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Hopmann KH. Full Reaction Mechanism of Nitrile Hydratase: A Cyclic Intermediate and an Unexpected Disulfide Switch. Inorg Chem 2014; 53:2760-2. [DOI: 10.1021/ic500091k] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Kathrin H. Hopmann
- Centre for Theoretical and
Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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The Active Site of Nitrile Hydratase: An Assembly of Unusual Coordination Features by Nature. MOLECULAR DESIGN IN INORGANIC BIOCHEMISTRY 2013. [DOI: 10.1007/430_2012_85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Rao S, Holz RC. Analyzing the catalytic mechanism of the Fe-type nitrile hydratase from Comamonas testosteroni Ni1. Biochemistry 2008; 47:12057-64. [PMID: 18942853 DOI: 10.1021/bi801623t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to gain insight into the catalytic mechanism of Fe-type nitrile hydratases (NHase), the pH and temperature dependence of the kinetic parameters k cat, K m, and k cat/ K m along with the solvent isotope effect were examined for the Fe-type NHase from Comamonas testosteroni Ni1 ( CtNHase). CtNHase was found to exhibit a bell-shaped curve for plots of relative activity vs pH over pH values 4-10 for the hydration of acrylonitrile and was found to display maximal activity at pH approximately 7.2. Fits of these data provided a p K ES1 value of 6.1 +/- 0.1, a p K ES2 value of 9.1 +/- 0.2 ( k' cat = 10.1 +/- 0.3 s (-1)), a p K E1 value of 6.2 +/- 0.1, and a p K E2 value of 9.2 +/- 0.1 ( k' cat/ K' m of 2.0 +/- 0.2 s (-1) mM (-1)). Proton inventory studies indicate that two protons are transferred in the rate-limiting step of the reaction at pH 7.2. Since CtNHase is stable to 25 degrees C, an Arrhenius plot was constructed by plotting ln( k cat) vs 1/ T, providing an E a of 33.3 +/- 1.5 kJ/mol. Delta H degrees of ionization values were also determined, thus helping to identify the ionizing groups exhibiting the p K ES1 and p K ES2 values. Based on Delta H degrees ion data, p K ES1 is assigned to betaTyr68 while p K ES2 is assigned to betaArg52, betaArg157, or alphaSer116 (NHases are alpha 2beta 2 heterotetramers). Given the strong similarities in the kinetic data obtained for both Co- and Fe-type NHase enzymes, both types of NHase enzymes likely hydrate nitriles in a similar fashion.
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Affiliation(s)
- Saroja Rao
- Department of Chemistry, Loyola University--Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, USA
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Kubiak K, Nowak W. Molecular dynamics simulations of the photoactive protein nitrile hydratase. Biophys J 2008; 94:3824-38. [PMID: 18234830 PMCID: PMC2367182 DOI: 10.1529/biophysj.107.116665] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 12/31/2007] [Indexed: 11/18/2022] Open
Abstract
Nitrile hydratase (NHase) is an enzyme used in the industrial biotechnological production of acrylamide. The active site, which contains nonheme iron or noncorrin cobalt, is buried in the protein core at the interface of two domains, alpha and beta. Hydrogen bonds between betaArg-56 and alphaCys-114 sulfenic acid (alphaCEA114) are important to maintain the enzymatic activity. The enzyme may be inactivated by endogenous nitric oxide (NO) and activated by absorption of photons of wavelength lambda < 630 nm. To explain the photosensitivity and to propose structural determinants of catalytic activity, differences in the dynamics of light-active and dark-inactive forms of NHase were investigated using molecular dynamics (MD) modeling. To this end, a new set of force field parameters for nonstandard NHase active sites have been developed. The dynamics of the photodissociated NO ligand in the enzyme channel was analyzed using the locally enhanced sampling method, as implemented in the MOIL MD package. A series of 1 ns trajectories of NHases shows that the protonation state of the active site affects the dynamics of the catalytic water and NO ligand close to the metal center. MD simulations support the catalytic mechanism in which a water molecule bound to the metal ion directly attacks the nitrile carbon.
