Enzyme mechanisms articles from across Nature Portfolio

Enzyme mechanisms are the chemical transformations, and the steps within them, generated by enzymatic action on substrates. The mechanism of enzyme catalysis is similar in principle to other types of chemical catalysis, for instance by involving a combination of several different types of catalysis. Determining enzyme mechanisms includes determining their kinetic and thermodynamic properties.

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News & Views | 18 May 2023

A look into the dynamic process of proofreading in DNA polymerase-γ at near-atomic resolution

Nature Structural & Molecular Biology, 1-2

Latest Research and Reviews

Research
02 June 2023 | Open Access

Human soluble CD39 displays substrate inhibition in a substrate-specific manner
- Venkat M. K. Vadlamani
- , Kavinda K. J. Gunasinghe
- & Matthew T. Harper
Scientific Reports 13, 8958
Research | 29 May 2023

Fragmentation and [4 + 3] cycloaddition in sodorifen biosynthesis

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
Nature Chemistry, 1-8
Research | 25 May 2023

Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN

The authors provide cryo-EM reconstructions of human transfer RNA splicing endonuclease during substrate recognition, rationalizing disease-relevant mutations.
- Samoil Sekulovski
- , Lukas Sušac
- & Simon Trowitzsch
Nature Structural & Molecular Biology, 1-7
Reviews | 24 May 2023

Loop dynamics and the evolution of enzyme activity

Enzyme conformational plasticity plays an important part in expanding the functional diversity of a limited repertoire of sequences. This Review discusses the role of flexible loops in enzyme evolution, focusing on both examples from natural evolution and engineering success stories.
- Marina Corbella
- , Gaspar P. Pinto
- & Shina C. L. Kamerlin
Nature Reviews Chemistry, 1-12
Research
23 May 2023 | Open Access

Discovery and biosynthesis of tricyclic copper-binding ribosomal peptides containing histidine-to-butyrine crosslinks

Cyclic peptides are important bioactive compounds and drugs, synthesised by enzymatic side-chain macrocyclization of ribosomal peptides, which rarely involves histidine residues. Here, the authors report the discovery and biosynthesis of tricyclic lanthipeptide noursin, constrained by a tri amino acid labionin crosslink and histidine-to-butyrine crosslink, which is important for copper binding of noursin.
- Yuqing Li
- , Yeying Ma
- & Huan Wang
Nature Communications 14, 2944
Research
22 May 2023 | Open Access

Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration

Two specific inhibitors for emerging cancer therapy target malic enzyme 2 (ME2) are identified and are shown to bind to one of ME2 allosteric sites, resulting in inactive open conformation, inhibiting ME2-mediated cellular respiration and ATP production in the cell
- Ju-Yi Hsieh
- , Kun-Chi Chen
- & Hui-Chih Hung
Communications Biology 6, 548

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News and Comment

News & Views | 18 May 2023

A look into the dynamic process of proofreading in DNA polymerase-γ at near-atomic resolution

The correction of errors during mitochondrial DNA replication by the proofreading function of DNA polymerase-γ is crucial for maintaining the integrity of the mitochondrial genome and the production of cellular energy. Using cryo-electron microscopy, several steps of the DNA polymerase-γ proofreading pathway have been revealed at near-atomic resolution.

Nature Structural & Molecular Biology, 1-2
News & Views | 20 April 2023

Human primase hangs on the primer–template and Polα to facilitate primer termination

We determined the structure of the Polα–primase complex trapped in a DNA elongation state. Cryo-electron microscopy showed that primase has a role in facilitating the timely termination of primer DNA elongation by Polα by hanging on the primer–template complex.

Nature Structural & Molecular Biology 30, 575-576
News & Views | 06 April 2023

GAPDH redox redux—rewiring pentose phosphate flux

GAPDH is highly sensitive to oxidation by reactive oxygen species, but how exactly its oxidation alters carbon flux is not known. Talwar et al. demonstrate that oxidative inactivation of GAPDH is required for maximal pentose phosphate pathway flux to support NADPH generation during oxidative stress.
- Laura Torrente
- & Gina M. DeNicola
Nature Metabolism 5, 538-539
News & Views | 31 March 2023

Structure of AlkB–AlkG shows details of alkane terminal C–H selectivity and functionalization

The cryo-EM structure of a natural AlkB–AlkG fusion from Fontimonas thermophila reveals the mechanistic basis for its selectivity towards, and functionalization of, alkane terminal C–H groups. AlkB contains an alkane entry tunnel and a diiron active site, and AlkG docks through electrostatic interactions and transfers electrons to the diiron center for catalysis.

Nature Structural & Molecular Biology 30, 413-414
News & Views | 06 February 2023

The cell cycle loops UTP around CAD

Cell division is a highly regulated process and requires a concurrent supply of energy and nutrients. Shin et al. provide critical insights into the allosteric mechanisms by which UTP regulates CAD activity and pyrimidine synthesis during the cell cycle.
- Umakant Sahu
- & Issam Ben-Sahra
Nature Metabolism 5, 199-200
Research Highlights | 30 January 2023

Protein C-mannosylation
- Jan-Stefan Völler
Nature Catalysis 6, 5

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Enzyme mechanisms articles from across Nature Portfolio

Featured

A look into the dynamic process of proofreading in DNA polymerase-γ at near-atomic resolution

Latest Research and Reviews

Human soluble CD39 displays substrate inhibition in a substrate-specific manner

Fragmentation and [4 + 3] cycloaddition in sodorifen biosynthesis

Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN

Loop dynamics and the evolution of enzyme activity

Discovery and biosynthesis of tricyclic copper-binding ribosomal peptides containing histidine-to-butyrine crosslinks

Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration

News and Comment

A look into the dynamic process of proofreading in DNA polymerase-γ at near-atomic resolution

Human primase hangs on the primer–template and Polα to facilitate primer termination

GAPDH redox redux—rewiring pentose phosphate flux

Structure of AlkB–AlkG shows details of alkane terminal C–H selectivity and functionalization

The cell cycle loops UTP around CAD

Protein C-mannosylation

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