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Bhalla TC, Thakur N, Kumar V. Arylacetonitrilases: Potential Biocatalysts for Green Chemistry. Appl Biochem Biotechnol 2024; 196:1769-1785. [PMID: 37453025 DOI: 10.1007/s12010-023-04643-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
Nitrilases are the enzymes that catalyze the hydrolysis of nitriles to corresponding carboxylic acid and ammonia. They are broadly categorized into aromatic, aliphatic, and arylacetonitrilases based on their substrate specificity. Most of the studies pertaining to these enzymes in the literature have focused on aromatic and aliphatic nitrilases. However, arylacetonitrilases have attracted the attention of academia and industry in the last several years due to their aryl specificity and enantioselectivity. They have emerged as interesting biocatalytic tools in green chemistry to synthesize useful aryl acids such as mandelic acid and derivatives of phenylacetic acid. The aim of the present review is to collate information on the arylacetonitrilases and their catalytic properties including enantioselectivity and potential applications in organic synthesis.
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Affiliation(s)
- Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India.
| | - Neerja Thakur
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India
- Department of Biotechnology and Microbiology, Himachal Pradesh, Rajkiya Kanya Mahavidyalaya, Longwood, Shimla, 171001, India
| | - Vijay Kumar
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Bian M, Zhao J, Xu W, Han X, Chen X, Wang P, Zhu G. Enzymatic Characterization of the Isocitrate Dehydrogenase with Dual Coenzyme Specificity from the Marine Bacterium Umbonibacter marinipuiceus. Int J Mol Sci 2023; 24:11428. [PMID: 37511187 PMCID: PMC10380307 DOI: 10.3390/ijms241411428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Isocitrate dehydrogenase (IDH) can be divided into NAD+-dependent and NADP+-dependent types based on the coenzyme specificity. It is worth noting that some IDHs exhibit dual coenzyme specificity characteristics. Herein, a dual coenzyme-dependent IDH from Umbonibacter Marinipuiceus (UmIDH) was expressed, purified, and identified in detail for the first time. SDS-PAGE and Gel filtration chromatography analyses showed that UmIDH is an 84.7 kDa homodimer in solution. The Km values for NAD+ and NADP+ are 1800.0 ± 64.4 μM and 1167.7 ± 113.0 μM in the presence of Mn2+, respectively. Meanwhile, the catalytic efficiency (kcat/Km) of UmIDH is only 2.3-fold greater for NADP+ than NAD+. The maximal activity for UmIDH occurred at pH 8.5 (with Mn2+) or pH 8.7 (with Mg2+) and at 35 °C (with Mn2+ or Mg2+). Heat inactivation assay revealed that UmIDH sustained 50% of maximal activity after incubation at 57 °C for 20 min with either Mn2+ or Mg2+. Moreover, three putative core coenzyme binding residues (R345, L346, and V352) of UmIDH were evaluated by site-directed mutagenesis. This recent work identified a unique dual coenzyme-dependent IDH and achieved the groundbreaking bidirectional modification of this specific IDH's coenzyme dependence for the first time. This provides not only a reference for the study of dual coenzyme-dependent IDH, but also a basis for the investigation of the coenzyme-specific evolutionary mechanisms of IDH.
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Affiliation(s)
- Mingjie Bian
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu 241000, China
| | - Jiaxin Zhao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu 241000, China
| | - Wenqiang Xu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu 241000, China
| | - Xueyang Han
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu 241000, China
| | - Xuefei Chen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu 241000, China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu 241000, China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu 241000, China
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Yuan L, Liu G, Zhao D, Zhu H, Qi J, Lu K. Interaction of p53 with BRC analogs: A comparative design assisted by ZDOCK and CABS-Dock simulation. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Kumar A, Shahul R, Singh R, Kumar S, Kumar A, Mehta PK. Geobacillus thermoleovorans MTCC 13131: An Amide-Hydrolyzing Thermophilic Bacterium Isolated from a Hot Spring of Manikaran. Indian J Microbiol 2022; 62:618-626. [PMID: 36458220 PMCID: PMC9705672 DOI: 10.1007/s12088-022-01042-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022] Open
Abstract
Geobacillus thermoleovorans MTCC 13131, an amide hydrolyzing bacteria was isolated from a hot spring in Himachal Pradesh and identified through 16S rRNA gene sequence analysis. The amidase derived from this bacterium exhibited hydrolyzing catalytic ability against aliphatic and aromatic amides. The isolate was characterized for morphological and biochemical properties. Further, the production of amidase enzyme from this isolate was evaluated using approach of one-variable-at-a-time and response surface method. The Response Surface Methodology based study indicated the importance of nitrogen sources and growth period for amidase production. Optimal production was achieved at a temperature 55 °C, and production pH 7.5 in the production medium comprising diammonium hydrogen phosphate (0.4%), peptone (0.45%) and yeast extract (0.3%). The wide substrate affinity of the strain suggests its potential role in biotransformation of amides to corresponding acids of industrial significance along with its strong capacity to degrade the toxic amide in polluted environmental samples. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-022-01042-9.
