Biocatalysis

  • Article
    | Open Access

    Isoflavonoids are a class of industrially important plant natural products, but their low abundance and structural complexity limits their availability. Here, the authors engineer Saccharomyces cerevisiae metabolism to become a platform for efficient production of daidzein which is core chemical scaffold for isoflavonoid biosynthesis, and show its application for production of bioactive glucosides from glucose.

    • Quanli Liu
    • , Yi Liu
    •  & Jens Nielsen
  • Article
    | Open Access

    Enzymes installing an intact hydropersulfide (-SSH) group into natural products have so far not been identified. Here, the authors report the characterization of an S-adenosyl methionine-dependent hydropersulfide methyltransferase (GnmP) for guangnanmycin biosynthesis, and identification of three SH domains within several NRPS-PKS assembly lines as thiocysteine lyases.

    • Song Meng
    • , Andrew D. Steele
    •  & Ben Shen
  • Article
    | Open Access

    5-Hydroxymethylfurfural (HMF) can be transformed to a range of industrially useful derivatives, such as 2,5-diformylfuran (DFF), but the reactions needed for efficient industrial production are hindered by several issues. Here, the authors perform reaction and enzyme engineering resulting in a galactose oxidase variant with high activity towards HMF, improved oxygen binding and high productivity.

    • William R. Birmingham
    • , Asbjørn Toftgaard Pedersen
    •  & Nicholas J. Turner
  • Article
    | Open Access

    Nucleic acid-based constitutional dynamic networks (CDNs) enable control of various catalytic processes, but it is challenging to achieve intercommunication between different CDNs and by that mimic complex cell biology networks. Here, the authors report two CDNs that control the integration of photochemical and dark-operating processes, and show their intercommunication afforded by environmental components.

    • Chen Wang
    • , Michael P. O’Hagan
    •  & Itamar Willner
  • Article
    | Open Access

    The chemical processes for the selective incorporation of deuterium into small molecules, of interest to organic and medicinal chemistry, are well established, while the enzymatic methods remain underdeveloped. Here, the authors use an enzymatic approach employing Chlorella variabilis NC64A photodecarboxylase that catalyses decarboxylative deuteration of various carboxylic acids with D2O, and identify enzyme variants that can employ substrates with different chain length acids.

    • Jian Xu
    • , Jiajie Fan
    •  & Qi Wu
  • Article
    | Open Access

    Enzyme reactions at interfaces are common in both Nature and industrial applications but no general kinetic framework exists for interfacial enzymes. Here, the authors kinetically characterize 83 cellulases and identify a scaling relationship between ligand binding strength and maximal turnover, a so-called linear free energy relationship, which may help rationalize cellulolytic mechanisms and guide the selection of technical enzymes.

    • Jeppe Kari
    • , Gustavo A. Molina
    •  & Peter Westh
  • Article
    | Open Access

    The authors generate the largest structural dataset of enzymatic and non-enzymatic metalloprotein sites to date. They use this dataset to train a decision-tree ensemble machine learning algorithm that allows them to distinguish between catalytic and non-catalytic metal sites. The computational model described here could also be useful for the identification of new enzymatic mechanisms and de novo enzyme design.

    • Ryan Feehan
    • , Meghan W. Franklin
    •  & Joanna S. G. Slusky
  • 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

    P450 oxidoreductase (POR) selectively activates numerous cytochromes P450 (CYP), crucial for metabolism of drugs, steroids and xenobiotics and natural product biosynthesis. Here, the authors identify ligands that bind POR and bias its specificity towards CYP redox partners, activating distinct metabolic cascades in cells.

    • Simon Bo Jensen
    • , Sara Thodberg
    •  & Nikos S. Hatzakis
  • 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

    Connecting conformational dynamics and epistasis has so far been limited to a few proteins and a single fitness trait. Here, the authors provide evidence of positive epistasis on multiple catalytic traits in the evolution and dynamics of engineered cytochrome P450 monooxygenase, offering insights for in silico protein design.

    • Carlos G. Acevedo-Rocha
    • , Aitao Li
    •  & Manfred T. Reetz
  • Article
    | Open Access

    Active-site loops are important for catalytic properties of enzymes, but challenging to engineer due to their high flexibility and diversity. Here, the authors identify and engineer hot-spots in the loops of cumene dioxygenase, obtain variants with changed activity, regio- and enantioselectivity, and present a Linker In Loop Insertion approach for loop modification.

    • Peter M. Heinemann
    • , Daniel Armbruster
    •  & Bernhard Hauer
  • Article
    | Open Access

    Multistep enzymatic reactions (cascades) can be achieved by confining enzymes in synthetic materials, but ways to simultaneously energize, control and observe the reactions in real time are lacking. Here, bidirectional interconversion between aspartate and pyruvate by a five enzyme cascade trapped in electrode nanopores, addressable by laptop commands, is demonstrated.

