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Facile protic hydration of acetonitrile to protonated acetamide at oxygen mediated by chloroauric acid: insights from experimental and calculations. RESEARCH ON CHEMICAL INTERMEDIATES 2020. [DOI: 10.1007/s11164-019-03979-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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2
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Wang Z, Liu Z, Cui W, Zhou Z. Establishment of Bioprocess for Synthesis of Nicotinamide by Recombinant Escherichia coli Expressing High-Molecular-Mass Nitrile Hydratase. Appl Biochem Biotechnol 2017; 182:1458-1466. [PMID: 28150192 DOI: 10.1007/s12010-017-2410-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/13/2017] [Indexed: 10/20/2022]
Abstract
Application of engineered bacteria expressing nitrile hydratase for the production of amide is getting tremendous attention due to the rapid development of recombinant DNA technique. This study evaluated the effect of 3-cyanopyridine concentrations on nicotinamide production using recombinant Escherichia coli strain (BAG) expressing high-molecular-mass nitrile hydratase from Rhodococcus rhodochrous J1, and established proper process of whole-cell catalysis of 3-cyanopyridine and high cell-density cultivation. The process of substrate fed-batch was applied in the production of nicotinamide, and the concentration of product reached 390 g/L under the condition of low cell-density. After the high cell-density cultivation of BAG in 5 L bioreactor, the OD600 of cell attained 200 and the total activity reached 2813 U/mL. Different high density of BAG after fermentation in the tank was used to catalyze 3-cyanopyridine, and the concentration of nicotinamide reached to 508 g/L in just 60 min. The productivity of BAG was 212% higher than that of R. rhodochrous J1, and it is possible that BAG is able to achieve industrial production of nicotinamide.
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Affiliation(s)
- Zhe Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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3
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Kayanuma M, Shoji M, Yohda M, Odaka M, Shigeta Y. Catalytic Mechanism of Nitrile Hydratase Subsequent to Cyclic Intermediate Formation: A QM/MM Study. J Phys Chem B 2016; 120:3259-66. [DOI: 10.1021/acs.jpcb.5b11363] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Megumi Kayanuma
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Mitsuo Shoji
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Masafumi Yohda
- Graduate
School of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masafumi Odaka
- Graduate
School of Engineering and Resource Science, Akita University, 1-1
Tegata Gakuen-machi, Akita, Akita 010-8502, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
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4
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Kayanuma M, Hanaoka K, Shoji M, Shigeta Y. A QM/MM study of the initial steps of catalytic mechanism of nitrile hydratase. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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Roy S, Mazinani SKS, Groy TL, Gan L, Tarakeshwar P, Mujica V, Jones AK. Catalytic Hydrogen Evolution by Fe(II) Carbonyls Featuring a Dithiolate and a Chelating Phosphine. Inorg Chem 2014; 53:8919-29. [DOI: 10.1021/ic5012988] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Souvik Roy
- Department of Chemistry and Biochemistry and ‡Center for Bio-Inspired Solar Fuel
Production, Arizona State University, Tempe, Arizona 85287, United States
| | - Shobeir K. S. Mazinani
- Department of Chemistry and Biochemistry and ‡Center for Bio-Inspired Solar Fuel
Production, Arizona State University, Tempe, Arizona 85287, United States
| | - Thomas L. Groy
- Department of Chemistry and Biochemistry and ‡Center for Bio-Inspired Solar Fuel
Production, Arizona State University, Tempe, Arizona 85287, United States
| | - Lu Gan
- Department of Chemistry and Biochemistry and ‡Center for Bio-Inspired Solar Fuel
Production, Arizona State University, Tempe, Arizona 85287, United States
| | - Pilarisetty Tarakeshwar
- Department of Chemistry and Biochemistry and ‡Center for Bio-Inspired Solar Fuel
Production, Arizona State University, Tempe, Arizona 85287, United States
| | - Vladimiro Mujica
- Department of Chemistry and Biochemistry and ‡Center for Bio-Inspired Solar Fuel
Production, Arizona State University, Tempe, Arizona 85287, United States