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Affiliation(s)
- Arun Kumar
- Center for Molecular Biology, Central University of Jammu, Bagla, Rahya Suchani, Jammu, Jammu and Kashmir 181143 India
| | - Refana Shahul
- Center for Molecular Biology, Central University of Jammu, Bagla, Rahya Suchani, Jammu, Jammu and Kashmir 181143 India
| | - Rajendra Singh
- Environmental Energy Engineering, College of Engineering, University of Suwon, Hwaseong, 18323 Republic of Korea
| | - Sanjay Kumar
- Department of Life Sciences, School of Basics Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh 201310 India
| | - Ashok Kumar
- Center for Molecular Biology, Central University of Jammu, Bagla, Rahya Suchani, Jammu, Jammu and Kashmir 181143 India
| | - Praveen Kumar Mehta
- Center for Molecular Biology, Central University of Jammu, Bagla, Rahya Suchani, Jammu, Jammu and Kashmir 181143 India
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A Novel NADP(H)-Dependent 7alpha-HSDH: Discovery and Construction of Substrate Selectivity Mutant by C-Terminal Truncation. Catalysts 2022. [DOI: 10.3390/catal12070781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
7α-Hydroxysteroid dehydrogenase (7α-HSDH) plays an important role in the biosynthesis of tauroursodeoxycholic acid (TUDCA) using complex substrate chicken bile powder as raw material. However, chicken bile powder contains 4.74% taurocholic acid (TCA), and a new by-product tauroursocholic acid (TUCA) will be produced, having the risk of causing colorectal cancer. Here, we obtained a novel NADP(H)-dependent 7α-HSDH with good thermostability from Ursus thibetanus gut microbiota (named St-2-2). St-2-2 could catalyze taurochenodeoxycholic acid (TCDCA) and TCA with the catalytic activity of 128.13 and 269.39 U/mg, respectively. Interestingly, by a structure-based C-terminal truncation strategy, St-2-2△C10 only remained catalytic activity on TCDCA (14.19 U/mg) and had no activity on TCA. As a result, it can selectively catalyze TCDCA in waste chicken bile powder. MD simulation and structural analysis indicated that enhanced surface hydrophilicity and improved C-terminal rigidity affected the entry and exit of substrates. Hydrogen bond interactions between different subunits and interaction changes in Phe249 of the C-terminal loop inverted the substrate catalytic activity. This is the first report on substrate selectivity of 7α-HSDH by C-terminal truncation strategy and it can be extended to other 7α-HSDHs (J-1-1, S1-a-1).
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Patel SKS, Shanmugam R, Lee JK, Kalia VC, Kim IW. Biomolecules Production from Greenhouse Gases by Methanotrophs. Indian J Microbiol 2021; 61:449-457. [PMID: 34744200 PMCID: PMC8542019 DOI: 10.1007/s12088-021-00986-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 12/24/2022] Open
Abstract
Harmful effects on living organisms and the environment are on the rise due to a significant increase in greenhouse gas (GHG) emissions through human activities. Therefore, various research initiatives have been carried out in several directions in relation to the utilization of GHGs via physicochemical or biological routes. An environmentally friendly approach to reduce the burden of significant emissions and their harmful effects is the bioconversion of GHGs, including methane (CH4) and carbon dioxide (CO2), into value-added products. Methanotrophs have enormous potential for the efficient biotransformation of CH4 to various bioactive molecules, including biofuels, polyhydroxyalkanoates, and fatty acids. This review highlights the recent developments in methanotroph-based systems for methanol production from GHGs and proposes future perspectives to improve process sustainability via biorefinery approaches.
