: Modeling Selectivities In Metalloenzymesmentioning

confidence: 99%

Computational Understanding of the Selectivities in Metalloenzymes

et al. 2018

Self Cite

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Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.

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“…In this paper, we investigate all proposed mechanisms for both the S and R substrates on an equal footing. We have used the quantum mechanical (QM) cluster approach, which has extensively been used to study catalytic mechanisms and structures of enzymes [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26] . In this approach, the most important residues are cut out from the active site of the enzyme.…”

Section: Introductionmentioning

confidence: 99%

Catalytic mechanism of human glyoxalase I studied by quantum-mechanical cluster calculations

Jafari

Ryde

Irani

2016

Journal of Molecular Catalysis B: Enzymatic

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Density functional theory has been used to study the mechanism and stereospeci7icity of the catalytic reaction of human glyoxalase I. We used the quantum mechanical cluster method to model the enzyme active site. Glyoxalase I accepts both enantiomers of the hemithioacetal between methylglyoxal and glutathione and converts them to the S-D enantiomer of lactoylglutathione. We have compared several previously suggested or alternative reaction mechanisms for both substrates on an equal footing. The results show that the coordination shell of the Zn ion in the optimized geometries is more symmetric than in some inhibitor crystal structures, which we assign to differences in the electronic structure and the protonation states. The symmetry of the active site model indicates that the enzyme can use the same reaction mechanism for the S and the R enantiomers of the substrate, but with exchanged roles of the two active-site glutamate residues. However, the calculations show some asymmetry (0-4 kcal mol -1 differences in reaction energies and activation barriers), caused by the different coordination states of the glutamate residues in the starting crystal structure. Our results indicate that the only possibility for the stereospeci7icity of GlxI is differences in the electrostatic surroundings and 7lexibility of the glutamate residues in the active site owing to their neighboring residues in the protein.

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Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations

Cited by 28 publications

References 78 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Computational Understanding of the Selectivities in Metalloenzymes

Catalytic mechanism of human glyoxalase I studied by quantum-mechanical cluster calculations

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