1
|
Miller C, Huntoon D, Kaley N, Ogutu I, Fiedler AT, Bennett B, Liu D, Holz R. Role of second-sphere arginine residues in metal binding and metallocentre assembly in nitrile hydratases. J Inorg Biochem 2024; 256:112565. [PMID: 38677005 DOI: 10.1016/j.jinorgbio.2024.112565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024]
Abstract
Two conserved second-sphere βArg (R) residues in nitrile hydratases (NHase), that form hydrogen bonds with the catalytically essential sulfenic and sulfinic acid ligands, were mutated to Lys and Ala residues in the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) and the Fe-type NHase from Rhodococcus equi TG328-2 (ReNHase). Only five of the eight mutants (PtNHase βR52A, βR52K, βR157A, βR157K and ReNHase βR61A) were successfully expressed and purified. Apart from the PtNHase βR52A mutant that exhibited no detectable activity, the kcat values obtained for the PtNHase and ReNHase βR mutant enzymes were between 1.8 and 12.4 s-1 amounting to <1% of the kcat values observed for WT enzymes. The metal content of each mutant was also significantly decreased with occupancies ranging from ∼10 to ∼40%. UV-Vis spectra coupled with EPR data obtained on the ReNHase mutant enzyme, suggest a decrease in the Lewis acidity of the active site metal ion. X-ray crystal structures of the four PtNHase βR mutant enzymes confirmed the mutation and the low active site metal content, while also providing insight into the active site hydrogen bonding network. Finally, DFT calculations suggest that the equatorial sulfenic acid ligand, which has been shown to be the catalytic nucleophile, is protonated in the mutant enzyme. Taken together, these data confirm the necessity of the conserved second-sphere βR residues in the proposed subunit swapping process and post-translational modification of the α-subunit in the α activator complex, along with stabilizing the catalytic sulfenic acid in its anionic form.
Collapse
Affiliation(s)
- Callie Miller
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Delanie Huntoon
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Nicholas Kaley
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Irene Ogutu
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, WI 53233, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Richard Holz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
| |
Collapse
|
2
|
Jeong D, Kim K, Lee Y, Cho J. Synthetic Advances for Mechanistic Insights: Metal-Oxygen Intermediates with a Macrocyclic Pyridinophane System. Acc Chem Res 2024; 57:120-130. [PMID: 38110355 DOI: 10.1021/acs.accounts.3c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
ConspectusMetalloenzymes, which are proteins containing earth-abundant transition-metal ions as cofactors in the active site, generate various metal-oxygen intermediates via activating a dioxygen molecule (O2) to mediate vital metabolic functions, such as the oxidative metabolism of xenobiotics and the biotransformation of naturally occurring molecules. By replicating the active sites of metalloenzymes, many bioinorganic chemists have studied the geometric and electronic properties and reactivities of model complexes to understand the nature of enzymatic intermediates and develop bioinspired metal catalysts. Among the reported model complexes, nonporphyrinic macrocyclic ligands are the predominant coordination system widely used in stabilizing and isolating diverse metal-oxygen intermediates, which allows us to extensively investigate the physicochemical characteristics of the analogs of reactive intermediates of metalloenzymes. In particular, it has been reported that the ring size of the macrocyclic ligands, defined by the number of atoms in the macrocyclic ring, drastically affects the identity of the metal-oxygen intermediate. Thus, systematic modification of the macrocyclic ligands has been a great subject being examined in various inorganic fields.In this Account, we describe synthetic advances of a macrocyclic ligand system by introducing pyridine donors into a 12-membered tetraazamacrocyclic ligand (12-TMC) that initially has 4 amine donors. Interestingly, the backbone of the pyridinophane ligand with 2 pyridine and 2 amine donors in a 12-membered ring is shown to be much more folded than in other macrocyclic ligands, thereby allowing the axial and equatorial donors to separately control the electronic structure of metal complexes. Then, we looked over independent electronic and steric effects on metal-oxygen species with thorough physicochemical analysis. The NiIII-peroxo complexes exhibit nucleophilic reactivity dependent on the steric hindrance of the second coordination sphere. Furthermore, the C-H bond strength of the second coordination sphere has also been an important factor in determining the stability of MnIV-bis(hydroxo) intermediates. Electronic tuning on CoIII-hydroperoxo intermediates results in a trend between the electron-donating abilities of para-substituents on pyridine in the pyridinophane ligand and electrophilic reactivities, from which mechanistic insights into the metal-hydroperoxo species have been gained. Importantly, the metal-oxygen intermediates supported by the pyridinophane ligand system have revealed quite challenging chemical reactions, including dioxygenase-like nitrile activation by CoIII-peroxo intermediates and the oxidation of aldehyde and aromatic compounds by manganese-oxygen intermediates. Based on the fine substitution of donors, we have addressed that those novel reactions originated from the unique framework of the pyridinophane system incorporating spin-crossover behavior and high redox potentials of the metal-oxygen intermediates. These results will be valuable for the structure-activity relationship of metal-oxygen intermediates, giving a better understanding on the enzymatic coordination system where amino acid ligands vary for specific chemical reactions.
