Enzyme mechanisms articles within Nature Chemistry

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  • Article |

    Ribosomally synthesized and post-translationally modified peptides (RiPPs) can have vast structural diversity and biological functions enabled by disparate post-translational modifications (PTMs). However, unconventional PTMs derived from non-RiPP biosynthesis are rarely reported. Now a class of lipopeptides featuring a distinct fatty-acyl-modified N terminus and the responsible RiPP/fatty-acid hybrid biosynthetic machinery have been characterized.

    • Hengqian Ren
    • , Chunshuai Huang
    •  & Huimin Zhao

  • Article |

    The use of biocatalysis to support early-stage drug discovery campaigns remains largely untapped. Here, engineered biocatalysts enable the synthesis of sp3-rich polycyclic compounds through an intramolecular cyclopropanation of benzothiophenes, affording a class of complex scaffolds potentially useful for fragment-based drug discovery campaigns.

    • David A. Vargas
    • , Xinkun Ren
    •  & Rudi Fasan

  • Article |

    Many natural products are produced by non-ribosomal peptide synthetases in an assembly-line fashion. How these molecular machines orchestrate the biochemical sequences has remained elusive. It is now understood that an extended-conformation ensemble is needed to coordinate chemical-transformation steps whereas the biosynthesis directionality is driven by the enzyme’s innate conformational free energies.

    • Xun Sun
    • , Jonas Alfermann
    •  & Haw Yang

  • News & Views |

    Tandem cycloaddition reactions have significant applications in organic synthetic chemistry. Now, two enzymes are shown to catalyse tandem hetero-Diels–Alder reactions with a synergistic interplay between a calcium cofactor and N-glycan post-translational modifications during the biosynthesis of bistropolone-sesquiterpene secondary metabolites.

    • Richiro Ushimaru
    •  & Ikuro Abe

  • Article
    | Open Access

    Allostery produces concerted functions of protein complexes by orchestrating the cooperative work between the constituent subunits. By restoring functions of pseudo-active sites that have been lost through evolution, allosteric sites have now been designed into a rotary molecular motor, V1-ATPase, resulting in its rotation being boosted allosterically.

    • Takahiro Kosugi
    • , Tatsuya Iida
    •  & Nobuyasu Koga

  • Article |

    Two glycosylated enzymes, EupfF and PycR1, have now been characterized and shown to independently catalyse the tandem intermolecular [4 + 2] cycloaddition in the biosynthesis of bistropolone-sesquiterpenes. Through analysis of enzyme–substrate co-crystal structures, together with computational and mutational studies, the origins of their catalytic activity and stereoselectivity were elucidated.

    • Jiawang Liu
    • , Jiayan Lu
    •  & Youcai Hu

  • Article
    | Open Access

    The metal-dependent, bifunctional isoprenyl diphosphate synthase PcIDS1 from the leaf beetle Phaedon cochleariae integrates substrate, product and metal-ion concentrations to tune its dynamic reactivity. Now structural and functional analyses reveal that this enzyme uses both catalytic centres to form geranyl pyrophosphate, while one domain is inactivated during farnesyl pyrophosphate production.

    • Felix Ecker
    • , Abith Vattekkatte
    •  & Michael Groll

  • Article |

    The biosynthesis of the methylated sesquiterpene sodorifen, which features a cryptic methylation pattern, has now been studied through extensive labelling experiments and computational chemistry. The methyl group formation is now understood to come from methylene carbons of the substrate farnesyl diphosphate and the absolute configuration of the biosynthetic intermediate presodorifen diphosphate has been revised.

    • Houchao Xu
    • , Lukas Lauterbach
    •  & Jeroen S. Dickschat

  • Article |

    A nanopore framework has been developed to reveal the crosstalk effect on the renin–angiotensin system. By reading the single-amino-acid differences in angiotensin peptides with high accuracy and high efficiency, the selective inhibition of angiotensin-converting enzyme by angiotensin-converting enzyme 2 was revealed. This activity was shown to be suppressed by the spike protein of SARS-CoV-2.

