Structural and functional models of nitrile hydratase

Hydrolytic metal-mediated coupling of dialkylcyanamides at a Pt(IV) center giving a new family of diimino ligands

Addition of excess R(2)NCN to an aqueous solution of K(2)[PtCl(4)] led to the precipitation of [PtCl(2)(NCNR(2))(2)] (R(2) = Me(2) 1; Et(2) 2; C(5)H(10) 3; C(4)H(8)O, 4) in a cis/trans isomeric ratio which depends on temperature. Pure isomers cis-1-3 and trans-1-3 were separated by column chromatography on SiO(2), while trans-4 was obtained by recrystallization. Complexes cis-1-3 isomerize to trans-1-3 on heating in the solid phase at 110 degrees C; trans-1 has been characterized by X-ray crystallography. Chlorination of the platinum(II) complexes cis-1-3 and trans-1-4 gives the appropriate platinum(IV) complexes [PtCl(4)(NCNR(2))(2)] (cis-5-7 and trans-5-8). The compound cis-6 was also obtained by treatment of [PtCl(4)(NCMe)(2)] with neat Et(2)NCN. The platinum(IV) complex trans-[PtCl(4)(NCNMe(2))(2)] (trans-5) in a mixture of undried Et(2)O and CH(2)Cl(2) undergoes facile hydrolysis to give trans-[PtCl(4)[(H)=C(NMe(2))OH](2)] (9; X-ray structure has been determined). The hydrolysis went to another direction with the cis-[PtCl(4)(NCNR(2))(2)] (cis-5-7) which were converted to the metallacycles [PtCl(4)[NH=C(NR(2))OC(NR(2))=NH]] (11-13) due to the unprecedented hydrolytic coupling of the two adjacent dialkylcyanamide ligands giving a novel (for both coordination and organic chemistry) diimino linkage. Compounds 11-13 and also 14 (R(2) = C(4)H(8)O) were alternatively obtained by the reaction between cis-[PtCl(4)(MeCN)(2)] and neat undried NCNR(2). The structures of complexes 11, 13, and 14 were determined by X-ray single-crystal diffraction. All the platinum compounds were additionally characterized by elemental analyses, FAB mass-spectrometry, and IR and (1)H and (13)C[(1)H] NMR spectroscopies.

Modeling carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS): a trinuclear nickel complex employing deprotonated amides and bridging thiolates

Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) utilizes a unique Ni-M bimetallic site in the biosynthesis of acetyl-CoA, where a square-planar Ni ion is coordinated to two thiolates and two deprotonated amides in a Cys-Gly-Cys motif. The identity of M is currently a matter of debate, although both Cu and Ni have been proposed. In an effort to model ACS's unusual active site and to provide insight into the mechanism of acetyl-CoA formation and the role of each of the metals ions, we have prepared and structurally characterized a number of Ni(II)-peptide mimic complexes. The mononuclear complexes Ni(II) N, N'-bis(2-mercaptoethyl)oxamide (1), Ni(II) N, N'-ethylenebis(2-mercaptoacetamide) (2), and Ni(II) N, N'-ethylenebis(2-mercaptopropionamide) (3) model the Ni(Cys-Gly-Cys) site and can be used as synthons for additional multinuclear complexes. Reaction of 2 with MeI resulted in the alkylation of the sulfur atoms and the formation of Ni(II) N, N'-ethylenebis(2-methylmercaptoacetamide) (4), demonstrating the nucleophilicity of the terminal alkyl thiolates. Addition of Ni(OAc)(2).4H(2)O to3 resulted in the formation of a trinuclear species (5), while 2 crystallizes as an unusual paddlewheel complex (6) in the presence of nickel acetate. The difference in reactivity between the similar complexes 2 and 3 highlights the importance of ligand design when synthesizing models of ACS. Significantly,5 maintains the key features observed in the active site of ACS, namely a square-planar Ni coordinated to two deprotonated amides and two thiolates, where the thiolates bridge to a second metal, suggesting that 5 is a reasonable structural model for this unique enzyme.

