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

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/H 2 O 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. Fe III -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 gvalues (g 1 = 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.

Insights into the catalytic mechanism of the chlorothalonil dehalogenase from Pseudomonas sp. CTN-3

“…Experimental (zχ″/zB) EPR spectra were recorded at 9.468 GHz, 12 K, 2 mW microwave power, and 12 G (1.2 mT) magnetic field modulation, using instrumentation described in earlier work (Karunagala Pathiranage et al, 2021). Second derivative (z 2 χ″/zB 2 ) EPR spectra were generated by pseudomodulation (Hyde et al, 1990) of the experimental spectra with a 22 G pseudomodulation amplitude (Xenon, Bruker).…”