| | - Anne K. Jones
- Department of Chemistry and Biochemistry and ‡Center for Bio-Inspired Solar Fuel
Production, Arizona State University, Tempe, Arizona 85287, United States
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6
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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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7
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Liu Y, Cui W, Liu Z, Cui Y, Xia Y, Kobayashi M, Zhou Z. Effect of flexibility and positive charge of the C-terminal domain on the activator P14K function for nitrile hydratase inPseudomonas putida. FEMS Microbiol Lett 2014; 352:38-44. [DOI: 10.1111/1574-6968.12376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 12/31/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yi Liu
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Youtian Cui
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry; The University of Tsukuba; Tsukuba Ibaraki Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
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8
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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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Liu Y, Cui W, Xia Y, Cui Y, Kobayashi M, Zhou Z. Self-subunit swapping occurs in another gene type of cobalt nitrile hydratase. PLoS One 2012; 7:e50829. [PMID: 23226397 PMCID: PMC3511329 DOI: 10.1371/journal.pone.0050829] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 10/25/2012] [Indexed: 11/30/2022] Open
Abstract
Self-subunit swapping is one of the post-translational maturation of the cobalt-containing nitrile hydratase (Co-NHase) family of enzymes. All of these NHases possess a gene organization of <β-subunit> <α-subunit> <activator protein>, which allows the activator protein to easily form a mediatory complex with the α-subunit of the NHase after translation. Here, we discovered that the incorporation of cobalt into another type of Co-NHase, with a gene organization of <α-subunit> <β-subunit> <activator protein>, was also dependent on self-subunit swapping. We successfully isolated a recombinant NHase activator protein (P14K) of Pseudomonas putida NRRL-18668 by adding a Strep-tag N-terminal to the P14K gene. P14K was found to form a complex [α(StrepP14K)2] with the α-subunit of the NHase. The incorporation of cobalt into the NHase of P. putida was confirmed to be dependent on the α-subunit substitution between the cobalt-containing α(StrepP14K)2 and the cobalt-free NHase. Cobalt was inserted into cobalt-free α(StrepP14K)2 but not into cobalt-free NHase, suggesting that P14K functions not only as a self-subunit swapping chaperone but also as a metallochaperone. In addition, NHase from P. putida was also expressed by a mutant gene that was designed with a <β-subunit> <α-subunit> <P14K> order. Our findings expand the general features of self-subunit swapping maturation.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Youtian Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
- * E-mail: (MK); (ZMZ)
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- * E-mail: (MK); (ZMZ)
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10
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González L, Escudero D, Serrano-Andrés L. Progress and Challenges in the Calculation of Electronic Excited States. Chemphyschem 2011; 13:28-51. [DOI: 10.1002/cphc.201100200] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 08/05/2011] [Indexed: 11/09/2022]
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11
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Zhou Z, Hashimoto Y, Cui T, Washizawa Y, Mino H, Kobayashi M. Unique Biogenesis of High-Molecular Mass Multimeric Metalloenzyme Nitrile Hydratase: Intermediates and a Proposed Mechanism for Self-Subunit Swapping Maturation. Biochemistry 2010; 49:9638-48. [DOI: 10.1021/bi100651v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhemin Zhou
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yoshiteru Hashimoto
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Tianwei Cui
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yumi Washizawa
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroyuki Mino
- Division of Material Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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12