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Affiliation(s)
- Karina Kubiak
- Institute of Physics, Nicolaus Copernicus University, 87-100 Torun, Poland
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Hopmann KH, Himo F. Theoretical Investigation of the Second-Shell Mechanism of Nitrile Hydratase. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200701137] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hopmann KH, Guo JD, Himo F. Theoretical Investigation of the First-Shell Mechanism of Nitrile Hydratase. Inorg Chem 2007; 46:4850-6. [PMID: 17497847 DOI: 10.1021/ic061894c] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first-shell mechanism of nitrile hydratase (NHase) is investigated theoretically using density functional theory. NHases catalyze the conversion of nitriles to amides and are classified into two groups, the non-heme Fe(III) NHases and the non-corrinoid Co(III) NHases. The active site of the non-heme iron NHase comprises a low-spin iron (S=1/2) with a remarkable set of ligands, including two deprotonated backbone nitrogens and both cysteine-sulfenic and cysteine-sulfinic acids. A widely proposed reaction mechanism of NHase is the first-shell mechanism in which the nitrile substrate binds directly to the low-spin iron in the sixth coordination site. We have used quantum chemical models of the NHase active site to investigate this mechanism. We present potential energy profiles for the reaction and provide characterization of the intermediates and transition-state structures for the NHase-mediated conversion of acetonitrile. The results indicate that the first-shell ligand Cys114-SO- could be a possible base in the nitrile hydration mechanism, abstracting a proton from the nucleophilic water molecule. The generally suggested role of the Fe(III) center as a Lewis acid, activating the substrate toward nucleophilic attack, is shown to be unlikely. Instead, the metal is suggested to provide electrostatic stabilization to the anionic imidate intermediate, thereby lowering the reaction barrier.
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Affiliation(s)
- Kathrin H Hopmann
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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Abstract
To elucidate a detailed catalytic mechanism for nitrile hydratases (NHases), the pH and temperature dependence of the kinetic constants k(cat) and K(m) for the cobalt-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) were examined. PtNHase was found to exhibit a bell-shaped curve for plots of relative activity versus pH at pH 3.2-11 and was found to display maximal activity between pH 7.2 and 7.8. Fits of these data provided pK(E)(S1) and pK(E)(S2) values of 5.9 +/- 0.1 and 9.2 +/- 0.1 (k(cat)' = 130 +/- 1 s(-1)), respectively, and pK(E)(1) and pK(E)(2) values of 5.8 +/- 0.1 and 9.1 +/- 0.1 (k(cat)'/K(m)' = (6.5 +/- 0.1) x 10(3) s(-1) mm(-1)), respectively. Proton inventory studies indicated that two protons are transferred in the rate-limiting step of the reaction at pH 7.6. Because PtNHase is stable at 60 degrees C, an Arrhenius plot was constructed by plotting ln(k(cat)) versus 1/T, providing E(a) = 23.0 +/- 1.2 kJ/mol. The thermal stability of PtNHase also allowed DeltaH(0) ionization values to be determined, thus helping to identify the ionizing groups exhibiting the pK(E)(S1) and pK(E)(S2) values. Based on DeltaH(0)(ion) data, pK(E)(S1) is assigned to betaTyr(68), whereas pK(E)(S2) is assigned to betaArg(52), betaArg(157), or alphaSer(112) (NHases are alpha(2)beta(2)-heterotetramers). A combination of these data with those previously reported for NHases and synthetic model complexes, along with sequence comparisons of both iron- and cobalt-type NHases, allowed a novel catalytic mechanism for NHases to be proposed.
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Affiliation(s)
- Sanghamitra Mitra
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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Greene SN, Richards NGJ. Electronic structure, bonding, spectroscopy and energetics of Fe-dependent nitrile hydratase active-site models. Inorg Chem 2006; 45:17-36. [PMID: 16390037 DOI: 10.1021/ic050965p] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fe-type nitrile hydratase (NHase) is a non-heme Fe(III)-dependent enzyme that catalyzes the hydration of nitriles to the corresponding amides. Despite experimental studies of the enzyme and model Fe(III)-containing complexes, many questions concerning the electronic structure and spectroscopic transitions of the metal center remain unanswered. In addition, the catalytic mechanism of nitrile hydration has not yet been determined. We now report density functional theory (B3LYP/6-31G) calculations on three models of the Fe(III) center in the active site of NHase corresponding to hypothetical intermediates in the enzyme-catalyzed hydration of acetonitrile. Together with natural bond orbital (NBO) analysis of the chemical bonding in these active-site models and INDO/S CIS calculations of their electronic spectra, this theoretical investigation gives new insight into the molecular origin of the unusual low-spin preference and spectroscopic properties of the Fe(III) center. In addition, the low-energy electronic transition observed for the active form of NHase is assigned to a dd transition that is coupled with charge-transfer transitions involving the metal and its sulfur ligands. Calculations of isodesmic ligand-exchange reaction energies provide support for coordination of the Fe(III) center in free NHase by a water molecule rather than a hydroxide ion and suggest that the activation of the nitrile substrate by binding to the metal in the sixth coordination site during catalytic turnover cannot yet be definitively ruled out.
