Enzyme mechanisms

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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Latest Research and Reviews

  • Research |

    Cryo-EM structures of the yeast P4-ATPase Drs2p–Cdc50p in three different states of activation provide insights into the function of this lipid flippase, including mechanisms of autoinhibition and PI4P-dependent activation.

    • Milena Timcenko
    • , Joseph A. Lyons
    • , Dovile Januliene
    • , Jakob J. Ulstrup
    • , Thibaud Dieudonné
    • , Cédric Montigny
    • , Miriam-Rose Ash
    • , Jesper Lykkegaard Karlsen
    • , Thomas Boesen
    • , Werner Kühlbrandt
    • , Guillaume Lenoir
    • , Arne Moeller
    •  & Poul Nissen
    Nature, 1-5
  • Research |

    A combination of structural and biochemical analyses of MlaC, the soluble periplasmic component of the Mla pathway, elucidate how this protein assists phospholipid movement between the bacterial inner and outer membranes.

    • Gareth W. Hughes
    • , Stephen C. L. Hall
    • , Claire S. Laxton
    • , Pooja Sridhar
    • , Amirul H. Mahadi
    • , Caitlin Hatton
    • , Thomas J. Piggot
    • , Peter J. Wotherspoon
    • , Aneika C. Leney
    • , Douglas G. Ward
    • , Mohammed Jamshad
    • , Vaclav Spana
    • , Ian T. Cadby
    • , Christopher Harding
    • , Georgia L. Isom
    • , Jack A. Bryant
    • , Rebecca J. Parr
    • , Yasin Yakub
    • , Mark Jeeves
    • , Damon Huber
    • , Ian R. Henderson
    • , Luke A. Clifton
    • , Andrew L. Lovering
    •  & Timothy J. Knowles
  • Research |

    HMCES protects abasic sites that block DNA replication via covalent protein attachment. Crystal structures of the Escherichia coli HMCES homolog YedK reveal that the conserved SRAP domain forms a thiazolidine linkage with the abasic site, explaining the stability of the DNA-protein cross-link and its specificity for DNA lesions at stalled replication forks.

    • Petria S. Thompson
    • , Katherine M. Amidon
    • , Kareem N. Mohni
    • , David Cortez
    •  & Brandt F. Eichman
  • Research |

    The fleeting nature of transition state ensembles of protein motions has precluded their experimental observation. This work provides an atomistic insight into the rate-determining structural transition of adenylate kinase during catalysis by high-pressure NMR and molecular dynamics simulations.

    • John B. Stiller
    • , S. Jordan Kerns
    • , Marc Hoemberger
    • , Young-Jin Cho
    • , Renee Otten
    • , Michael F. Hagan
    •  & Dorothee Kern
  • Research | | open

    Shiuan-Woei LinWu et al. presents a DNA sequencing technology with high accuracy, using 9°N DNA polymerase. This study expands the current portfolio of enzymes equipped with 3′-esterase activity and shows the feasibility of a 3′-editing-based DNA sequencing.

    • Shiuan-Woei LinWu
    • , Yu-Hsuan Tu
    • , Ting-Yueh Tsai
    • , Manuel Maestre-Reyna
    • , Mu-Sen Liu
    • , Wen-Jin Wu
    • , Jyun-Yuan Huang
    • , Hung-Wen Chi
    • , Wei-Hsin Chang
    • , Chung-Fan Chiou
    • , Andrew H.-J. Wang
    • , Johnsee Lee
    •  & Ming-Daw Tsai

News and Comment

  • News and Views |

    A synthetic DNA enzyme catalyses the formation of a native phosphodiester bond between two RNA fragments, but the molecular details of the mechanism remained elusive. Research using computational and biochemical approaches now suggests that the DNA enzyme recruits two magnesium ions to assist in the catalysis of RNA ligation.

    • Claudia Höbartner
    Nature Catalysis 2, 483-484
  • News and Views |

    Hydrogenases are very powerful biocatalysts for dihydrogen cleavage. Now, X-ray crystallography shows how [Fe]-hydrogenase requires ligand exchanges at the metal centre and significant molecular motions to open and close its active site to effectively transfer a hydride to an electrophilic organic substrate.

    • Yvain Nicolet
    Nature Catalysis 2, 481-482
  • News and Views |

    High-yield production of a functionally active mimic of particulate methane monooxygenase in Escherichia coli has been presented. Investigation of its catalytic mode clarifies the role of duroquinol in biomimetic methanol production.

    • Sunney I. Chan
    •  & Steve S.-F Yu
    Nature Catalysis 2, 286-287
  • News and Views |

    Bacteriophage-encoded anti-CRISPR (Acr) proteins were previously thought to inhibit CRISPR-mediated immunity by acting as physical barriers against the binding or cleavage of DNA. Two new studies report that recently discovered type V Acr proteins use enzymatic activities to shut down the Cas12a endonuclease, providing a multi-turnover ‘off switch’ for CRISPR-based immunity and technology.

    • Shravanti K. Suresh
    • , Karthik Murugan
    •  & Dipali G. Sashital
  • Research Highlights |

    Formylglycine residues are important functional handles on native and synthetic proteins. The formation of these residues is mediated by a copper enzyme operating via a superoxo intermediate.

    • David Schilter