Identification of an Intermediate Species along the Nitrile Hydratase Reaction Pathway by EPR Spectroscopy

Biochemistry. 2021 Dec 14;60(49):3771-3782. doi: 10.1021/acs.biochem.1c00574. Epub 2021 Nov 29.

Abstract

A new method to trap catalytic intermediate species was employed with Fe-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase). ReNHase was incubated with substrates in a 23% (w/w) NaCl/H2O eutectic system that remained liquid at -20 °C, thereby permitting the observation of transient species that were present at electron paramagnetic resonance (EPR)-detectable levels in samples frozen while in the steady state. FeIII-EPR signals from the resting enzyme were unaffected by the presence of 23% NaCl, and the catalytic activity was ∼55% that in the absence of NaCl at the optimum pH of 7.5. The reaction of ReNHase in the eutectic system at -20 °C with the substrates acetonitrile or benzonitrile induced significant changes in the EPR spectra. A previously unobserved signal with highly rhombic g-values (g1 = 2.31) was observed during the steady state but did not persist beyond the exhaustion of the substrate, indicating that it arises from a catalytically competent intermediate. Distinct signals due to product complexes provide a detailed mechanism for product release, the rate-limiting step of the reaction. Assignment of the observed EPR signals was facilitated by density functional theory calculations, which provided candidate structures and g-values for various proposed ReNHase intermediates. Collectively, these results provide new insights into the catalytic mechanism of NHase and offer a new approach for isolating and characterizing EPR-active intermediates in metalloenzymes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetonitriles / chemistry*
  • Acetonitriles / metabolism
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Biocatalysis
  • Catalytic Domain
  • Cold Temperature
  • Deep Eutectic Solvents / chemistry
  • Density Functional Theory
  • Electron Spin Resonance Spectroscopy
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Hydro-Lyases / chemistry*
  • Hydro-Lyases / genetics
  • Hydro-Lyases / metabolism
  • Hydrogen-Ion Concentration
  • Iron / chemistry*
  • Iron / metabolism
  • Kinetics
  • Nitriles / chemistry*
  • Nitriles / metabolism
  • Protein Subunits / chemistry
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Rhodococcus equi / chemistry*
  • Rhodococcus equi / enzymology
  • Sodium Chloride / chemistry
  • Substrate Specificity
  • Water / chemistry

Substances

  • Acetonitriles
  • Bacterial Proteins
  • Deep Eutectic Solvents
  • Nitriles
  • Protein Subunits
  • Recombinant Proteins
  • Water
  • Sodium Chloride
  • benzonitrile
  • Iron
  • Hydro-Lyases
  • nitrile hydratase
  • acetonitrile