Oxidoreductases articles within Nature Communications

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  • Article
    | Open Access

    Enzymes involve structural flexibility in their function, but understanding enzyme catalysis as connected to protein motions is a major challenge. Here, the authors obtain energetic description of C-H activation in nicotinamide coenzyme-dependent UDP-glucuronic acid C4 epimerase based on temperature kinetic studies and isotope effect measurements.

    • Christian Rapp
    • , Annika Borg
    •  & Bernd Nidetzky

  • Article
    | Open Access

    Understanding the complex relationships between enzyme sequence, folding stability and catalytic activity is essential for applications, but current technologies cannot simultaneously resolve both stability and activity phenotypes and couple these to gene sequences at large scale. Here, the authors report Enzyme Proximity Sequencing (EP-Seq), a deep mutational scanning method to assay both expression level and catalytic activity of thousands of oxidoreductase variants from a cellular pool in a single experiment.

    • Rosario Vanella
    • , Christoph Küng
    •  & Michael A. Nash

  • Article
    | Open Access

    Previous genetically encoded H2O2 probes are based on reversible thiol oxidation. Here, a heme peroxidase is introduced as a thiol-independent H2O2 probe. APEX2 converts H2O2 into fluorescent or luminescent signals, allowing its quantification.

    • Mohammad Eid
    • , Uladzimir Barayeu
    •  & Tobias P. Dick

  • Article
    | Open Access

    In this work, Bay et al describe the construction of the first genome-scale metabolic model for the parasitic whipworm, Trichuris muris and use it to identify novel metabolic pathways and predict critical enzymes and essential metabolites for worm survival.

    • Ömer F. Bay
    • , Kelly S. Hayes
    •  & Ian S. Roberts

  • Article
    | Open Access

    Currently the structure and biological function of Lactate Dehydrogenase D (LDHD) are unclear. Here the authors report the structure of LDHD bound with various ligands and show that LDHD is a general dehydrogenase for D-2-hydroxyacids with small to moderate-size hydrophobic moieties and investigate loss-of-function mutations that play an important role in D-lactic acidosis.

    • Shan Jin
    • , Xingchen Chen
    •  & Jianping Ding

  • Article
    | Open Access

    MonCI, a flavin-dependent monooxygenase, transforms all three C = C groups in the polyene substrate into epoxides during monensin A biosynthesis. Here, the authors present the structural basis for this enzyme’s regio- and stereoselective epoxidation activity.

    • Qian Wang
    • , Ning Liu
    •  & Chu-Young Kim

  • Article
    | Open Access

    Glutaredoxin (GLRX) is a key enzyme in redox regulation via oxidation of protein cysteines and its activity is disrupted in diverse human diseases. This study integrates molecular modeling and biochemical validation to provide insights into the mechanisms of oxidative inactivation of GLRX.

    • Elizabeth M. Corteselli
    • , Mona Sharafi
    •  & Yvonne M. W. Janssen-Heininger

  • Article
    | Open Access

    Digoxin is a heart medicine extracted from plants, but how plants synthesize it is largely unknown. Here Carroll et al. identify a novel enzyme for digoxin biosynthesis, paving the way to produce digoxin and other structurally similar drugs in microbes.

    • Emily Carroll
    • , Baradwaj Ravi Gopal
    •  & Zhen Q. Wang

  • Article
    | Open Access

    Quinol-dependent nitric oxide reductases, unique to bacteria, are considered members of respiratory heme copper oxidases. A 2.2 Å cryoEM structure of qNOR is reported shedding light on key aspects of enzyme mechanism including quinol binding and pathways for electron, substrate, and proton transport.

    • Alex J. Flynn
    • , Svetlana V. Antonyuk
    •  & S. Samar Hasnain

  • Article
    | Open Access

    Biological nitrogen fixation is achieved by nitrogenase, but the mechanism remains enigmatic. Here, the authors report high resolution single particle cryoEM structures of homocitrate-compromised MoFe-proteins and unveil a new binding partner.

    • Rebeccah A. Warmack
    • , Ailiena O. Maggiolo
    •  & Douglas C. Rees

  • Article
    | Open Access

    Detoxification enzymes are crucial for the survival of animals in new environments. Here, the authors study the molecular mechanism behind the catalytic diversification of a major family of tetrapod detoxification enzymes—the FMOs—during evolution.