    • Jie Jiang
    • , Meng-Yin Li
    •  & Yi-Tao Long

  • Article |

    Enzymes with identical sequences of amino acids can display varying activities when encoded with mRNA with different properties, but why this is the case has been a mystery. Now, it has been shown that synonymous mutations in mRNA alter the partitioning of proteins into long-lived soluble misfolded states with varying activities.

    • Yang Jiang
    • , Syam Sundar Neti
    •  & Edward P. O’Brien

  • Article |

    Sterically demanding 2′-modified nucleotides used in antisense therapeutics have thus far been challenging to synthesise enzymatically. Now, it has been shown that mutation of two gatekeeper residues in an archaeal DNA polymerase unlocks efficient synthesis of the modified nucleic acid oligomers 2′-O-methyl-RNA and 2′-O-(2-methoxyethyl)-RNA and enables the evolution of 2′-O-methyl-RNA enzymes.

    • Niklas Freund
    • , Alexander I. Taylor
    •  & Philipp Holliger

  • Article |

    A genetically encoded phototrigger based on a xanthone amino acid can expand the scope of time-resolved serial femtosecond crystallography beyond naturally photoactive proteins. This approach has been used to uncover metastable reaction intermediates that occur prior to C–H bond activation in a human liver fatty-acid-binding protein mutant.

    • Xiaohong Liu
    • , Pengcheng Liu
    •  & Jiangyun Wang

  • Article |

    A reduction reaction is usually equated with an electron transfer reaction. Now, ultrafast time-resolved serial femtosecond X-ray crystallography has enabled the visualization of the stepwise structural changes that occur after electron transfers have been observed in the light-triggered reduction of flavin adenine dinucleotide catalysed by DNA photolyase.

    • Manuel Maestre-Reyna
    • , Cheng-Han Yang
    •  & Ming-Daw Tsai

  • Article |

    Directed evolution of a primitive computationally designed enzyme has produced an efficient and enantioselective biocatalyst for the Morita–Baylis–Hillman reaction. The engineered enzyme uses a designed histidine nucleophile operating in synergy with a catalytic arginine that emerged during evolution and serves as a genetically encoded surrogate of privileged bidentate hydrogen-bonding catalysts.

    • Rebecca Crawshaw
    • , Amy E. Crossley
    •  & Anthony P. Green

  • Article |

    O-methyl nitronate is a rare functional group in natural products. Now, the biosynthetic pathway to O-methyl nitronate, which involves O-methylation of a peptidyl carrier protein (PCP)-tethered nitronate, has been revealed. In some bacteria, the same PCP-tethered nitronate is shown to be oxidized by nitronate monooxygenases to provide nitrite and a PCP-tethered glyoxylate.

    • Hai-Yan He
    •  & Katherine S. Ryan

  • Article |

    The biosynthesis of goadvionins—hybrid lipopeptide antibiotics—is not fully understood. An unusual acyltransferase, GdvG, has now been identified and shown to catalyse a condensation reaction between an acyl-carrier-protein-tethered very-long-chain fatty acid and an eight-residue ribosomally synthesized and post-translationally modified peptide. The position of functional groups in the very-long acyl chain have been determined by tandem mass spectrometry.

    • Ryosuke Kozakai
    • , Takuto Ono
    •  & Hiroyasu Onaka

  • Article |

    The Varkud satellite ribozyme, which catalyses site-specific RNA cleavage and ligation, is an important model to understand RNA catalysis. Now, a combination of theoretical and experimental work has revealed new details about its catalytic mechanism. Mg2+ is shown to play an important role in organizing the active site, and the proton transfers in the transition state have also been identified.

    • Abir Ganguly
    • , Benjamin P. Weissman
    •  & Darrin M. York

  • Article |

    The complete biosynthesis of the fungal indole alkaloid malbrancheamide, which culminates in an intramolecular [4+2] hetero-Diels–Alder cyclization to produce the bicyclo[2.2.2]diazaoctane scaffold, has now been discovered. Chemical synthesis and protein structural analysis were used to provide mechanistic insight into this enzyme-dependent diastereo- and enantioselective cycloaddition.