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Affiliation(s)
- Shannon N Greene
- Department of Chemistry, University of Florida, Gainesville, 32611-7200, USA
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Morgado CA, Mcnamara JP, Hillier * IH, Sundararajan M. The structure and spin-states of some Fe(III) mimics of nitrile hydratase, studied by DFT and ONIOM(DFT:PM3) calculations. Mol Phys 2005. [DOI: 10.1080/00268970512331340583] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kovacs JA. Synthetic analogues of cysteinate-ligated non-heme iron and non-corrinoid cobalt enzymes. Chem Rev 2004; 104:825-48. [PMID: 14871143 PMCID: PMC4487544 DOI: 10.1021/cr020619e] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julie A Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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Chang CH, Boone AJ, Bartlett RJ, Richards NGJ. Toward a Computational Description of Nitrile Hydratase: Studies of the Ground State Bonding and Spin-Dependent Energetics of Mononuclear, Non-Heme Fe(III) Complexes. Inorg Chem 2003; 43:458-72. [PMID: 14731008 DOI: 10.1021/ic0350032] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Christopher H Chang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA
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Shearer J, Jackson HL, Schweitzer D, Rittenberg DK, Leavy TM, Kaminsky W, Scarrow RC, Kovacs JA. The first example of a nitrile hydratase model complex that reversibly binds nitriles. J Am Chem Soc 2002; 124:11417-28. [PMID: 12236756 PMCID: PMC4485622 DOI: 10.1021/ja012555f] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitrile hydratase (NHase) is an iron-containing metalloenzyme that converts nitriles to amides. The mechanism by which this biochemical reaction occurs is unknown. One mechanism that has been proposed involves nucleophilic attack of an Fe-bound nitrile by water (or hydroxide). Reported herein is a five-coordinate model compound ([Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+)) containing Fe(III) in an environment resembling that of NHase, which reversibly binds a variety of nitriles, alcohols, amines, and thiocyanate. XAS shows that five-coordinate [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) reacts with both methanol and acetonitrile to afford a six-coordinate solvent-bound complex. Competitive binding studies demonstrate that MeCN preferentially binds over ROH, suggesting that nitriles would be capable of displacing the H(2)O coordinated to the iron site of NHase. Thermodynamic parameters were determined for acetonitrile (DeltaH = -6.2(+/-0.2) kcal/mol, DeltaS = -29.4(+/-0.8) eu), benzonitrile (-4.2(+/-0.6) kcal/mol, DeltaS = -18(+/-3) eu), and pyridine (DeltaH = -8(+/-1) kcal/mol, DeltaS = -41(+/-6) eu) binding to [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) using variable-temperature electronic absorption spectroscopy. Ligand exchange kinetics were examined for acetonitrile, iso-propylnitrile, benzonitrile, and 4-tert-butylpyridine using (13)C NMR line-broadening analysis, at a variety of temperatures. Activation parameters for ligand exchange were determined to be DeltaH(+ +) = 7.1(+/-0.8) kcal/mol, DeltaS(+ +) = -10(+/-1) eu (acetonitrile), DeltaH(+ +) = 5.4(+/-0.6) kcal/mol, DeltaS(+ +) = -17(+/-2) eu (iso-propionitrile), DeltaH(+ +) = 4.9(+/-0.8) kcal/mol, DeltaS(+ +) = -20(+/-3) eu (benzonitrile), and DeltaH(+ +) = 4.7(+/-1.4) kcal/mol DeltaS(+ +) = -18(+/-2) eu (4-tert-butylpyridine). The thermodynamic parameters for pyridine binding to a related complex, [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))](+) (DeltaH = -5.9(+/-0.8) kcal/mol, DeltaS = -24(+/-3) eu), are also reported, as well as kinetic parameters for 4-tert-butylpyridine exchange (DeltaH(+ +) = 3.1(+/-0.8) kcal/mol, DeltaS(+ +) = -25(+/-3) eu). These data show for the first time that, when it is contained in a ligand environment similar to that of NHase, Fe(III) is capable of forming a stable complex with nitriles. Also, the rates of ligand exchange demonstrate that low-spin Fe(III) in this ligand environment is more labile than expected. Furthermore, comparison of [Fe(III)(S(2)(Me2)N(3)(Et,Pr))](+) and [Fe(III)(S(2)(Me2)N(3)(Pr,Pr))](+) demonstrates how minor distortions induced by ligand constraints can dramatically alter the reactivity of a metal complex.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Henry L. Jackson
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Dirk Schweitzer
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Durrell K. Rittenberg
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | - Tanya M. Leavy
- Department of Chemistry, Haverford College, Haverford, PennsylVania 19041
| | | | - Robert C. Scarrow
- Department of Chemistry, Haverford College, Haverford, PennsylVania 19041
| | - Julie A. Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
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