    • Gautier Bailleul
    • , Guang Yang
    •  & Maria Laura Mascotti

  • Article
    | Open Access

    Treatment of hypertension entails use of angiotensin-converting enzyme inhibitors. Here, the authors show a series of karnamicins with significant inhibitory activity and identify two unusual flavoprotein hydroxylases involved in the assembly of the fully-substituted hydroxypyridine core of karnamicins.

    • Zhiyin Yu
    • , Jian-Ping Huang
    •  & Sheng-Xiong Huang

  • Article
    | Open Access

    In mammals, hypoxia causes dilation of small arteries for increased metabolic demand. Keller et al used novel transgenic mice to show alpha hemoglobin in endothelium, once thought only in red blood cells, can regulate hypoxic-mediated dilation.

    • T. C. Stevenson Keller IV
    • , Christophe Lechauve
    •  & Brant E. Isakson

  • Article
    | Open Access

    NADPH oxidase NOX2 produces superoxide, a reactive oxygen species essential in innate immunity. Here, the authors reveal the structure of the NOX2 core, rationalize disease-causing mutations, and suggest avenues for selective NOX2 pharmacological modulation.

    • Sigrid Noreng
    • , Naruhisa Ota
    •  & James T. Koerber

  • Article
    | Open Access

    The development of IDH variant inhibitors is a breakthrough as it is the first time metabolism has been successfully targeted by small molecule drugs in cancer. Here the authors report studies on resistance to the pioneer drug ivosidenib leading to identification of inhibitors retaining activity.

    • Raphael Reinbold
    • , Ingvild C. Hvinden
    •  & Christopher J. Schofield

  • Article
    | Open Access

    Cyclic five-membered disulfides (1,2-dithiolanes) have been reported either as nonspecific redox motifs, or as highly specific cellular probes for thioredoxin reductase (TrxR). Here the authors show that 1,2-dithiolane probes are nonspecifically reduced by a range of thiol reductants and are not sensitive to TrxR modulation, thus they are unsuitable as cellular probes for TrxR.

    • Jan G. Felber
    • , Lena Poczka
    •  & Oliver Thorn-Seshold

  • Article
    | Open Access

    Cytochalasans are a large family of fungal polyketide-nonribosomal peptide hybrid natural products that exhibit important pharmaceutical activities, but the mechanism of conversion of the monocytochalasans to the polycyclic, fused analogues is unclear. Here the authors reconstitute the core backbone of the cytochalasin family and describe an oxidase that catalyzes an unusual double-bond isomerization reaction.

    • Jin-Mei Zhang
    • , Xuan Liu
    •  & Yi Zou

  • Article
    | Open Access

    Antibiotic-producing organisms need to co-evolve self-protection mechanisms to avoid any damage to themselves caused by the antibiotic pharmacophore (the reactive part of the compound). In this study, the authors report a self-defense strategy in naphthyridinomycin (NDM)-producing Streptomyces lusitanus, that comprises reductive inactivation of the hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and HomW.

    • Wan-Hong Wen
    • , Yue Zhang
    •  & Gong-Li Tang

  • Article
    | Open Access

    The human 2-oxoglutarate (2OG) oxygenases FIH and AspH are relevant drug targets. Here, the authors show that synthetic and naturally occurring 2OG derivatives can selectively modulate FIH and AspH activities, suggesting that these compounds may serve as a basis to develop 2OG oxygenase-targeting probes and drugs.

    • Yu Nakashima
    • , Lennart Brewitz
    •  & Christopher J. Schofield

  • Article
    | Open Access

    Catalytic enantioselective halocyclization of alkenes is an important bond forming tool and a key step in natural product biosynthesis, but so far no examples of the enzymatic counterpart of this reaction on simple achiral olefins have been reported. Here, the authors describe examples of engineered flavin-dependent halogenases that catalyze halolactonization of olefins with high enantioselectivity and near-native catalytic activity.

