Cyanobacterial aldehyde deformylating oxygenase: Structure, function, and potential in biofuels production

Basri, Rose Syuhada; Rahman, Raja Noor Zaliha Raja Abd; Leow, Adam Thean Chor; Ali, Mohd Shukuri Mohamad

doi:10.1016/j.ijbiomac.2020.08.162

Cited by 14 publications

(9 citation statements)

References 91 publications

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“…Aldehyde deformylations are chemical reactions taking place in organisms during metabolism and biosynthesis. , These biochemical reactions are catalyzed by metalloenzymes such as cytochrome P450 and aldehyde decarbonylase (ADO). − By binding to molecular oxygen, the metal cofactors of the metalloenzymes form metal–dioxygen active cores that perform these reactions. − Inspired by these biological processes, much effort has been devoted to the study of small-molecule transition-metal–dioxygen complexes (denoted TM–O 2 complexes hereafter). − On the one hand, TM–O 2 complexes serve as biomimetic models to deeply understand the relevant biological processes like deformylations; on the other hand, studying the chemistry of TM–O 2 complexes could lead to the discovery of aerobic catalytic transformations. − The use of abundant molecular O 2 as an oxidant offers a green and sustainable approach to produce valuable chemical products.…”

Section: Introductionsupporting

confidence: 50%

DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal–Dioxygen Complexes: Distinct Mechanisms and Reaction Rules

Zhao

Zhang

Liu

et al. 2022

JACS Au

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Aldehyde deformylations occurring in organisms are catalyzed by metalloenzymes through metal–dioxygen active cores, attracting great interest to study small-molecule metal–dioxygen complexes for understanding relevant biological processes and developing biomimetic catalysts for aerobic transformations. As the known deformylation mechanisms, including nucleophilic attack, aldehyde α-H-atom abstraction, and aldehyde hydrogen atom abstraction, undergo outer-sphere pathways, we herein report a distinct inner-sphere mechanism based on density functional theory (DFT) mechanistic studies of aldehyde deformylations with a copper (II)–superoxo complex. The inner-sphere mechanism proceeds via a sequence mainly including aldehyde end-on coordination, homolytic aldehyde C–C bond cleavage, and dioxygen O–O bond cleavage, among which the C–C bond cleavage is the rate-determining step with a barrier substantially lower than those of outer-sphere pathways. The aldehyde C–C bond cleavage, enabled through the activation of the dioxygen ligand radical in a second-order nucleophilic substitution (SN2)-like fashion, leads to an alkyl radical and facilitates the subsequent dioxygen O–O bond cleavage. Furthermore, we deduced the rules for the reactions of metal–dioxygen complexes with aldehydes and nitriles via the inner-sphere mechanism. Expectedly, our proposed inner-sphere mechanisms and the reaction rules offer another perspective to understand relevant biological processes involving metal–dioxygen cores and to discover metal–dioxygen catalysts for aerobic transformations.

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Section: Introductionsupporting

confidence: 50%

DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal–Dioxygen Complexes: Distinct Mechanisms and Reaction Rules

Zhao

Zhang

Liu

et al. 2022

JACS Au

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“…Mononuclear metal–oxygen species such as metal–oxo, −superoxo, −peroxo, and −hydroperoxo complexes are key intermediates in a variety of reactions by metalloenzymes. − Among them, metal–peroxo and −hydroperoxo intermediates have received much attention recently due to their important role in biological oxidative reactions. − For example, in cytochrome P450 aromatase, the iron(III)–peroxo intermediate is known to be responsible for the biotransformation of androgens to estrogens by mediating the nucleophilic aldehyde deformylation reaction. − In contrast, the iron(III)–hydroperoxo intermediate has been proposed as an electrophilic oxidant capable of hydrogen-atom transfer (HAT) in DNA scission reactions by bleomycin or oxygen-atom transfer (OAT) in sulfoxidation of thioether substrates by cytochrome P450. − …”

Section: Introductionmentioning

confidence: 99%

Systematic Electronic Tuning on the Property and Reactivity of Cobalt–(Hydro)peroxo Intermediates

Kim

Jeong

et al. 2023

Inorg. Chem.