Toward a Computational Description of Nitrile Hydratase: Studies of the Ground State Bonding and Spin-Dependent Energetics of Mononuclear, Non-Heme Fe(III) Complexes

The metal coordination and spin state of the Fe(III) center in nitrile hydratase (NHase) has stimulated the synthesis of model complexes in efforts to understand the reactivity and spectroscopic properties of the enzyme. We report density functional theory (DFT) calculations on a number of Fe(III) complexes that have been prepared as models of the NHase metal center, together with others having similar ligands but different ground state spin multiplicities. Our results suggest that a DFT description of specific spin configurations in these systems does not suffer from significant amounts of spin contamination. In particular, B3LYP calculations not only reproduce the observed spin state preferences of these Fe(III) complexes but also predict spin-dependent structural properties consistent with those expected on the basis of ligand field models. An analysis of the natural bond orbital (NBO) transformation of the Kohn-Sham wave functions has enabled quantitation of the overall contribution to covalency of ligand-to-metal sigma-donation and pi-donation, and metal-to-ligand pi-back-bonding in these Fe(III) complexes at their BLYP-optimized geometries. Although sulfur ligands are the primary source of covalency in the Fe(III) complexes, our quantitative analysis suggests that hyperbonding between metal-bound nitrogens and an Fe-S bond represents a mechanism by which Fe-N covalency may arise. These studies establish the computational methodology for future theoretical investigations of the NHase Fe(III) center.

Protonation Structures of Cys-Sulfinic and Cys-Sulfenic Acids in the Photosensitive Nitrile Hydratase Revealed by Fourier Transform Infrared Spectroscopy†

Nitrile hydratase (NHase) from Rhodococcus N-771, which catalyzes hydration of nitriles to the corresponding amides, exhibits novel photosensitivity; in the dark, it is in the inactive form that binds an endogenous nitric oxide (NO) molecule at the non-heme iron center, and photodissociation of the NO activates the enzyme. NHase is also known to have a unique active site structure. Two cysteine ligands to the iron center, alphaCys112 and alphaCys114, are post-translationally modified to sulfinic acid (Cys-SO(2)H) and sulfenic acid (Cys-SOH), respectively, which are thought to play a crucial role in the catalytic reaction. Here, we have determined the protonation structures of these Cys-SO(2)H and Cys-SOH groups using Fourier transform infrared (FTIR) spectroscopy in combination with density functional theory (DFT) calculations. The light-induced FTIR difference spectrum of NHase between the dark inactive and light active forms exhibited two prominent signals at (1154-1148)/1126 and (1040-1034)/1019 cm(-1), which downshifted to 1141/1114 and 1026/1012 cm(-1), respectively, in the uniformly (34)S-labeled NHase. In addition, a minor signal at 915/908 cm(-1) also showed a considerable downshift upon (34)S labeling. These (34)S-sensitive signals were basically conserved in D(2)O buffer with only slight shifts. Vibrational frequencies of methanesulfenic acid (CH(3)SOH) and methanesulfinic acid (CH(3)SO(2)H), simple model compounds of Cys-SOH and Cys-SO(2)H, respectively, were calculated using the DFT method in both the protonated and deprotonated forms and in metal complexes. Comparison of the calculated frequencies and isotope shifts with the observed ones provided the assignment of the two major signals around 1140 and 1030 cm(-1) to the asymmetric and symmetric SO(2) stretching vibrations, respectively, of the S-bonded Cys-SO(2)(-) complex, and the assignment of the minor signal around 910 cm(-1) most likely to the SO stretch of the S-bonded Cys-SO(-) complex. These assignments and the small frequency shifts upon deuteration are consistent with the view that the deprotonated alphaCys112-SO(2)(-) and alphaCys114-SO(-) are hydrogen-bonded with the protons from betaArg56 and/or betaArg141, forming a reactive cavity at the interface of the alpha and beta subunits. There is further speculation that either of these groups is hydrogen bonded to a reactant water molecule, increasing its basicity to facilitate the nucleophilic attack on the nitrile substrate bound to the iron center.