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Shearer J, Callan PE, Amie J. Use of metallopeptide based mimics demonstrates that the metalloprotein nitrile hydratase requires two oxidized cysteinates for catalytic activity. Inorg Chem 2010; 49:9064-77. [PMID: 20831172 PMCID: PMC3570060 DOI: 10.1021/ic101765h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrile hydratases (NHases) are non-heme Fe(III) or non-corrin Co(III) containing metalloenzymes that possess an N(2)S(3) ligand environment with nitrogen donors derived from amidates and sulfur donors derived from cysteinates. A closely related enzyme is thiocyanate hydrolase (SCNase), which possesses a nearly identical active-site coordination environment as CoNHase. These enzymes are redox inactive and perform hydrolytic reactions; SCNase hydrolyzes thiocyanate anions while NHase converts nitriles into amides. Herein an active CoNHase metallopeptide mimic, [Co(III)NHase-m1] (NHase-m1 = AcNH-CCDLP-CGVYD-PA-COOH), that contains Co(III) in a similar N(2)S(3) coordination environment as CoNHase is reported. [Co(III)NHase-m1] was characterized by electrospray ionization-mass spectrometry (ESI-MS), gel-permeation chromatography (GPC), Co K-edge X-ray absorption spectroscopy (Co-S: 2.21 Å; Co-N: 1.93 Å), vibrational, and optical spectroscopies. We find that [Co(III)NHase-m1] will perform the catalytic conversion of acrylonitrile into acrylamide with up to 58 turnovers observed after 18 h at 25 °C (pH 8.0). FTIR data used in concert with calculated vibrational data (mPWPW91/aug-cc-TZVPP) demonstrates that the active form of [Co(III)NHase-m1] has a ligated SO(2) (ν = 1091 cm(-1)) moiety and a ligated protonated SO(H) (ν = 928 cm(-1)) moiety; when only one oxygenated cysteinate ligand (i.e., a mono-SO(2) coordination motif) or the bis-SO(2) coordination motif are found within [Co(III)NHase-m1] no catalytic activity is observed. Calculations of the thermodynamics of ligand exchange (B3LYP/aug-cc-TZVPP) suggest that the reason for this is that the SO(2)/SO(H) equatorial ligand motif promotes both water dissociation from the Co(III)-center and nitrile coordination to the Co(III)-center. In contrast, the under- or overoxidized motifs will either strongly favor a five coordinate Co(III)-center or strongly favor water binding to the Co(III)-center over nitrile binding.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA.
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13
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Zhou Z, Hashimoto Y, Kobayashi M. Self-subunit swapping chaperone needed for the maturation of multimeric metalloenzyme nitrile hydratase by a subunit exchange mechanism also carries out the oxidation of the metal ligand cysteine residues and insertion of cobalt. J Biol Chem 2009; 284:14930-8. [PMID: 19346246 DOI: 10.1074/jbc.m808464200] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The incorporation of cobalt into low molecular mass nitrile hydratase (L-NHase) of Rhodococcus rhodochrous J1 has been found to depend on the alpha-subunit exchange between cobalt-free L-NHase (apo-L-NHase lacking oxidized cysteine residues) and its cobalt-containing mediator (holo-NhlAE containing Cys-SO(2)(-) and Cys-SO(-) metal ligands), this novel mode of post-translational maturation having been named self-subunit swapping, and NhlE having been recognized as a self-subunit swapping chaperone (Zhou, Z., Hashimoto, Y., Shiraki, K., and Kobayashi, M. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 14849-14854). We discovered here that cobalt was inserted into both the cobalt-free NhlAE (apo-NhlAE) and the cobalt-free alpha-subunit (apo-alpha-subunit) in an NhlE-dependent manner in the presence of cobalt and dithiothreitol in vitro. Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy analysis revealed that the non-oxidized cysteine residues in apo-NhlAE were post-translationally oxidized after cobalt insertion. These findings suggested that NhlE has two activities, i.e. cobalt insertion and cysteine oxidation. NhlE not only functions as a self-subunit swapping chaperone but also a metallochaperone that includes a redox function. Cobalt insertion and cysteine oxidation occurred under both aerobic and anaerobic conditions when Co(3+) was used as a cobalt donor, suggesting that the oxygen atoms in the oxidized cysteines were derived from water molecules but not from dissolved oxygen. Additionally, we isolated apo-NhlAE after the self-subunit swapping event and found that it was recycled for cobalt transfer into L-NHase.