    • Qingyun Dan
    • , Sean A. Newmister
    •  & Robert M. Williams

  • Article |

    The UbiD family of reversible decarboxylases interconvert propenoic or aromatic acids with the corresponding alkenes or aromatic compounds, using a transient 1,3-dipolar cycloaddition between the substrate and the prenylated flavin mononucleotide cofactor. Atomic-resolution crystallography shows targeted destabilization of the intermediate covalent adducts, allowing the enzyme to harness 1,3-dipolar cycloaddition as a readily reversible reaction.

    • Samuel S. Bailey
    • , Karl A. P. Payne
    •  & David Leys

  • Article |

    LepI is an S-adenosylmethionine-dependent pericyclase that catalyses the dehydration, hetero-Diels–Alder reaction and retro-Claisen rearrangement reactions that occur in the formation of the 2-pyridone natural product leporin C. Now, the mechanistic details that underpin this range of catalytic reactions have been uncovered from the crystal structures of LepI and LepI in complex with ligands.

    • Yujuan Cai
    • , Yang Hai
    •  & Yi Tang

  • Article |

    The biosynthesis of the [FeFe] hydrogenase active site H-cluster requires several Fe–S proteins that perform poorly understood reactions. Now, a reaction intermediate trapped in the enzyme HydG is shown to contain a [(Cys)Fe(CO)(CN)] species identified as the first organometallic Fe moiety en route to the catalytic H-cluster.

    • Guodong Rao
    • , Lizhi Tao
    •  & R. David Britt

  • Article |

    Enzymes that form a metabolic pathway in which the product of one enzyme is the substrate for the next have now been shown to associate through a process of sequential, directed chemotactic movement. The extent of enzyme migration is proportional to the exposure time to the substrate gradient.

    • Xi Zhao
    • , Henri Palacci
    •  & Ayusman Sen

  • Article |

    Radical SAM enzymes are versatile enzymes catalysing chemically challenging reactions. Now, a radical SAM enzyme that post-translationally modifies ribosomally synthesized peptides to contain D-amino acids has been discovered in Bacillus subtilis, and its mechanism has been deciphered. These peptides, called epipeptides, efficiently inhibit bacterial growth.

    • Alhosna Benjdia
    • , Alain Guillot
    •  & Olivier Berteau

  • Article |

    An artificial aldolase has been optimized using an ultrahigh-throughput microfluidic screening assay. The evolved enzyme exhibits excellent stereoselectivity and broad substrate scope. Structural studies suggest that a Lys-Tyr-Asn-Tyr catalytic tetrad, which emerged during directed evolution, is responsible for the >109 rate enhancement achieved by this catalyst.

    • Richard Obexer
    • , Alexei Godina
    •  & Donald Hilvert

  • Article |

    FeFe hydrogenases are highly efficient H2 producing enzymes; however, they can be inactivated by O2. Now, a mechanism for O2 diffusion within FeFe hydrogenases and its reactions at the active site of the enzyme has been proposed. These findings could help with the design of hydrogenase mutants with increased resistance to oxidative damage.

    • Adam Kubas
    • , Christophe Orain
    •  & Christophe Léger

  • Article |

    A temperature-dependent kinetic study of ground-state proton transfer in the green fluorescent protein highlights the role of ‘deep tunnelling’ in proton wires. A potential mechanism for directional proton transport is proposed, where high-pKa amino acid residues act as ‘tunnel diodes’ and as stabilizing elements within protein water wires.

    • Bridget Salna
    • , Abdelkrim Benabbas
    •  & Paul M. Champion

  • Article |

    L-Cysteine-derived thiazolidines have now been shown to be artificial substrates of the radical SAM enzyme HydE, which converts them into S-adenosyl-L-cysteine. Carbon–sulfur bonds are formed in a concerted mechanism that involves the formation of a C-centred radical that concomitantly attacks the S atom of a thioether. This is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting an H-atom.