A novel inhibitor for Fe-type nitrile hydratase: 2-cyano-2-propyl hydroperoxide

Nitrile hydratase (NHase) is a non-heme iron or non-corrin cobalt enzyme having two post-translationally modified ligand residues, cysteine-sulfinic acid (alphaCys112-SO(2)H) and -sulfenic acid (alphaCys114-SOH). We studied the interaction between Fe-type NHase and isobutyronitrile (iso-BN) which had been reported as a competitive inhibitor with a K(i) value of 5 microM. From detailed kinetic studies of the inhibitory effect of iso-BN on Fe-type NHase, we found that authentic iso-BN was hydrated normally and that the impurity present in commercially available iso-BN inhibited NHase activity strongly. The inhibitory compound induced significant changes in the UV-vis absorption spectrum of NHase, suggesting its interaction with the iron center. This compound was purified by using reversed-phase HPLC and identified as 2-cyano-2-propyl hydroperoxide (Cpx) by (1)H and PFG-HMBC NMR spectroscopy. Upon addition of a stoichiometric amount of Cpx, NHase was irreversibly inactivated, probably by the oxidation of alphaCys114-SOH to Cys-SO(2)H. This result suggests that the -SOH structure of alphaCys114 is essential for the catalytic activity. The oxygen atom in Cys-SO(2)H is confirmed to come from the solvent H(2)O. The oxidized NHase was found to induce the UV-vis absorption spectral changes by addition of Cpx, suggesting that Cpx strongly interacted with iron(III) in the oxidized NHase to form a stable complex. Thus, Cpx functions as a novel irreversible inhibitor for NHase.

Modulation of the pK(a) of metal-bound water via oxidation of thiolato sulfur in model complexes of Co(III) containing nitrile hydratase: insight into possible effect of cysteine oxidation in Co-nitrile hydratase

The Co(III) complexes of N,N'-bis(2-mercaptophenyl)pyridine-2,6-dicarboxamide (PyPSH(4)), a designed pentadentate ligand with built-in carboxamide and thiolate groups, have been synthesized and studied to gain insight into the role of Cys-S oxidation in Co-containing nitrile hydratase (Co-NHase). Reaction of [Co(NH(3))(5)Cl]Cl(2) with PyPS(4)(-) in DMF affords the thiolato-bridged dimeric Co(III) complex (Et(4)N)(2)[Co(2)(PyPS)(2)] (1). Although the bridged structure is quite robust, reaction of (Et(4)N)(CN) with 1 in acetonitrile affords the monomeric species (Et(4)N)(2)[Co(PyPS)(CN)] (2). Oxidation of 2 with H(2)O(2) in acetonitrile gives rise to a mixture which, upon chromatographic purification, yields K(2)[Co(PyPSO(2)(OSO(2))(CN] (3), a species containing asymmetrically oxidized thiolates. The Co(III) metal center in 3 is coordinated to a S-bound sulfinate and an O-bound sulfonate (OSO(2)) group. Upon oxidation with H(2)O(2), 1 affords an asymmetrically oxidized dimer (Et(4)N)(2)[Co(2)(PyPS(SO(2)))(2)] (4) in which only the terminal thiolates are oxidized to form S-bound sulfinate groups while the bridging thiolates remain unchanged. The thiolato-bridge in 4 is also cleaved upon reaction with (Et(4)N)(CN) in acetonitrile, and one obtains (Et(4)N)(2)[Co(PyPS(SO(2)))(CN)] (5), a species that contains both coordinated thiolate and S-bound sulfinate around Co(III). The structures of 1-4 have been determined. The spectroscopic properties and reactivity of all the complexes have been studied to understand the behavior of the Co(III) site in Co-NHase. Unlike typical Co(III) complexes with bound CN(-) ligands, the Co(III) centers in 2 and 5 are labile and rapidly lose CN(-) in aqueous solutions. Since 3 does not show this lability, it appears that at least one thiolato sulfur donor is required in the first coordination sphere for the Co(III) center in such species to exhibit lability. Both 2 and 5 are converted to the aqua complexes [Co(PyPS)(H(2)O)](-) and [Co(PyPS(SO(2))(H(2)O)](-) in aqueous solutions. The pK(a) values of the bound water in these two species, determined by spectrophotometry, are 8.3 +/- 0.03 and 7.2 +/- 0.06, respectively. Oxidation of the thiolato sulfur (to sulfinate) therefore increases the acidity of the bound water. Since 2 and 5 promote hydrolysis of acetonitrile at pH values above their corresponding pK(a) values, it is also evident that a metal-bound hydroxide is a key player in the mechanism of hydrolysis by these model complexes of Co-NHase. The required presence of a Cys-sulfinic residue and one water molecule at the Co(III) site of Co-NHase as well as the optimal pH of the enzyme near 7 suggests that (i) modulation of the pK(a) of the bound water molecule at the active site of the enzyme could be one role of the oxidized Cys-S residue(s) and (ii) a cobalt-bound hydroxide could be responsible for the hydrolysis of nitriles by Co-NHase.