    • Giorgio Morello
    • , Clare F. Megarity
    •  & Fraser A. Armstrong
  • Article
    | Open Access

    Artificial enzymes with reprogrammed and augmented catalytic activity and substrate selectivity have emerged to tackle limitations of noble metals or transition metal oxides. Here, the authors report Au25 clusterzymes which are endowed with high catalytic activity and selectivity in a range of enzyme-mimicking reactions.

    • Haile Liu
    • , Yonghui Li
    •  & Xiao-Dong Zhang
  • Article
    | Open Access

    C-nucleosides are analogues of the canonical N-nucleosides and, despite their synthetic value, biocatalysis has not targeted them yet. Here, the authors report a pseudouridine monophosphate C-glycosidase enzyme for selective 5-β-C-glycosylation of uracil and its derivatives from pentose 5- phosphate substrates.

    • Martin Pfeiffer
    •  & Bernd Nidetzky
  • Article
    | Open Access

    Bacterial heterodimeric tryptophan-containing diketopiperazines (HTDKPs) are bioactive natural products that are difficult to access chemically. Here, the authors identify a family of three related HTDKP-forming cytochrome P450s and engineer key amino acid residues to produce distinct diketopiperazines frameworks.

    • Chenghai Sun
    • , Zhenyao Luo
    •  & Xudong Qu
  • Article
    | Open Access

    The success of protein evolution is dependent on the sequence context mutations are introduced into. Here the authors present UMIC-seq that allows consensus generation for closely related genes by using unique molecular identifiers linked to gene variants.

    • Paul Jannis Zurek
    • , Philipp Knyphausen
    •  & Florian Hollfelder
  • Article
    | Open Access

    Current efforts to establish synthetic carbon fixation in model heterotrophs rely on expression of heterologous enzymes. Here, the authors explore the presence and activity of a latent CO2-assimilation pathway in E. coli based only on endogenous enzymes and a reversible decarboxylase.

    • Ari Satanowski
    • , Beau Dronsella
    •  & Arren Bar-Even
  • 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

    β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for catabolism of trehalose and maltose. Coupled analyses of multiple βPGM structures and enzymatic activity lead to the proposal of allomorphy — a post-translational mechanism controlling enzyme activity.

    • Henry P. Wood
    • , F. Aaron Cruz-Navarrete
    •  & Jonathan P. Waltho
  • Article
    | Open Access

    The extreme oxygen sensitive character of hydrogenases is a longstanding issue for hydrogen production in bacteria. Here, the authors build carboxysome shells in E. coli and incorporate catalytically active hydrogenases and functional partners within the empty shell for the production of hydrogen.

    • Tianpei Li
    • , Qiuyao Jiang
    •  & Lu-Ning Liu
  • Article
    | Open Access

    C-glycosides are of pharmaceutical interest due to their stability against in vivo hydrolysis, however their enzymatic synthesis faces challenges. Here, the authors report a C-glycosyltransferase from Aloe barbadensis catalysing the C-glycosylation of drug-like acceptors to generate bioactive C-glycosides.

    • Kebo Xie
    • , Xiaolin Zhang
    •  & Jungui Dai
  • Article
    | Open Access

    Aliphatic α,ω-dicarboxylic acids (DCAs) are widely used chemicals that are synthesised by multistage chemical oxidations. Here, the authors report an artificially designed biocatalytic cascade for the oxidation of cycloalkanes or cycloalkanols to DCAs in the form of microbial consortia, composed of three Escherichia coli cell modules.

    • Fei Wang
    • , Jing Zhao
    •  & Aitao Li
  • Article
    | Open Access

    Thioglycoligases have proved useful for bonding carbohydrates to non-sugar acceptors, however, the scope of these biocatalysts is usually limited. Here, the authors engineer a xylosidase into a thioglycoligase with the ability to form O-, N-, S- and Se- glycosides together with sugar esters and phosphoesters.

    • Manuel Nieto-Domínguez
    • , Beatriz Fernández de Toro
    •  & María Jesús Martínez
  • Article
    | Open Access

    Kemp eliminases are artificial enzymes that catalyze the concerted deprotonation and ring-opening of benzisoxazoles. Here, the authors use room-temperature X-ray crystallography to investigate changes to the conformational ensemble of the Kemp eliminase HG3 along a directed evolutionary trajectory, and develop an experimentally guided, ensemble-based computational enzyme design procedure.

    • Aron Broom
    • , Rojo V. Rakotoharisoa
    •  & Roberto A. Chica
  • 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

    DOCK2 is a guanine nucleotide exchange factor (GEF) that activates RHO GTPases and interacts with ELMO1, which stimulates its GEF activity. Here, the authors provide mechanistic insights into how ELMO1 regulates DOCK2 activity by determining the structure of the DOCK2–ELMO1 binary complex representing the closed, auto-inhibited state and the DOCK2−ELMO1−RAC1 ternary complex structure, where DOCK2−ELMO1 adopts an open, active conformation.