Collapse
Affiliation(s)
- Donghyun Jeong
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyungmin Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yujeong Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaeheung Cho
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| |
Collapse
|
3
|
Modification of nitrile hydratase from Rhodococcus erythropolis CCM2595 by semirational design to enhance its substrate affinity. Biointerphases 2022; 17:061007. [PMID: 36456206 DOI: 10.1116/6.0002061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is an excellent biocatalyst that catalyzes the hydration of nitrile substances to their corresponding amides. Given its catalytic specificity and eco-friendliness, NHase has extensive applications in the chemical, pharmaceutical, and cosmetic industries. To improve the affinity between Rhodococcus erythropolis CCM2595-derived NHase (ReNHase) and adiponitrile, this study used a semirational design to improve the efficiency of ReNHase in catalyzing the generation of 5-cyanopentanamide from adiponitrile. Enzyme kinetics analysis showed that Km of the mutant ReNHaseB:G196Y was 3.265 mmol l-1, which was lower than that of the wild-type NHase. The affinity of the mutant ReNHaseB:G196Y to adiponitrile was increased by 36.35%, and the efficiency of the mutant ReNHaseB:G196Y in catalyzing adiponitrile to 5-cyanopentamide was increased by 10.11%. The analysis of the enzyme-substrate interaction showed that the hydrogen bond length of the mutant ReNHaseB:G196Y to adiponitrile was shortened by 0.59 Å, which enhanced the interaction between the mutant and adiponitrile and, thereby, increased the substrate affinity. Similarly, the structural analysis showed that the amino acid flexibility near the mutation site of ReNHaseB:G196Y was increased, which enhanced the binding force between the enzyme and adiponitrile. Our work may provide a new theoretical basis for the modification of substrate affinity of NHase and increase the possibility of industrial applications of the enzyme.
Collapse
|
4
|
Pathiranage WLK, Gumataotao N, Fiedler AT, Holz RC, Bennett B. Identification of an Intermediate Species along the Nitrile Hydratase Reaction Pathway by EPR Spectroscopy. Biochemistry 2021; 60:3771-3782. [PMID: 34843221 PMCID: PMC8721871 DOI: 10.1021/acs.biochem.1c00574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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/H2O 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. FeIII-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 g-values (g1 = 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.
Collapse
Affiliation(s)
| | - Natalie Gumataotao
- Department of Chemistry and Biochemistry, Loyola University, Chicago, Illinois 60660, United States
| | - Adam T. Fiedler
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Richard C. Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233, United States
| |
Collapse
|
5
|
Meyer F, Frey R, Ligibel M, Sager E, Schroer K, Snajdrova R, Buller R. Modulating Chemoselectivity in a Fe(II)/α-Ketoglutarate-Dependent Dioxygenase for the Oxidative Modification of a Nonproteinogenic Amino Acid. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00678] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fabian Meyer
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Raphael Frey
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Mathieu Ligibel
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Emine Sager
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Kirsten Schroer
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - Rebecca Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| |
Collapse
|
6
|
Effect and mechanism analysis of different linkers on efficient catalysis of subunit-fused nitrile hydratase. Int J Biol Macromol 2021; 181:444-451. [PMID: 33753198 DOI: 10.1016/j.ijbiomac.2021.03.103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/21/2022]
Abstract
Protein fusion using a linker plays an important role for protein evolution. However, designing suitable linkers for protein evolution is yet challenging and under-explored. To further clarify the regular pattern of suitable type of linker for fusion proteins, one nitrile hydratase (NHase) was used as a target protein and subunit fusion strategy was carried out to improve its efficient catalysis. Subunit-fused variants with three different types of linkers were constructed and characterized. All variants exhibited higher stability than that of the wild type. The longer the linker was, the higher stability NHase showed, however, too long linker affected NHase activity and expression. Among the three types of linkers, the α-helical linker seemed more suitable for NHase than flexible or rigid linkers. Though it is not clear how the linkers affecting the activity, structure analysis indicated that the stability improvement is dependent on the additional salt bridge, H-bond, and the subunit interface area increasing due to the linker insertion, among which the additional salt bridge and interface area were more important factors. The results described here may be useful for redesigning other enzymes through subunit fusion.
Collapse
|
7
|
Du W, Huang J, Cui B, Guo Y, Wang L, Liang C. Efficient biodegradation of nitriles by a novel nitrile hydratase derived from Rhodococcus erythropolis CCM2595. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1941253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Wenjing Du
- Lab of Advanced Materials and Catalytic Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning, PR China
| | - Jiao Huang
- Lab of Biocalyalysis and Transformation, School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, Liaoning, PR China
| | - Baocheng Cui
- Lab of Biocalyalysis and Transformation, School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, Liaoning, PR China
| | - Yi Guo
- Lab of Biocalyalysis and Transformation, School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, Liaoning, PR China
| | - Li Wang
- Lab of Biocalyalysis and Transformation, School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, Liaoning, PR China
| | - Changhai Liang
- Lab of Advanced Materials and Catalytic Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning, PR China
| |
Collapse
|
8
|
Cheng Z, Xia Y, Zhou Z. Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications. Front Bioeng Biotechnol 2020; 8:352. [PMID: 32391348 PMCID: PMC7193024 DOI: 10.3389/fbioe.2020.00352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.
Collapse
Affiliation(s)
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
9
|
Knossow N, Siebner H, Bernstein A. Isotope Fractionation (δ 13C, δ 15N) in the Microbial Degradation of Bromoxynil by Aerobic and Anaerobic Soil Enrichment Cultures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1546-1554. [PMID: 31986047 DOI: 10.1021/acs.jafc.9b07653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bromoxynil is an increasingly applied nitrile herbicide. Under aerobic conditions, hydration, nitrilation, or hydroxylation of the nitrile group commonly occurs, whereas under anaerobic conditions reductive dehalogenation is common. This work studied the isotope effects associated with these processes by soil cultures. The aerobic soil enrichment culture presented a significant increase in Stenotrophomonas, Pseudomonas, Chryseobacterium, Achromobacter, Azospirillum, and Arcticibacter, and degradation products indicated that nitrile hydratase was the dominant degradation route. The anaerobic culture was dominated by Proteobacteria and Firmicutes phyla with a significant increase in Dethiosulfatibacter, and degradation products indicated reductive debromination as a major degradation route. Distinct dual-isotope trends (δ13C, δ15N) were determined for the two routes: a strong inverse nitrogen isotope effect (εN = 10.56 ± 0.36‰) and an insignificant carbon isotope effect (εC = 0.37 ± 0.36‰) for the aerobic process versus a negligible effect for both elements in the anaerobic process. These trends differ from formerly reported trends for the photodegradation of bromoxynil and enable one to distinguish between the processes in the field.