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A series of cobalt(III)–peroxo complexes, [CoIII(R2-TBDAP)(O2)]+ (1 R2 ; R2 = Cl, H, and OMe), and cobalt(III)–hydroperoxo complexes, [CoIII(R2-TBDAP)(O2H)(CH3CN)]2+ (2 R2 ), bearing electronically tuned tetraazamacrocyclic ligands (R2-TBDAP = N,N′-di-tert-butyl-2,11-diaza[3.3](2,6)-p-R2-pyridinophane) were prepared from their cobalt(II) precursors and characterized by various physicochemical methods. The X-ray diffraction and spectroscopic analyses unambiguously showed that all 1 R2 compounds have similar octahedral geometry with a side-on peroxocobalt(III) moiety, but the O–O bond lengths of 1 Cl [1.398(3) Å] and 1 OMe [1.401(4) Å] were shorter than that of 1 H [1.456(3) Å] due to the different spin states. For 2 R2 , the O–O bond vibration energies of 2 Cl and 2 OMe were identical at 853 cm–1 (856 cm–1 for 2 H ), but their Co–O bond vibration frequencies were observed at 572 cm–1 for 2 Cl and 550 cm–1 for 2 OMe , respectively, by resonance Raman spectroscopy (560 cm–1 for 2 H ). Interestingly, the redox potentials (E 1/2) of 2 R2 increased in the order of 2 OMe (0.19 V) < 2 H (0.24 V) < 2 Cl (0.34 V) according to the electron richness of the R2-TBDAP ligands, but the oxygen-atom-transfer reactivities of 2 R2 showed a reverse trend (k 2: 2 Cl < 2 H < 2 OMe ) with a 13-fold rate enhancement at 2 OMe over 2 Cl in a sulfoxidation reaction with thioanisole. Although the reactivity trend contradicts the general consideration that electron-rich metal–oxygen species with low E 1/2 values have sluggish electrophilic reactivity, this could be explained by a weak Co–O bond vibration of 2 OMe in the unusual reaction pathway. These results provide considerable insight into the electronic nature–reactivity relationship of metal–oxygen species.

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“…[66] In light of these structural discoveries, several protein engineering studies have been carried out to improve enzyme activity and substrate specificity. [67,68] For example, residues at the substrate-binding tunnel were mutated to modulate the enzyme's preference for shorter chain substrates. [69] In another study, based on the observation that hydrogen peroxide inhibits ADO, a chimeric protein comprising of ADO and catalase was constructed, which converted H 2 O 2 to O 2 , leading to the prolonged activity of ADO.…”

Section: Structural Featuresmentioning

confidence: 99%

“…In another recent study, the crystal structure of the ADO complexed with FAAR was obtained, and the aldehyde substrate transferring channel from FAAR to ADO has been proposed [66] . In light of these structural discoveries, several protein engineering studies have been carried out to improve enzyme activity and substrate specificity [67,68] . For example, residues at the substrate‐binding tunnel were mutated to modulate the enzyme‘s preference for shorter chain substrates [69] .…”

Section: Aldehyde Decarbonylasesmentioning

confidence: 99%

Metalloenzymes for Fatty Acid‐Derived Hydrocarbon Biosynthesis: Nature's Cryptic Catalysts

Iqbal

Chakraborty

Murugan

et al. 2022

Chemistry An Asian Journal

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Waning resources, massive energy consumption, ever‐deepening global warming crisis, and climate change have raised grave concerns regarding continued dependence on fossil fuels as the predominant source of energy and generated tremendous interest for developing biofuels, which are renewable. Hydrocarbon‐based ′drop‐in′ biofuels can be a proper substitute for fossil fuels such as gasoline or jet fuel. In Nature, hydrocarbons are produced by diverse organisms such as insects, plants, bacteria, and cyanobacteria. Metalloenzymes play a crucial role in hydrocarbons biosynthesis, and the past decade has witnessed discoveries of a number of metalloenzymes catalyzing hydrocarbon biosynthesis from fatty acids and their derivatives employing unprecedented mechanisms. These discoveries elucidated the enigma related to the divergent chemistries involved in the catalytic mechanisms of these metalloenzymes. There is substantial diversity in the structure, mode of action, cofactor requirement, and substrate scope among these metalloenzymes. Detailed structural analysis along with mutational studies of some of these enzymes have contributed significantly to identifying the key amino acid residues that dictate substrate specificity and catalytic intricacy. In this Review, we discuss the metalloenzymes that catalyze fatty acid‐derived hydrocarbon biosynthesis in various organisms, emphasizing the active site architecture, catalytic mechanism, cofactor requirements, and substrate specificity of these enzymes. Understanding such details is essential for successfully implementing these enzymes in emergent biofuel research through protein engineering and synthetic biology approaches.

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Cyanobacterial aldehyde deformylating oxygenase: Structure, function, and potential in biofuels production

Cited by 14 publications

References 91 publications

DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal–Dioxygen Complexes: Distinct Mechanisms and Reaction Rules

DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal–Dioxygen Complexes: Distinct Mechanisms and Reaction Rules

Systematic Electronic Tuning on the Property and Reactivity of Cobalt–(Hydro)peroxo Intermediates

Metalloenzymes for Fatty Acid‐Derived Hydrocarbon Biosynthesis: Nature's Cryptic Catalysts

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