    • Leifu Chang
    • , Jing Yang
    •  & David Barford
  • Article
    | Open Access

    Glutaredoxins are a family of essential enzymes divided into two major classes with either a CGFS or a CxxC active site, of which only the latter exhibits oxidoreductase activity. Here the authors address the structural basis for the functional difference between the two classes of glutaredoxins.

    • Daniel Trnka
    • , Anna D. Engelke
    •  & Christopher Horst Lillig
  • Article
    | Open Access

    Plasmodium falciparum IMP-specific 5′-nucleotidase 1 (PfISN1) is of interest as a potential malaria drug target. Here, the authors report that IMP is a substrate, and ATP an allosteric activator, of PfISN1 and present PfISN1 crystal structures in the ligand-free state and bound to either IMP or ATP.

    • Loïc Carrique
    • , Lionel Ballut
    •  & Nushin Aghajari
  • Article
    | Open Access

    Rieske oxygenases are iron-dependent enzymes that catalyse C–H mono- and dihydroxylation reactions. Here, the authors characterise two cyanobacterial Rieske oxygenases, SxtT and GxtA that are involved in the biosynthesis of paralytic shellfish toxins and determine their substrate free and saxitoxin analog-bound crystal structures and by using mutagenesis experiments identify residues, which are important for substrate positioning and reaction selectivity.

    • April L. Lukowski
    • , Jianxin Liu
    •  & Alison R. H. Narayan
  • Article
    | Open Access

    Self-sufficient cytochrome P450 monooxygenases, which contain all redox partners in a single polypeptide chain, are of interest for biotechnological applications. Here, the authors present the crystal structure of full-length Thermobispora bispora CYP116B46 and discuss the potential electron transfer pathway.

    • Lilan Zhang
    • , Zhenzhen Xie
    •  & Chun-Chi Chen
  • 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

    Rhodobacter capsulatus NAD+ dependent formate dehydrogenase (RcFDH) is a molybdoenzyme that catalyses the reversible oxidation of formate to carbon dioxide, and is of interest for biotechnological applications. Here the authors present the cryo-EM structures of RcFDH as isolated from R. capsulatus and in the reduced state with bound NADH, and discuss the enzyme mechanism.

    • Christin Radon
    • , Gerd Mittelstädt
    •  & Petra Wendler
  • Article
    | Open Access

    Halogenated plant natural products are rare and plant halogenation enzymes are thus far unknown. Here Kim et al. identify a dechloroacutumine halogenase from Common Moonseed that catalyzes the final chlorination step in the biosynthesis of acutumine, a chloroalkaloid with selective cytotoxicity to cultured T cells.

    • Colin Y. Kim
    • , Andrew J. Mitchell
    •  & Jing-Ke Weng
  • Article
    | Open Access

    Deuterated chemicals are widely exploited in analytical chemistry and increasingly in the synthesis of pharmaceutical compounds. Here, the authors developed a mild biocatalytic method for the selective asymmetric reductive deuteration of organic compounds, by using H2 and 2H2O to generate 2H-NADH.

    • J. S. Rowbotham
    • , M. A. Ramirez
    •  & K. A. Vincent
  • Article
    | Open Access

    O-alkylation of carboxylates by alkyl halides has only been observed transiently in enzymatic processes. Here, the authors show a carboxylate alkylating enzyme, BrtB, that catalyzes C-O bond formation between free fatty acids and secondary alkyl chlorides.

    • João P. A. Reis
    • , Sandra A. C. Figueiredo
    •  & Pedro N. Leão
  • Article
    | Open Access

    Metabolic engineering is often hampered by non-linear kinetics and allosteric regulatory mechanisms. Here, the authors construct a quantitative model for the pentose degradation Weimberg pathway in Caulobacter crescentus and demonstrate its biotechnological applications in cell-free system and standard metabolic engineering.

    • Lu Shen
    • , Martha Kohlhaas
    •  & Bettina Siebers
  • Article
    | Open Access

    Glucuronoyl esterases have the potential to be used in the biocatalytic conversion of lignin-carbohydrate complexes to obtain pure lignin for downstream biofuel conversion. Here the authors present a detailed structural analysis of the glucuronoyl esterase from Cerrena unicolor, providing the basis for its activity on natural substrate and for how lignin can be selectively separated from lignocellulosic materials.

    • Heidi A. Ernst
    • , Caroline Mosbech
    •  & Sine Larsen
  • Article
    | Open Access

    Lytic polysaccharide (mono)oxygenases (LPMOs) perform oxidative cleavage of polysaccharides. Here, the authors showed that the light-driven activity of LPMOs is dependent on hydrogen peroxide availability and can be controlled via the light intensity provided.

    • Bastien Bissaro
    • , Eirik Kommedal
    •  & Vincent G. H. Eijsink