    • Dibyendu Mondal
    • , Brian F. Fisher
    •  & Jared C. Lewis

  • Article
    | Open Access

    Microbial oxidoreductases are key in biomass breakdown. Here, the authors expand the specificity and redox scope within fungal auxiliary activity 7 family (AA7) enzymes and show that AA7 oligosaccharide dehydrogenases can directly fuel cellulose degradation by lytic polysaccharide monooxygenases.

    • Majid Haddad Momeni
    • , Folmer Fredslund
    •  & Maher Abou Hachem

  • Article
    | Open Access

    Streptoseomycin is a potent antibiotic that contains a pentacyclic 5/14/10/6/6 ring system. Here, the authors report the enzymatic and non-enzymatic steps of the downstream modification of streptoseomycin biosynthesis and show a [6 + 4]-cycloaddition adduct as an unexpected biosynthetic intermediate.

    • Kai Biao Wang
    • , Wen Wang
    •  & Hui Ming Ge

  • Article
    | Open Access

    Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn3+SOD and Mn2+SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.

    • Jahaun Azadmanesh
    • , William E. Lutz
    •  & Gloria E. O. Borgstahl

  • Article
    | Open Access

    One goal of potato breeding is to reduce the accumulation of toxic solanidane glycoalkaloids. Here the authors show that potato DPS, a 2-oxoglutarate dependent dioxygenase, catalyzes ring rearrangement of a biosynthetic precursor to differentiate solanidanes from spirosolanes that are found in other solanaceous plants.

    • Ryota Akiyama
    • , Bunta Watanabe
    •  & Masaharu Mizutani

  • Article
    | Open Access

    Bacterial malic enzymes (ME) transform malate to pyruvate. One group, hybrid ME enzymes, are regulated by acetyl-CoA, linking the enzyme activity to the metabolic state of the cell. Structures of a representative hybrid ME MaeB reveal large conformational rearrangements that provide insight into the mechanism of allosteric inhibition by acetyl-CoA.

    • Christopher John Harding
    • , Ian Thomas Cadby
    •  & Andrew Lee Lovering

  • Article
    | Open Access

    The Pseudomonas aeruginosa lytic polysaccharide monooxygenase CbpD, prevalent in clinical isolates, has been proposed to act as a virulence factor. Here, the authors combine structural work, in silico simulations, enzymatic activity and in vitro and in vivo experiments to further delineate the role of CbpD and show that its deletion renders P. aeruginosa unable to establish a lethal systemic infection, leading to enhanced bacterial clearance in a mouse model of infection.

    • Fatemeh Askarian
    • , Satoshi Uchiyama
    •  & Gustav Vaaje-Kolstad

  • Article
    | Open Access

    An important type of post-translational protein modification is the conversion of peptidyl amino acid into enzyme cofactor. Here, the authors report functional and structural characterization of a flavoprotein monooxygenase essential for biosynthesis of cysteine tryptophylquinone (CTQ) cofactor.

    • Toshinori Oozeki
    • , Tadashi Nakai
    •  & Toshihide Okajima

  • Article
    | Open Access

    Dual oxidases (DUOXs), assembled from the catalytic DUOX and the auxiliary DUOXA subunits, produce hydrogen peroxide by transferring electrons from intracellular NADPH to extracellular oxygen in a calcium-activated manner. Here authors report the cryo-EM structures of human DUOX1-DUOXA1 complex in both high-calcium and low-calcium states.

    • Jing-Xiang Wu
    • , Rui Liu
    •  & Lei Chen

  • Article
    | Open Access

    Lytic polysaccharide monooxygenases (LPMOs) catalyze the hydroxylation of glycosidic bonds in polysaccharides, but the catalytic properties of these monocopper enzymes remain poorly characterized. Here authors employ competition between reference enzymes and LPMOs for the H2O2 co-substrate to kinetically characterize LPMO-catalyzed cellulose oxidation.

    • Riin Kont
    • , Bastien Bissaro
    •  & Priit Väljamäe

  • Article
    | Open Access

    The respiratory complex I (NADH:ubiquinone oxidoreductase) is a large redox-driven proton pump that initiates respiration in mitochondria. Here, the authors present the 3.0 Å cryo-EM structure of complex I from mouse heart mitochondria with the ubiquinone-analogue inhibitor piericidin A bound in the active site and with kinetic measurements and MD simulations they further show that this inhibitor acts competitively against the native ubiquinone-10 substrate.