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Affiliation(s)
- Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Ramsamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Vipin C. Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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Anaerobic Digestion of Agri-Food Wastes for Generating Biofuels. Indian J Microbiol 2021; 61:427-440. [PMID: 34744198 DOI: 10.1007/s12088-021-00977-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022] Open
Abstract
Presently, fossil fuels are extensively employed as major sources of energy, and their uses are considered unsustainable due to emissions of obnoxious gases on the burning of fossil fuels, which can lead to severe environmental complications, including human health. To tackle these issues, various processes are developing to waste as a feed to generate eco-friendly fuels. The biological production of fuels is considered to be more beneficial than physicochemical methods due to their environmentally friendly nature, high rate of conversion at ambient physiological conditions, and less energy-intensive. Among various biofuels, hydrogen (H2) is considered as a wonderful due to high calorific value and generate water molecule as end product on the burning. The H2 production from biowaste is demonstrated, and agri-food waste can be potentially used as a feedstock due to their high biodegradability over lignocellulosic-based biomass. Still, the H2 production is uneconomical from biowaste in fuel competing market because of low yields and increased capital and operational expenses. Anaerobic digestion is widely used for waste management and the generation of value-added products. This article is highlighting the valorization of agri-food waste to biofuels in single (H2) and two-stage bioprocesses of H2 and CH4 production.
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Tacias-Pascacio VG, Morellon-Sterling R, Castañeda-Valbuena D, Berenguer-Murcia Á, Kamli MR, Tavano O, Fernandez-Lafuente R. Immobilization of papain: A review. Int J Biol Macromol 2021; 188:94-113. [PMID: 34375660 DOI: 10.1016/j.ijbiomac.2021.08.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Papain is a cysteine protease from papaya, with many applications due to its broad specificity. This paper reviews for first time the immobilization of papain on different supports (organic, inorganic or hybrid supports) presenting some of the features of the utilized immobilization strategies (e.g., epoxide, glutaraldehyde, genipin, glyoxyl for covalent immobilization). Special focus is placed on the preparation of magnetic biocatalysts, which will permit the simple recovery of the biocatalyst even if the medium is a suspension. Problems specific to the immobilization of proteases (e.g., steric problems when hydrolyzing large proteins) are also defined. The benefits of a proper immobilization (enzyme stabilization, widening of the operation window) are discussed, together with some artifacts that may suggest an enzyme stabilization that may be unrelated to enzyme rigidification.
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Affiliation(s)
- Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Roberto Morellon-Sterling
- Departamento de Biocatálisis. ICP-CSIC./Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid. Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid. Spain
| | - Daniel Castañeda-Valbuena
- Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Majid Rasool Kamli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddad 21589, Saudi Arabia; Center of excellence in Bionanoscience Research, King Abdulaziz University, Jeddad 21589, Saudi Arabia
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC./Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid. Spain; Center of Excellence in Bionanoscience Research, External advisory board, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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Devi N, Patel SKS, Kumar P, Singh A, Thakur N, Lata J, Pandey D, Thakur V, Chand D. Bioprocess Scale-up for Acetohydroxamic Acid Production by Hyperactive Acyltransferase of Immobilized Rhodococcus Pyridinivorans. Catal Letters 2021. [DOI: 10.1007/s10562-021-03696-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Guo LB, Zhu CY, Wu YB, Fan XM, Zhang YW. A novel chondroitin AC lyase from Pedobacter xixiisoli: Cloning, expression, characterization and the application in the preparation of oligosaccharides. Enzyme Microb Technol 2021; 146:109765. [PMID: 33812567 DOI: 10.1016/j.enzmictec.2021.109765] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 01/22/2023]
Abstract
Chondroitin AC lyase can efficiently hydrolyze chondroitin sulfate (CS) to low molecule weight chondroitin sulfate, which has been widely used in clinical therapy, including anti-tumor, anti-oxidation, hypolipidemic, and anti-inflammatory. In this work, a novel chondroitin AC lyase from Pedobacter xixiisoli (PxchonAC) was cloned and overexpressed in Escherichia coli BL21 (DE3). The characterization of PxchonAC showed that it has specific activities on chondroitin sulfate A, Chondroitin sulfate C and hyaluronic acid with 428.77, 270.57, and 136.06 U mg-1, respectively. The Km and Vmax of PxchonAC were 0.61 mg mL-1 and 670.18 U mg-1 using chondroitin sulfate A as the substrate. The enzyme had a half-life of roughly 660 min at 37 °C in the presence of Ca2+ and remained a residual activity of 54 % after incubated at 4 °C for 25 days. Molecular docking revealed that Asn123, His223, Tyr232, Arg286, Arg290, Asn372, and Glu374 were mainly involved in the substrate binding. The enzymatic hydrolysis product was analyzed by gel permeation chromatography, demonstrating PxchonAC could hydrolyze CS efficiently.
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Affiliation(s)
- Li-Bin Guo
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Chen-Yuan Zhu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Yi-Bei Wu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Xiao-Man Fan
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Ye-Wang Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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