Collapse
Affiliation(s)
- Nadav Knossow
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology , Ben-Gurion University of the Negev , Sede Boqer Campus , Sede Boqer 8499000 , Israel
| | - Hagar Siebner
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology , Ben-Gurion University of the Negev , Sede Boqer Campus , Sede Boqer 8499000 , Israel
| | - Anat Bernstein
- Zuckerberg Institute for Water Research, Department of Environmental Hydrology and Microbiology , Ben-Gurion University of the Negev , Sede Boqer Campus , Sede Boqer 8499000 , Israel
| |
Collapse
|
10
|
Yang X, Bennett B, Holz RC. Insights into the catalytic mechanism of a bacterial hydrolytic dehalogenase that degrades the fungicide chlorothalonil. J Biol Chem 2019; 294:13411-13420. [PMID: 31331935 DOI: 10.1074/jbc.ra119.009094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Indexed: 11/06/2022] Open
Abstract
Chlorothalonil (2,4,5,6-tetrachloroisophtalonitrile; TPN) is one of the most commonly used fungicides in the United States. Given TPN's widespread use, general toxicity, and potential carcinogenicity, its biodegradation has garnered significant attention. Here, we developed a direct spectrophotometric assay for the Zn(II)-dependent, chlorothalonil-hydrolyzing dehalogenase from Pseudomonas sp. CTN-3 (Chd), enabling determination of its metal-binding properties; pH dependence of the kinetic parameters k cat, Km , and k cat/Km ; and solvent isotope effects. We found that a single Zn(II) ion binds a Chd monomer with a Kd of 0.17 μm, consistent with inductively coupled plasma MS data for the as-isolated Chd dimer. We observed that Chd was maximally active toward chlorothalonil in the pH range 7.0-9.0, and fits of these data yielded a pK ES1 of 5.4 ± 0.2, a pK ES2 of 9.9 ± 0.1 (k'cat = 24 ± 2 s-1), a pK E1 of 5.4 ± 0.3, and a pK E2 of 9.5 ± 0.1 (k'cat/k' m = 220 ± 10 s-1 mm-1). Proton inventory studies indicated that one proton is transferred in the rate-limiting step of the reaction at pD 7.0. Fits of UV-visible stopped-flow data suggested a three-step model and provided apparent rate constants for intermediate formation (i.e. a k'2 of 35.2 ± 0.1 s-1) and product release (i.e. a k'3 of 1.1 ± 0.2 s-1), indicating that product release is the slow step in catalysis. On the basis of these results, along with those previously reported, we propose a mechanism for Chd catalysis.
Collapse
Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233
| | - Richard C Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881; Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401.
| |
Collapse
|
11
|
Parrot A, Collin S, Bruylants G, Reinaud O. The 3 rd degree of biomimetism: associating the cavity effect, Zn II coordination and internal base assistance for guest binding and activation. Chem Sci 2018; 9:5479-5487. [PMID: 30079177 PMCID: PMC6048688 DOI: 10.1039/c8sc01129j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022] Open
Abstract
The synthesis and characterization of a resorcinarene-based tetra(imidazole) ligand is reported. The properties of the corresponding ZnII complex are studied in depth, notably by NMR spectroscopy. In MeCN, acid-base titration reveals that one out of the four imidazole arms is hemi-labile and can be selectively protonated, thereby opening a coordination site in the exo position. Quite remarkably, the 4th imidazole arm promotes binding of an acidic molecule (a carboxylic acid, a β-diketone or acetamide), by acting as an internal base, which allows guest binding as an anion to the metal center in the endo position. Most importantly, the presence of this labile imidazole arm makes the ZnII complex active for the catalyzed hydration of acetonitrile. It is proposed that it acts as a general base for activating a water molecule in the vicinity of the metal center during its nucleophilic attack to the endo-bound MeCN substrate. This system presents a unique degree of biomimetism when considering zinc enzymes: a pocket for guest binding, a similar first coordination sphere, a coordination site available for water activation in the cis position relative to the substrate and finally an internal imidazole residue that plays the role of a general base.
Collapse
Affiliation(s)
- A Parrot
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , CNRS UMR8601 , Université Paris Descartes , Sorbonne Paris Cité , 45 rue des Saints Pères , 75006 Paris , France .
| | - S Collin
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , CNRS UMR8601 , Université Paris Descartes , Sorbonne Paris Cité , 45 rue des Saints Pères , 75006 Paris , France .
| | - G Bruylants
- Engineering of Molecular NanoSystems , Ecole Polytechnique de Bruxelles , Université Libre de Bruxelles (ULB) , Avenue F. D. Roosevelt 50, CP165/64 , B-1050 Brussels , Belgium
| | - O Reinaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , CNRS UMR8601 , Université Paris Descartes , Sorbonne Paris Cité , 45 rue des Saints Pères , 75006 Paris , France .