    • Hannah R. Bridges
    • , Justin G. Fedor
    •  & Judy Hirst

  • Article
    | Open Access

    Monooxygenases catalyse the hydroxylation of C-H bonds using oxygen as a co-substrate, which, in turn, is unavailable for anaerobic bacteria. Here, the authors report a three-step reaction cascade involving two hydroxylases and one dehydratase which hydroxylate the C26 methyl group of cholesterol with water as a co-substrate.

    • Christian Jacoby
    • , Sascha Ferlaino
    •  & Matthias Boll

  • Article
    | Open Access

    The number of usable light-responsive enzymes is limited, despite the potential biotechnological applications. Here, the authors report a flavoprotein monooxygenase which is controllable by blue light illumination, and propose a mechanism involving protein-mediated radical photoreduction of FAD via a semiquinone intermediate.

    • Simon Ernst
    • , Stefano Rovida
    •  & Steffen L. Drees

  • Article
    | Open Access

    Production of inflammatory mediators by M1-polarized macrophages is thought to rely on suppression of mitochondrial metabolism in favor of glycolysis. Refining this concept, here the authors define metabolic targets of nitric oxide as responsible for the mitochondrial rewiring resulting from polarization.

    • Erika M. Palmieri
    • , Marieli Gonzalez-Cotto
    •  & Daniel W. McVicar

  • Article
    | Open Access

    Understanding enzyme active sites can elucidate fundamental enzymatic reaction pathways and inform designs for synthetic catalysts. Here, authors employ operando X-ray absorption spectroelectrochemistry to assess copper ions in bilirubin oxidase during oxygen reduction electrocatalysis.

    • Lucyano J. A. Macedo
    • , Ayaz Hassan
    •  & Frank N. Crespilho

  • Article
    | Open Access

    Reactive oxygen species (ROS) stimulate GLUT4-mediated glucose transport following contraction of isolated muscle, but it is not clear if this occurs in vivo. Here, the authors show in human volunteers that exercise induces ROS increase in muscle and, using loss of-function animal models, they demonstrate that NOX2 is a major ROS source required to stimulate glucose uptake during exercise.

    • Carlos Henríquez-Olguin
    • , Jonas R. Knudsen
    •  & Thomas E. Jensen

  • Article
    | Open Access

    Sulfonamide is in many important drugs yet is rare in nature and little is known about the synthesis of sulfonamide containing antibiotics. Here, the authors report on a detailed analysis of the biosynthesis machineries of the aminoacyl sulfonamide antibiotics.

    • Zhijuan Hu
    • , Takayoshi Awakawa
    •  & Ikuro Abe

  • Article
    | Open Access

    Soluble fumarate reductases are essential for eukaryotic cell survival under anaerobic conditions but their mechanism is not fully understood. Here, the authors present structural and enzymatic analyses of yeast fumarate reductase Osm1, elucidating the molecular basis of maintaining redox balance during anaerobiosis.

    • Sunghwan Kim
    • , Chang Min Kim
    •  & Hyun Ho Park

  • Article
    | Open Access

    The human enzyme MTHFR links the folate and methionine cycles, which are essential for the biosynthesis of nucleotides and proteins. Here, the authors present the crystal structure and biochemical analysis of human MTHFR, providing molecular insights into its function and regulation in higher eukaryotes.

    • D. Sean Froese
    • , Jolanta Kopec
    •  & Wyatt W. Yue

  • Article
    | Open Access

    Some prokaryotes use alternative respiratory chain complexes, such as the alternative complex III (ACIII), to generate energy. Here authors provide the cryoEM structure of ACIII from Rhodothermus marinus which shows the arrangement of cofactors and provides insights into the mechanism for energy transduction.

    • Joana S. Sousa
    • , Filipa Calisto
    •  & Manuela M. Pereira

  • Article
    | Open Access

    The mechanism for covalent flavinylation of flavoenzymes is still unclear. Here, the authors propose a mechanism based on the crystal structure of a flavinylation assembly intermediate of the E. coli respiratory Complex II comprising the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor SdhE.

    • Pankaj Sharma
    • , Elena Maklashina
    •  & T. M. Iverson

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