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Affiliation(s)
- Zhemin Zhou
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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O’Toole MG, Bennett B, Mashuta MS, Grapperhaus CA. Substrate binding preferences and pka determinations of a nitrile hydratase model complex: variable solvent coordination to [(bmmp-TASN)Fe]OTf. Inorg Chem 2009; 48:2300-8. [PMID: 19166306 PMCID: PMC2754792 DOI: 10.1021/ic802180d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The five-coordinate iron-dithiolate complex (N,N'-4,7-bis-(2'-methyl-2'-mercatopropyl)-1-thia-4,7-diazacyclononane)iron(III), [LFe]+, has been isolated as the triflate salt from reaction of the previously reported LFeCl with thallium triflate. Spectroscopic characterization confirms an S = 1/2 ground state in non-coordinating solvents with room temperature microeff = 1.78 microB and electron paramagnetic resonance (EPR) derived g-values of g1 = 2.04, g2 = 2.02 and g3 = 2.01. [LFe]+ binds a variety of coordinating solvents resulting in six-coordinate complexes [LFe-solvent]+. In acetonitrile the low-spin [LFe-NCMe]+ (g1 = 2.27, g2 = 2.18, and g3 = 1.98) is in equilibrium with [LFe]+ with a binding constant of Keq = 4.7 at room temperature. Binding of H2O, DMF, methanol, DMSO, and pyridine to [LFe]+ yields high-spin six-coordinate complexes with EPR spectra that display significant strain in the rhombic zero-field splitting term E/D. Addition of 1 equiv of triflic acid to the previously reported diiron species (LFe)2O results in the formation of [(LFe)2OH]OTf, which has been characterized by X-ray crystallography. The aqueous chemistry of [LFe]+ reveals three distinct species as a function of pH: [LFe-OH2]+, [(LFe)2OH]OTf, and (LFe)2O. The pKa values for [LFe-OH2]+ and [(LFe)2OH]OTf are 5.4 +/- 0.1 and 6.52 +/- 0.05, respectively.
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Affiliation(s)
- Martin G. O’Toole
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Brian Bennett
- National Biomedical EPR Center, Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226-0509
| | - Mark S. Mashuta
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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Lugo-Mas P, Taylor W, Schweitzer D, Theisen RM, Xu L, Shearer J, Swartz RD, Gleaves MC, Dipasquale A, Kaminsky W, Kovacs JA. Properties of square-pyramidal alkyl-thiolate Fe(III) complexes, including an analogue of the unmodified form of nitrile hydratase. Inorg Chem 2008; 47:11228-36. [PMID: 18989922 PMCID: PMC2659597 DOI: 10.1021/ic801704n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The syntheses and structures of three new coordinatively unsaturated, monomeric, square-pyramidal thiolate-ligated Fe(III) complexes are described, [Fe(III)((tame-N(3))S(2)(Me2))](+) (1), [Fe(III)(Et-N(2)S(2)(Me2))(py)](1-) (3), and [Fe(III)((tame-N(2)S)S(2)(Me2))](2-) (15). The anionic bis-carboxamide, tris-thiolate N(2)S(3) coordination sphere of 15 is potentially similar to that of the yet-to-be characterized unmodified form of NHase. Comparison of the magnetic and reactivity properties of these reveals how anionic charge build up (from cationic 1 to anionic 3 and dianionic 15) and spin-state influence apical ligand affinity. For all of the ligand-field combinations examined, an intermediate S = 3/2 spin state was shown to be favored by a strong N(2)S(2) basal plane ligand field, and this was found to reduce the affinity for apical ligands, even when they are built in. This is in contrast to the post-translationally modified NHase active site, which is low spin and displays a higher affinity for apical ligands. Cationic 1 and its reduced Fe(II) precursor are shown to bind NO and CO, respectively, to afford [Fe(III)((tame-N(3))S(2)(Me))(NO)](+) (18, nu(NuO) = 1865 cm(-1)), an analogue of NO-inactivated NHase, and [Fe(II)((tame-N(3))S(2)(Me))(CO)] (16; nu(CO) stretch (1895 cm(-1)). Anions (N(3)(-), CN(-)) are shown to be unreactive toward 1, 3, and 15 and neutral ligands unreactive toward 3 and 15, even when present in 100-fold excess and at low temperatures. The curtailed reactivity of 15, an analogue of the unmodified form of NHase, and its apical-oxygenated S = 3/2 derivative [Fe(III)((tame-N(2)SO(2))S(2)(Me2))](2-) (20) suggests that regioselective post-translational oxygenation of the basal plane NHase cysteinate sulfurs plays an important role in promoting substrate binding. This is supported by previously reported theoretical (DFT) calculations.