| |
Collapse
|
12
|
Iron-Dependent Enzyme Catalyzes the Initial Step in Biodegradation of N-Nitroglycine by Variovorax sp. Strain JS1663. Appl Environ Microbiol 2017; 83:AEM.00457-17. [PMID: 28526789 DOI: 10.1128/aem.00457-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/06/2017] [Indexed: 01/29/2023] Open
Abstract
Nitramines are key constituents of most of the explosives currently in use and consequently contaminate soil and groundwater at many military facilities around the world. Toxicity from nitramine contamination poses a health risk to plants and animals. Thus, understanding how nitramines are biodegraded is critical to environmental remediation. The biodegradation of synthetic nitramine compounds such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has been studied for decades, but little is known about the catabolism of naturally produced nitramine compounds. In this study, we report the isolation of a soil bacterium, Variovorax sp. strain JS1663, that degrades N-nitroglycine (NNG), a naturally produced nitramine, and the key enzyme involved in its catabolism. Variovorax sp. JS1663 is a Gram-negative, non-spore-forming motile bacterium isolated from activated sludge based on its ability to use NNG as a sole growth substrate under aerobic conditions. A single gene (nnlA) encodes an iron-dependent enzyme that releases nitrite from NNG through a proposed β-elimination reaction. Bioinformatics analysis of the amino acid sequence of NNG lyase identified a PAS (Per-Arnt-Sim) domain. PAS domains can be associated with heme cofactors and function as signal sensors in signaling proteins. This is the first instance of a PAS domain present in a denitration enzyme. The NNG biodegradation pathway should provide the basis for the identification of other enzymes that cleave the N-N bond and facilitate the development of enzymes to cleave similar bonds in RDX, nitroguanidine, and other nitramine explosives.IMPORTANCE The production of antibiotics and other allelopathic chemicals is a major aspect of chemical ecology. The biodegradation of such chemicals can play an important ecological role in mitigating or eliminating the effects of such compounds. N-Nitroglycine (NNG) is produced by the Gram-positive filamentous soil bacterium Streptomyces noursei This study reports the isolation of a Gram-negative soil bacterium, Variovorax sp. strain JS1663, that is able to use NNG as a sole growth substrate. The proposed degradation pathway occurs via a β-elimination reaction that releases nitrite from NNG. The novel NNG lyase requires iron(II) for activity. The identification of a novel enzyme and catabolic pathway provides evidence of a substantial and underappreciated flux of the antibiotic in natural ecosystems. Understanding the NNG biodegradation pathway will help identify other enzymes that cleave the N-N bond and facilitate the development of enzymes to cleave similar bonds in synthetic nitramine explosives.
Collapse
|
13
|
Jiang S, Zhang L, Yao Z, Gao B, Wang H, Mao X, Wei D. Switching a nitrilase from Syechocystis sp. PCC6803 to a nitrile hydratase by rationally regulating reaction pathways. Catal Sci Technol 2017. [DOI: 10.1039/c7cy00060j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Based on this mechanism, a nitrilase was engineered to shift the reaction pathway from formation of acid to formation of amide.
Collapse
Affiliation(s)
- Shuiqin Jiang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Lujia Zhang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Zhiqiang Yao
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Xiangzhao Mao
- Ocean Univ China
- Coll Food Sci & Engn
- Qingdao 266003
- China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| |
Collapse
|
14
|
Villar-Acevedo G, Lugo-Mas P, Blakely MN, Rees JA, Ganas AS, Hanada EM, Kaminsky W, Kovacs JA. Metal-Assisted Oxo Atom Addition to an Fe(III) Thiolate. J Am Chem Soc 2016; 139:119-129. [PMID: 28033001 DOI: 10.1021/jacs.6b03512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cysteinate oxygenation is intimately tied to the function of both cysteine dioxygenases (CDOs) and nitrile hydratases (NHases), and yet the mechanisms by which sulfurs are oxidized by these enzymes are unknown, in part because intermediates have yet to be observed. Herein, we report a five-coordinate bis-thiolate ligated Fe(III) complex, [FeIII(S2Me2N3(Pr,Pr))]+ (2), that reacts with oxo atom donors (PhIO, IBX-ester, and H2O2) to afford a rare example of a singly oxygenated sulfenate, [FeIII(η2-SMe2O)(SMe2)N3(Pr,Pr)]+ (5), resembling both a proposed intermediate in the CDO catalytic cycle and the essential NHase Fe-S(O)Cys114 proposed to be intimately involved in nitrile hydrolysis. Comparison of the reactivity of 2 with that of a more electron-rich, crystallographically characterized derivative, [FeIIIS2Me2NMeN2amide(Pr,Pr)]- (8), shows that oxo atom donor reactivity correlates with the metal ion's ability to bind exogenous ligands. Density functional theory calculations suggest that the mechanism of S-oxygenation does not proceed via direct attack at the thiolate sulfurs; the average spin-density on the thiolate sulfurs is approximately the same for 2 and 8, and Mulliken charges on the sulfurs of 8 are roughly twice those of 2, implying that 8 should be more susceptible to sulfur oxidation. Carboxamide-ligated 8 is shown to be unreactive towards oxo atom donors, in contrast to imine-ligated 2. Azide (N3-) is shown to inhibit sulfur oxidation with 2, and a green intermediate is observed, which then slowly converts to sulfenate-ligated 5. This suggests that the mechanism of sulfur oxidation involves initial coordination of the oxo atom donor to the metal ion. Whether the green intermediate is an oxo atom donor adduct, Fe-O═I-Ph, or an Fe(V)═O remains to be determined.
