Density functional study on geometry and electronic structure of nitrile hydratase active site model

Abstract

Nitrile Hydratase (R. Sp. 771, NHase, EC. 4.2.1.84, CAS registration no. 82391-37-5), the enzyme that plays an important role in the industrial production of acrylamide, is studied theoretically in this article. For the first time the electronic structure of the active site of nitrosylated form with a proper oxidation state of the cysteine ligands is calculated using the density functional theory (DFT) method with the Becke, Lee, Yang, and Paar (B3LYP)6-31G* functional. The optimized geometries of six and five coordinated complexes are different, showing that the photodissociation of NO triggers a substantial relaxation of the NHase active site. The major structural change is a shift of the position of iron with respect to the four equatorial ligands, which resembles a heme doming observed in myoglobins. Calculated charge distribution supports the role of Fe as a possible Lewis acid in catalytic cycle. We found that the cysteine-sulfinic residue (Cys112) is very strongly polarized in NHase. Sulfur atom S ␥ Cys112 is predicted to be the most positively charged center. This result gives independent support to a very recent finding of the critical role of an oxidation in the position Cys112 for preserving catalytic activity of the enzyme (Endo, I.; Nojiri, M.; Tsujimura, M.; Nakasako, M.; Nagashima, S.; Yohda, M.; Odaka, M. J Inorgan Biochem 2001, 83, 247).

Synthetic Analogues of Cysteinate‐Ligated Non‐Heme Iron and Non‐Corrinoid Cobalt Enzymes

“…The fact that the pK a of a M 3+ -bound water has been shown to decrease upon oxygenation of a thiolate (in an NHase model complex) supports this possibility. 124 Also consistent with this, recent DFT calculations indicate that the iron ion of NHase is moderately positively charged (calculated Mulliken charge = +0.49), 112 supporting its possible role as a Lewis acid. The last two mechanisms shown in Figure 6 are differentiated from the first in that they involve metalbound intermediates and require that the metal ion release product at reasonably fast rates.…”

The structure and spin-states of some Fe(III) mimics of nitrile hydratase, studied by DFT and ONIOM(DFT:PM3) calculations

“…The change in the d-orbital energies with the L ax -M-L ba angle in an idealized square pyramidal complex suggests that variations in this geometrical parameter might help to yield a low spin electronic state in five-coordinate Fe-NHase. A previous computational study [21] suggested that the photodissociation of NO triggers a substantial relaxation of the Fe-NHase active site, the major structural change being a shift of the position of the metal centre with respect to the four equatorial ligands. Further experimental and theoretical studies are needed to elucidate the structural basis of this highly unusual low spin preference.…”

“…Some models for the active site of Fe-NHase have been employed in previous computational studies, where some approximations were made in order to reduce the number of atoms involved in the calculation, such as the replacement of the aCys109 residue by a SCH 3 mercaptide group [21] or the modelling of the bArg56 and bArg141 residues as methyl guanidinium moieties [22].…”

“…During the past few years, research efforts pursuing a computational description of this enzyme have been directed towards studying the spin-dependent energetics and structures of a series of Fe(III) complexes [18][19][20], most of which have been synthesized to mimic the metal centre in Fe-NHase, although some calculations on the active site of the enzyme have also been reported [21,22]. Here we focus on the assessment of the capability of DFT alone, and when used in conjunction with PM3 in an ONIOM method, to predict the structure of some of the model complexes of Fe-NHase as well as a correct description of their spin-states.…”

A comparative DFT study of substrates and products of industrial enzyme nitrile hydratase

“…Relevant data on aliphatic ligands of NHases will be reported elsewhere. The same computational approach was used in recent studies of the Fe-NHase models of the active site [7,21,22]. The optimized structures of the reference compounds: NCN, NCA, benzonitrile (BNT), benzamide (BAM) are shown in Figure 3 The DFT data on structures, IR spectra and molecular electrostatic potential (MEP) maps presented here will be used to develop force field parameters for classical or quantum-classical molecular dynamics (MDs) studies of NHases.…”