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Affiliation(s)
- Priscilla Lugo-Mas
- The Department of Chemistry, University of Washington, Box 351700 Seattle, Washington 98195-1700, USA
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16
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Peplowski L, Kubiak K, Nowak W. Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.10.072] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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18
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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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19
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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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20
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van Duijnen PT, Greene SN, Richards NGJ. Time-dependent density functional theory/discrete reaction field spectra of open shell systems: The visual spectrum of [FeIII(PyPepS)2]− in aqueous solution. J Chem Phys 2007; 127:045105. [PMID: 17672728 DOI: 10.1063/1.2751164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the calculated visible spectrum of [FeIII(PyPepS)2]- in aqueous solution. From all-classical molecular dynamics simulations on the solute and 200 water molecules with a polarizable force field, 25 solute/solvent configurations were chosen at random from a 50 ps production run and subjected the systems to calculations using time-dependent density functional theory (TD-DFT) for the solute, combined with a solvation model in which the water molecules carry charges and polarizabilities. In each calculation the first 60 excited states were collected in order to span the experimental spectrum. Since the solute has a doublet ground state several excitations to states are of type "three electrons in three orbitals," each of which gives rise to a manifold of a quartet and two doublet states which cannot properly be represented by single Slater determinants. We applied a tentative scheme to analyze this type of spin contamination in terms of Delta and Delta transitions between the same orbital pairs. Assuming the associated states as pure single determinants obtained from restricted calculations, we construct conformation state functions (CFSs), i.e., eigenfunctions of the Hamiltonian Sz and S2, for the two doublets and the quartet for each Delta,Delta pair, the necessary parameters coming from regular and spin-flip calculations. It appears that the lower final states remain where they were originally calculated, while the higher states move up by some tenths of an eV. In this case filtering out these higher states gives a spectrum that compares very well with experiment, but nevertheless we suggest investigating a possible (re)formulation of TD-DFT in terms of CFSs rather than determinants.
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Affiliation(s)
- Piet Th van Duijnen
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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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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Peplowski L, Kubiak K, Nowak W. Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides. J Mol Model 2007; 13:725-30. [PMID: 17333306 DOI: 10.1007/s00894-007-0181-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Accepted: 01/29/2007] [Indexed: 12/01/2022]
Abstract
Nitrile hydratase (NHase) is an enzyme containing non-corrin Co3+ in the non-standard active site. NHases from Pseudonocardia thermophila JCM 3095 catalyse hydration of nitriles to corresponding amides. The efficiency of the enzyme is 100 times higher for aliphatic nitriles then aromatic ones. In order to understand better this selectivity dockings of a series of aliphatic and aromatic nitriles and related amides into a model protein based on an X-ray structure were performed. Substantial differences in binding modes were observed, showing better conformational freedom of aliphatic compounds. Distinct interactions with postranslationally modified cysteines present in the active site of the enzyme were observed. Modeling shows that water molecule activated by a metal ion may easily directly attack the docked acrylonitrile to transform this molecule into acryloamide. Thus docking studies provide support for one of the reaction mechanisms discussed in the literature.
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Affiliation(s)
- Lukasz Peplowski
- Theoretical Molecular Biophysics Group, Institute of Physics, N. Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
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Neese F, Petrenko T, Ganyushin D, Olbrich G. Advanced aspects of ab initio theoretical optical spectroscopy of transition metal complexes: Multiplets, spin-orbit coupling and resonance Raman intensities. Coord Chem Rev 2007. [DOI: 10.1016/j.ccr.2006.05.019] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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