Collapse
Affiliation(s)
- Gloria Villar-Acevedo
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Priscilla Lugo-Mas
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Maike N Blakely
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julian A Rees
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Abbie S Ganas
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Erin M Hanada
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Werner Kaminsky
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| |
Collapse
|
15
|
CO synthesized from the central one-carbon pool as source for the iron carbonyl in O2-tolerant [NiFe]-hydrogenase. Proc Natl Acad Sci U S A 2016; 113:14722-14726. [PMID: 27930319 DOI: 10.1073/pnas.1614656113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrogenases are nature's key catalysts involved in both microbial consumption and production of molecular hydrogen. H2 exhibits a strongly bonded, almost inert electron pair and requires transition metals for activation. Consequently, all hydrogenases are metalloenzymes that contain at least one iron atom in the catalytic center. For appropriate interaction with H2, the iron moiety demands for a sophisticated coordination environment that cannot be provided just by standard amino acids. This dilemma has been overcome by the introduction of unprecedented chemistry-that is, by ligating the iron with carbon monoxide (CO) and cyanide (or equivalent) groups. These ligands are both unprecedented in microbial metabolism and, in their free form, highly toxic to living organisms. Therefore, the formation of the diatomic ligands relies on dedicated biosynthesis pathways. So far, biosynthesis of the CO ligand in [NiFe]-hydrogenases was unknown. Here we show that the aerobic H2 oxidizer Ralstonia eutropha, which produces active [NiFe]-hydrogenases in the presence of O2, employs the auxiliary protein HypX (hydrogenase pleiotropic maturation X) for CO ligand formation. Using genetic engineering and isotope labeling experiments in combination with infrared spectroscopic investigations, we demonstrate that the α-carbon of glycine ends up in the CO ligand of [NiFe]-hydrogenase. The α-carbon of glycine is a building block of the central one-carbon metabolism intermediate, N10-formyl-tetrahydrofolate (N10-CHO-THF). Evidence is presented that the multidomain protein, HypX, converts the formyl group of N10-CHO-THF into water and CO, thereby providing the carbonyl ligand for hydrogenase. This study contributes insights into microbial biosynthesis of metal carbonyls involving toxic intermediates.
Collapse
|
16
|
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
| |
Collapse
|
17
|
Sun W, Zhu L, Chen X, Chen P, Yang L, Ding W, Zhou Z, Liu Y. Successful expression of the Bordetella petrii nitrile hydratase activator P14K and the unnecessary role of Ser115. BMC Biotechnol 2016; 16:21. [PMID: 26897378 PMCID: PMC4761151 DOI: 10.1186/s12896-016-0252-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 02/15/2016] [Indexed: 11/28/2022] Open
Abstract
Background The activator P14K is necessary for the activation of nitrile hydratase (NHase). However, it is hard to be expressed heterogeneously. Although an N-terminal strep tagged P14K could be successfully expressed from Pseudomonas putida, various strategies for the over-expression of P14K are needed to facilitate further application of NHase. Results P14K was successfully expressed through fusing a his tag (his-P14K), and was over-expressed through fusing a gst tag (gst-P14K) at its N-terminus in the NHase of Bordetella petrii DSM 12804. The stability of gst-P14K was demonstrated to be higher than that of the his-P14K. In addition, the Ser115 in the characteristic motif CXLC-Ser115-C of the active center of NHase was found to be unnecessary for NHase maturation. Conclusions Our results are not only useful for the NHase activator expression and the understanding of the role of Ser115 during NHase activation, but also helpful for other proteins with difficulty in heterologous expression.
Collapse
Affiliation(s)
- Weifeng Sun
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Longbao Zhu
- School of Biochemical Engineering, Anhui Polytechnic University, Anhui, 241000, China.
| | - Xianggui Chen
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Ping Chen
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Lingling Yang
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Wenwu Ding
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Yi Liu
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| |
Collapse
|
18
|
Nelp MT, Song Y, Wysocki VH, Bandarian V. A Protein-derived Oxygen Is the Source of the Amide Oxygen of Nitrile Hydratases. J Biol Chem 2016; 291:7822-9. [PMID: 26865634 DOI: 10.1074/jbc.m115.704791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 11/06/2022] Open
Abstract
Nitrile hydratase metalloenzymes are unique and important biocatalysts that are used industrially to produce high value amides from their corresponding nitriles. After more than three decades since their discovery, the mechanism of this class of enzymes is becoming clear with evidence from multiple recent studies that the cysteine-derived sulfenato ligand of the active site metal serves as the nucleophile that initially attacks the nitrile. Herein we describe the first direct evidence from solution phase catalysis that the source of the product carboxamido oxygen is the protein. Using(18)O-labeled water under single turnover conditions and native high resolution protein mass spectrometry, we show that the incorporation of labeled oxygen into both product and protein is turnover-dependent and that only a single oxygen is exchanged into the protein even under multiple turnover conditions, lending significant support to proposals that the post-translationally modified sulfenato group serves as the nucleophile to initiate hydration of nitriles.