Post-translational modification of Rhodococcus R312 and Comamonas NI1 nitrile hydratases

Nitrile hydratases (NHases) are industrially significant iron- and cobalt-containing enzymes used in the large-scale synthesis of acrylamide. Previous reports have shown that the active site peptides of NHases are post-translationally modified by oxidation of cysteine residues, and that these modifications are essential for catalysis. We report mass spectrometric evidence of the oxidation states of the active site cysteines in the iron coordination spheres of two iron-containing nitrile hydratases, namely R312 NHase from Rhodococcus rhodochrous strain R312 and NI1 NHase from Comamonas testosteroni. At least one of these cysteines is oxidised to a sulfinic acid (SO(2)H) and there is also evidence suggesting an additional oxidation to a sulfenic acid (SOH). This is the first evidence for the presence of these oxidation states for full-length NHases and for Fe-NHases from different microorganisms. The presence of these covalent modifications was confirmed by performing mass spectrometry on the active site peptide of R312 NHase, under native, reduced and carboxymethylated conditions. We also show the nitrosylation of the iron by mass spectrometry, as well as the release of NO by photoirradiation.

Capture of Ni(II), Cu(I) and Z(II) by thiolate sulfurs of an N2S2Ni complex: a role for a metallothiolate ligand in the acetyl-coenzyme A synthase active site

The metal binding affinity of an (N2S2)Ni bridging metallothiolate ligand (Zn2+ < Ni2+ < Cu+) gives precedent for the observed heterogeneity in ACS/CODH.

Structural analogues of the bimetallic reaction center in acetyl CoA synthase: a Ni--Ni model with bound CO

Models for the active site of the acetyl CoA synthase (ACS) were synthesized by attachment of Cu+ and Ni(0) to nickel diaminodithiolate (S2N2) and diamidodithiolate (S2N2') complexes. The Ni-Ni species form stable CO adducts, i.e., [{(CO)2Ni}{NiS2N2'}]2-, whereas the Cu-NiS2N2 and Cu-NiS2N2' models do not. These results provide supporting evidence for a biological role for reduced nickel in ACS.

Synthesis and characterization of N2S3X-Fe models of iron-containing nitrile hydratase

A series of iron complexes based on the pentadentate ligand 4,7-bis(2'-methyl-2'-mercaptopropyl)-1-thia-4,7-diazacyclononane), (bmmp-TASN)(2)(-), have been synthesized and characterized as models of iron-containing nitrile hydratase (NHase). The chloro derivative [(bmmp-TASN)Fe(III)Cl].0.5EtOH (1) contains a labile chloride which facilitates synthesis of related complexes via substitution reactions. Complex 1 is high-spin, g = 4.28. Addition of NEt(4)CN with 1 in CH(2)Cl(2) results in the cyanide ligated complex [(bmmp-TASN)Fe(III)CN] x 0.5EtOH (2), which shows a single intense nu(CN) band at 2083 cm(-)(1) in the IR region. Complex 2 is low-spin, g(1) = 2.31, g(2) = 2.16, and g(3) = 1.96. Under basic conditions complex 1 affords a mu-oxo bridged dimeric Fe(III) complex [(bmmp-TASN)Fe(III)](2)O (3), which shows an intense band at 799 cm(-)(1). Complex 3 was recrystallized from CH(2)Cl(2)/hexane solution in the triclinic space group P1, with a = 10.5486(15) A, b = 13.0612(19) A, c = 8.1852(12) A, alpha = 96.923(2) degrees, beta = 112.729(2) degrees, gamma = 81.048(2) degrees, and Z = 1. Density functional theory (DFT) calculations of the previously communicated iron-nitrosyl complex [(bmmp-TASN)Fe(III)(NO)][BPh(4)] (4) (Inorg. Chem. 2002, 41, 1039-1041) reveal that the HOMO region is dominated by Fe-S bonding. Complexes 1-4 display irreversible or quasi-reversible reductions in the cyclic voltammograms. All of the iron complexes and the zinc derivative, (bmmp-TASN)Zn (5), display an irreversible oxidation. Complex 5 was crystallized in the monoclinic space group P2(1)/n with a = 9.5759(6) A, b = 20.9790(13) A, c = 10.7113(7) A, beta = 91.283(1) degrees, and Z = 4.