    • Roman Rohac
    • , Patricia Amara
    •  & Yvain Nicolet

  • Article |

    [Fe]-hydrogenase has an iron-guanylylpyridinol cofactor and catalyses the reversible hydrogenation of a methenyl-tetrahydromethanopterin. Now, [Fe]-hydrogenase has been reconstituted using synthetic cofactor mimics. The enzyme containing a mimic with a 2-hydroxy-pyridine group was active, whereas one containing a 2-methoxy-pyridine group was inactive. This result, together with DFT computations, supports a catalytic mechanism involving the deprotonated pyridinol hydroxy group as a proton acceptor.

    • Seigo Shima
    • , Dafa Chen
    •  & Xile Hu

  • Article |

    The reactivity of a monooxygenase (P450 PikC) has been modified through protein and substrate engineering, and applied to the oxidation of unactivated methylene C–H bonds. The protein engineering was guided by using molecular dynamics and quantum mechanical calculations to develop a predictive model for substrate scope, site selectivity and stereoselectivity of the C–H hydroxylation.

    • Alison R. H. Narayan
    • , Gonzalo Jiménez-Osés
    •  & David H. Sherman

  • Article |

    Structural elucidation of a peptide natural product has revealed an unprecedented post-translational modification involving formation of a carbon–carbon bond between the side-chains of lysine and tryptophan. This motif defines a new family of cyclic peptides. Biochemical studies reveal that this C-C bond is generated by a radical SAM enzyme, and delineate its catalytic mechanism.

    • Kelsey R. Schramma
    • , Leah B. Bushin
    •  & Mohammad R. Seyedsayamdost

  • News & Views |

    A combined experimental and theoretical study of the biosynthesis of a family of antibacterial natural products has uncovered some of the finer details of unusual stereoselectivity observed in a peptide cyclization.

    • Bryan Jones
    •  & Romas J. Kazlauskas

  • Article |

    The stereochemical outcome of enzyme-catalysed reactions with physiological substrates is typically governed by the well-defined geometry of the enzyme active site. Now, a rare example is reported where the substrate controls the stereoselectivity of a Michael-type addition during lanthipeptide biosynthesis.

    • Weixin Tang
    • , Gonzalo Jiménez-Osés
    •  & Wilfred A. van der Donk

  • Article |

    FeFe hydrogenases, the enzymes that oxidize or produce H2, are inactivated under oxidizing conditions. Here, it is shown that this inactivation results from H2 binding to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the active site prevents irreversible oxidative damage.

    • Vincent Fourmond
    • , Claudio Greco
    •  & Christophe Léger

  • Article |

    Structural analysis of the enzyme transketolase at sub-ångström resolution shows the existence of physically distorted covalent intermediates with elongated scissile substrate bonds. These observations highlight the ability of enzymes to enhance the reactivity of reaction intermediates leading to a more efficient process.

    • Stefan Lüdtke
    • , Piotr Neumann
    •  & Kai Tittmann

  • News & Views |

    The metal cofactors responsible for the activity of CDK2 — a representative member of the kinase superfamily of enzymes — have now been shown to also have inhibitory effects during the catalytic cycle.

    • Ivaylo Ivanov

  • Editorial |

    Disagreements are common in science and can lead to better understanding, but must be handled carefully.

  • Perspective |

    Enzyme-catalysed reactions can involve significant quantum tunnelling and show kinetic isotope effects with complex temperature dependences. In this Perspective, reaction dynamics and enzyme catalysis are linked to transition-state-theory frameworks. It is shown that a multi-state model using standard transition-state theory can account for complex experimental data without invoking a role for enzyme dynamics.

    • David R. Glowacki
    • , Jeremy N. Harvey
    •  & Adrian J. Mulholland

  • Research Highlights |

    The isolation of pure quantities of the active intermediate in cytochrome P450 enzymes — known as compound I — has led to this elusive species being characterized in detail.

    • Neil Withers

  • Research Highlights |

    A computational investigation into how environmental factors influence phosphoester hydrolysis reveals differences between the mechanisms observed in aqueous solution and within an enzyme active site.

    • Gavin Armstrong

  • Research Highlights |

    A synthetic functional model of the oxygen reduction site in the enzyme cytochrome c oxidase has been used to investigate the effects of hydrogen sulfide on respiration.

    • Stephen Davey

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