Collapse
Affiliation(s)
- Micah T Nelp
- From the Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112 and
| | - Yang Song
- the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Vicki H Wysocki
- the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Vahe Bandarian
- From the Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112 and
| |
Collapse
|
19
|
Gong JS, Shi JS, Lu ZM, Li H, Zhou ZM, Xu ZH. Nitrile-converting enzymes as a tool to improve biocatalysis in organic synthesis: recent insights and promises. Crit Rev Biotechnol 2015; 37:69-81. [DOI: 10.3109/07388551.2015.1120704] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
20
|
Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M. Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
21
|
Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M. Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile. Angew Chem Int Ed Engl 2015; 54:10763-7. [DOI: 10.1002/anie.201502731] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/26/2015] [Indexed: 11/07/2022]
|
22
|
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]
|
23
|
Kumar D, Nguyen TN, Grapperhaus CA. Kinetic Effects of Sulfur Oxidation on Catalytic Nitrile Hydration: Nitrile Hydratase Insights from Bioinspired Ruthenium(II) Complexes. Inorg Chem 2014; 53:12372-7. [DOI: 10.1021/ic501695n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Davinder Kumar
- Department of Chemistry, University of Louisville, 2320 South
Brook Street, Louisville, Kentucky 40292, United States
| | - Tho N. Nguyen
- Department of Chemistry, University of Louisville, 2320 South
Brook Street, Louisville, Kentucky 40292, United States
| | - Craig A. Grapperhaus
- Department of Chemistry, University of Louisville, 2320 South
Brook Street, Louisville, Kentucky 40292, United States
| |
Collapse
|
24
|
Domingos SR, Sanders HJ, Hartl F, Buma WJ, Woutersen S. Switchable Amplification of Vibrational Circular Dichroism as a Probe of Local Chiral Structure. Angew Chem Int Ed Engl 2014; 53:14042-5. [DOI: 10.1002/anie.201407376] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 01/13/2023]
|
25
|
Domingos SR, Sanders HJ, Hartl F, Buma WJ, Woutersen S. Switchable Amplification of Vibrational Circular Dichroism as a Probe of Local Chiral Structure. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407376] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
26
|
Chen S, Gao H, Chen J, Wu J. Surface modification of polyacrylonitrile fibre by nitrile hydratase from Corynebacterium nitrilophilus. Appl Biochem Biotechnol 2014; 174:2058-66. [PMID: 25163886 DOI: 10.1007/s12010-014-1186-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 08/15/2014] [Indexed: 11/24/2022]
Abstract
Previously, nitrile hydratase (NHase) from Corynebacterium nitrilophilus was obtained and showed potential in polyacrylonitrile (PAN) fibre modification. In the present study, the modification conditions of C. nitrilophilus NHase on PAN were investigated. In the optimal conditions, the wettability and dyeability (anionic and reactive dyes) of PAN treated by C. nitrilophilus NHase reached a similar level of those treated by alkali. In addition, the chemical composition and microscopically observable were changed in the PAN surface after NHase treatment. Meanwhile, it revealed that cutinase combined with NHase facilitates the PAN hydrolysis slightly because of the ester existed in PAN as co-monomer was hydrolyzed. All these results demonstrated that C. nitrilophilus NHase can modify PAN efficiently without textile structure damage, and this study provides a foundation for the further application of C. nitrilophilus NHase in PAN modification industry.
Collapse
Affiliation(s)
- Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave., Wuxi, Jiangsu, 214122, China
| | | | | | | |
Collapse
|
27
|
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
| |
Collapse
|
28
|
Pawar SV, Yadav GD. PVA/chitosan–glutaraldehyde cross-linked nitrile hydratase as reusable biocatalyst for conversion of nitriles to amides. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
29
|
Martinez S, Kuhn ML, Russell JT, Holz RC, Elgren TE. Acrylamide production using encapsulated nitrile hydratase from Pseudonocardia thermophila in a sol–gel matrix. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.11.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Martinez S, Wu R, Sanishvili R, Liu D, Holz R. The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile. J Am Chem Soc 2014; 136:1186-9. [PMID: 24383915 PMCID: PMC3968781 DOI: 10.1021/ja410462j] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Indexed: 01/10/2023]
Abstract
Nitrile hydratase (NHase) catalyzes the hydration of nitriles to their corresponding commercially valuable amides at ambient temperatures and physiological pH. Several reaction mechanisms have been proposed for NHase enzymes; however, the source of the nucleophile remains a mystery. Boronic acids have been shown to be potent inhibitors of numerous hydrolytic enzymes due to the open shell of boron, which allows it to expand from a trigonal planar (sp(2)) form to a tetrahedral form (sp(3)). Therefore, we examined the inhibition of the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) by boronic acids via kinetics and X-ray crystallography. Both 1-butaneboronic acid (BuBA) and phenylboronic acid (PBA) function as potent competitive inhibitors of PtNHase. X-ray crystal structures for BuBA and PBA complexed to PtNHase were solved and refined at 1.5, 1.6, and 1.2 Å resolution. The resulting PtNHase-boronic acid complexes represent a "snapshot" of reaction intermediates and implicate the cysteine-sulfenic acid ligand as the catalytic nucleophile, a heretofore unknown role for the αCys(113)-OH sulfenic acid ligand. Based on these data, a new mechanism of action for the hydration of nitriles by NHase is presented.
Collapse
Affiliation(s)
- Salette Martinez
- Department
of Chemistry, Marquette
University, Milwaukee, Wisconsin 53201, United States
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rui Wu
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Ruslan Sanishvili
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Dali Liu
- Department of Chemistry and
Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Richard Holz
- Department
of Chemistry, Marquette
University, Milwaukee, Wisconsin 53201, United States
| |
Collapse
|
31
|
Yamanaka Y, Arakawa T, Watanabe T, Namima S, Sato M, Hori S, Ohtaki A, Noguchi K, Katayama Y, Yohda M, Odaka M. Two arginine residues in the substrate pocket predominantly control the substrate selectivity of thiocyanate hydrolase. J Biosci Bioeng 2013; 116:22-7. [DOI: 10.1016/j.jbiosc.2013.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/20/2013] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
|
32
|
Gumataotao N, Kuhn ML, Hajnas N, Holz RC. Identification of an active site-bound nitrile hydratase intermediate through single turnover stopped-flow spectroscopy. J Biol Chem 2013; 288:15532-6. [PMID: 23589282 DOI: 10.1074/jbc.m112.398909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stopped-flow kinetic data were obtained for the iron-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase) using methacrylonitrile as the substrate. Multiple turnover experiments suggest a three-step kinetic model that allows for the reversible binding of substrate, the presence of an intermediate, and the formation of product. Microscopic rate constants determined from these data are in good agreement with steady state data confirming that the stopped-flow method used was appropriate for the reaction. Single turnover stopped-flow experiments were used to identify catalytic intermediates. These data were globally fit confirming a three-step kinetic model. Independent absorption spectra acquired between 0.005 and 0.5 s of the reaction reveal a significant increase in absorbance at 375, 460, and 550 nm along with the hypsochromic shift of an Fe(3+)←S ligand-to-metal charge transfer band from 700 to 650 nm. The observed UV-visible absorption bands for the Fe(3+)-nitrile intermediate species are similar to low spin Fe(3+)-enzyme and model complexes bound by NO or N3((-)). These data provide spectroscopic evidence for the direct coordination of the nitrile substrate to the nitrile hydratase active site low spin Fe(3+) center.
Collapse
Affiliation(s)
- Natalie Gumataotao
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, USA
| | | | | | | |
Collapse
|
33
|
Liao RZ, Thiel W. Determinants of Regioselectivity and Chemoselectivity in Fosfomycin Resistance Protein FosA from QM/MM Calculations. J Phys Chem B 2013; 117:1326-36. [DOI: 10.1021/jp4002719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| |
Collapse
|
34
|
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]
|
35
|
Abstract
Cobalt is an essential trace element in both prokaryotes and eukaryotes. Nevertheless, it occurs less frequently in metalloproteins than other transition metals. This low occurrence appears to be due to the metal's low abundance in nature as well as its competition with iron, whose biologically critical functions include respiration and photosynthesis. In this review, we discuss the biological role of cobalt, the major effects of cobalt on iron utilization, as well as several mechanisms that cells have developed to circumvent the toxicity of cobalt while still exploiting its chemistry.
Collapse
Affiliation(s)
- Sachi Okamoto
- University of British Columbia - Microbiology and Immunology, Vancouver, British Columbia, Canada
| | | |
Collapse
|
36
|
Galstyan A, Sanz Miguel PJ, Lippert B. A “directed” approach toward a cationic molecular square containing four isonicotinamidate ligands and (4+2) (en)PtII metal entities. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.02.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
37
|
Swartz RD, Coggins MK, Kaminsky W, Kovacs JA. Nitrile hydration by thiolate- and alkoxide-ligated Co-NHase analogues. Isolation of Co(III)-amidate and Co(III)-iminol intermediates. J Am Chem Soc 2011; 133:3954-63. [PMID: 21351789 DOI: 10.1021/ja108749f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrile hydratases (NHases) are thiolate-ligated Fe(III)- or Co(III)-containing enzymes, which convert nitriles to the corresponding amide under mild conditions. Proposed NHase mechanisms involve M(III)-NCR, M(III)-OH, M(III)-iminol, and M(III)-amide intermediates. There have been no reported crystallographically characterized examples of these key intermediates. Spectroscopic and kinetic data support the involvement of a M(III)-NCR intermediate. A H-bonding network facilitates this enzymatic reaction. Herein we describe two biomimetic Co(III)-NHase analogues that hydrate MeCN, and four crystallographically characterized NHase intermediate analogues, [Co(III)(S(Me2)N(4)(tren))(MeCN)](2+) (1), [Co(III)(S(Me2)N(4)(tren))(OH)](+) (3), [Co(III)(S(Me2)N(4)(tren))(NHC(O)CH(3))](+) (2), and [Co(III)(O(Me2)N(4)(tren))(NHC(OH)CH(3))](2+) (5). Iminol-bound 5 represents the first example of a Co(III)-iminol compound in any ligand environment. Kinetic parameters (k(1)(298 K) = 2.98(5) M(-1) s(-1), ΔH(‡) = 12.65(3) kcal/mol, ΔS(‡) = -14(7) e.u.) for nitrile hydration by 1 are reported, and the activation energy E(a) = 13.2 kcal/mol is compared with that (E(a) = 5.5 kcal/mol) of the NHase enzyme. A mechanism involving initial exchange of the bound MeCN for OH- is ruled out by the fact that nitrile exchange from 1 (k(ex)(300 K) = 7.3(1) × 10(-3) s(-1)) is 2 orders of magnitude slower than nitrile hydration, and that hydroxide bound 3 does not promote nitrile hydration. Reactivity of an analogue that incorporates an alkoxide as a mimic of the highly conserved NHase serine residue shows that this moiety facilitates nitrile hydration under milder conditions. Hydrogen-bonding to the alkoxide stabilizes a Co(III)-iminol intermediate. Comparison of the thiolate versus alkoxide intermediate structures shows that C≡N bond activation and C═O bond formation proceed further along the reaction coordinate when a thiolate is incorporated into the coordination sphere.
Collapse
Affiliation(s)
- Rodney D Swartz
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | | | | | | |
Collapse
|
38
|
Nitrile hydratases (NHases): At the interface of academia and industry. Biotechnol Adv 2010; 28:725-41. [DOI: 10.1016/j.biotechadv.2010.05.020] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 11/19/2022]
|
39
|
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.
Collapse
Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA.
| | | | | |
Collapse
|
40
|
Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase. J Biol Inorg Chem 2010; 15:655-65. [DOI: 10.1007/s00775-010-0632-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 01/17/2010] [Indexed: 10/19/2022]
|
41
|
Arakawa T, Kawano Y, Katayama Y, Nakayama H, Dohmae N, Yohda M, Odaka M. Structural basis for catalytic activation of thiocyanate hydrolase involving metal-ligated cysteine modification. J Am Chem Soc 2010; 131:14838-43. [PMID: 19785438 DOI: 10.1021/ja903979s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiocyanate hydrolase (SCNase) is a member of a family of nitrile hydratase proteins, each of which contains a unique noncorrin cobalt center with two post-translationally modified cysteine ligands, cysteine-sulfenic acid or -sulfenate (Cys-SO(H)), and cysteine-sulfininate (Cys-SO(2)(-)), respectively. We have found that a partially matured recombinant SCNase was activated during storage. The crystal structures of SCNase before and after storage demonstrated that Cys-SO(2)(-) modification of gammaCys131 proceeded to completion prior to storage, while Cys-SO(H) modification of gammaCys133 occurred during storage. SCNase activity was suppressed when gammaCys133 was further oxidized to Cys-SO(2)(-). The correlation between the catalytic activity and the extent of the gammaCys133 modification indicates that the cysteine sulfenic acid modification of gammaCys133 is of primary importance in determining the activity of SCNase.
Collapse
Affiliation(s)
- Takatoshi Arakawa
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | | | | | | | | | | | | |
Collapse
|
42
|
Hsieh CC, Chao WJ, Horng YC. An unique stair-like infinite chain polymer containing dimeric N2S3 square-pyramidal iron(III) complex. INORG CHEM COMMUN 2009. [DOI: 10.1016/j.inoche.2009.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
43
|
van Pelt S, van Rantwijk F, Sheldon R. Synthesis of Aliphatic (S)-α-Hydroxycarboxylic Amides using a One-Pot Bienzymatic Cascade of Immobilised Oxynitrilase and Nitrile Hydratase. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200800625] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
44
|
Foerstner KU, Doerks T, Muller J, Raes J, Bork P. A nitrile hydratase in the eukaryote Monosiga brevicollis. PLoS One 2008; 3:e3976. [PMID: 19096720 PMCID: PMC2603476 DOI: 10.1371/journal.pone.0003976] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 11/18/2008] [Indexed: 11/19/2022] Open
Abstract
Bacterial nitrile hydratase (NHases) are important industrial catalysts and waste water remediation tools. In a global computational screening of conventional and metagenomic sequence data for NHases, we detected the two usually separated NHase subunits fused in one protein of the choanoflagellate Monosiga brevicollis, a recently sequenced unicellular model organism from the closest sister group of Metazoa. This is the first time that an NHase is found in eukaryotes and the first time it is observed as a fusion protein. The presence of an intron, subunit fusion and expressed sequence tags covering parts of the gene exclude contamination and suggest a functional gene. Phylogenetic analyses and genomic context imply a probable ancient horizontal gene transfer (HGT) from proteobacteria. The newly discovered NHase might open biotechnological routes due to its unconventional structure, its new type of host and its apparent integration into eukaryotic protein networks.
Collapse
Affiliation(s)
| | - Tobias Doerks
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jean Muller
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jeroen Raes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
| |
Collapse
|
45
|
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.
Collapse
Affiliation(s)
- Priscilla Lugo-Mas
- The Department of Chemistry, University of Washington, Box 351700 Seattle, Washington 98195-1700, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
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]
|
47
|
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.
Collapse
Affiliation(s)
- Saroja Rao
- Department of Chemistry, Loyola University--Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, USA
| | | |
Collapse
|
48
|
Hashimoto K, Suzuki H, Taniguchi K, Noguchi T, Yohda M, Odaka M. Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile. J Biol Chem 2008; 283:36617-23. [PMID: 18948265 DOI: 10.1074/jbc.m806577200] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrile hydratases (NHases) have an unusual iron or cobalt catalytic center with two oxidized cysteine ligands, cysteine-sulfinic acid and cysteine-sulfenic acid, catalyzing the hydration of nitriles to amides. Recently, we found that the NHase of Rhodococcus erythropolis N771 exhibited an additional catalytic activity, converting tert-butylisonitrile (tBuNC) to tert-butylamine. Taking advantage of the slow reactivity of tBuNC and the photoreactivity of nitrosylated NHase, we present the first structural evidence for the catalytic mechanism of NHase with time-resolved x-ray crystallography. By monitoring the reaction with attenuated total reflectance-Fourier transform infrared spectroscopy, the product from the isonitrile carbon was identified as a CO molecule. Crystals of nitrosylated inactive NHase were soaked with tBuNC. The catalytic reaction was initiated by photo-induced denitrosylation and stopped by flash cooling. tBuNC was first trapped at the hydrophobic pocket above the iron center and then coordinated to the iron ion at 120 min. At 440 min, the electron density of tBuNC was significantly altered, and a new electron density was observed near the isonitrile carbon as well as the sulfenate oxygen of alphaCys114. These results demonstrate that the substrate was coordinated to the iron and then attacked by a solvent molecule activated by alphaCys114-SOH.
Collapse
Affiliation(s)
- Koichi Hashimoto
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | | | | | | | | | | |
Collapse
|
49
|
|
50
|
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.
Collapse
Affiliation(s)
- Karina Kubiak
- Institute of Physics, Nicolaus Copernicus University, 87-100 Torun, Poland
| | | |
Collapse
|