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Das KK, Pattnaik S. Bioactivity of Microbacterium barkeri (LMA4) In Vitro and Candidate Gene Annotation In Silico. Appl Biochem Biotechnol 2024; 196:2839-2850. [PMID: 37166647 DOI: 10.1007/s12010-023-04519-5] [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] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
Actinomycetes are considered a never-ending treasure trove of biometabolites, which always fascinated researchers. However, to combat with newly emerging bacterial strains, the search for novel or analogs of existing therapeutic agents is recommended. In this context, this research work was carried out to search for a biopotent Actinomycetal strain grown in untapped soil, near the Hirakud dam. This Gram-positive bacteria was subjected to screening for its bioactivity against the medically important bacteria, isolated from local hospital sample using "co-culture" method, following both qualitative and quantitative assays. Further, the 16 s rRNA sequencing, BLASTn analysis, and GC% calculation were carried out. Based upon its bioactivity, a prediction-based genomics work was pursued, considering the gene sequence deposited in public domain. The reverse translation, elution of protein structural file, and the putative protein were predicted. The strain was identified as Microbacterium barkeri, with 54.1% GC content. From Gene Ontology term annotation, it was predicted that the α/β hydrolase fold of hydrolase protein could have been responsible for antibiotic/biometabolite synthesis, in silico. The in vitro-based sequence (from Whole Genome Sequence data) had inferred that there was elution of alpha/beta hydrolase fold, substantiated with conserved domain analysis, ORF finding more over Gene Ontology (GO) terminology annotations. The GO annotations had suggested that the protein had been produced in response to a bacteria, under the influence of external stimuli more so in stress.
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Affiliation(s)
- Krishna Kumar Das
- Laboratory of Medical Microbiology, Department of Biotechnology and Bioinformatics, School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, Odisha, India
| | - Smaranika Pattnaik
- Laboratory of Medical Microbiology, Department of Biotechnology and Bioinformatics, School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, Odisha, India.
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2
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Busch MR, Rajendran C, Sterner R. Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli. Biochemistry 2023; 62:863-872. [PMID: 36599150 DOI: 10.1021/acs.biochem.2c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli, which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 Å and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number (kcat) and/or the Michaelis constant (KM). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.
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Affiliation(s)
- Markus R Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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3
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Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
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Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
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4
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Chen Y, Gao F, Zheng G, Gao S. Enantioselective synthesis of a chiral intermediate of himbacine analogs by Burkholderia cepacia lipase A. Biotechnol Lett 2020; 42:2643-2651. [DOI: 10.1007/s10529-020-02969-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
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5
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Zheng Q, Wang M, Zhang L, Ahmad W, Li H, Tong Y, Zheng G, Zhu S. Topology engineering via protein catenane construction to strengthen an industrial biocatalyst. J Biotechnol 2020; 325:271-279. [PMID: 33065139 DOI: 10.1016/j.jbiotec.2020.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 12/24/2022]
Abstract
Protein topology engineering has emerged as a new dimension to alter protein stability and function. Inspired by the art of nature, where backbone cyclization is frequently adopted to enhance the stability of natural peptide products and thermostable enzymes; herein, we report protein topology engineering of an industrial thermolabile gamma lactamase via catenation. Two different protein catenanes were successfully constructed via SpyTag/SpyCatcher modules and two different peptide dimer domains. The designed protein catenanes were functionally synthesized in Escherichia coli. A comparison of their biochemical properties revealed that protein topology played a key role in the stability of gamma lactamase. Protein catenation enhanced both the thermo- and proteolytic stabilities of gamma lactamase. Gamma lactamase was stabilized by ∼8 °C in one of the catenated forms. Moreover, Cat1-MhIHL-V54L and Cat2-MhIHL-V54L displayed 1.8- and 2.4-fold higher enzyme efficiencies (Kcat/Km), respectively, than the unattenuated enzyme. Therefore, our results proved that protein catenane construction could be a general strategy to strengthen industrial biocatalysts by mechanisms distinct from those of the conventional direct evolution schemes, whereby our results offer wide applications in the fine chemical industry.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China
| | - Mengjiao Wang
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China
| | - Lin Zhang
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China
| | - Waqas Ahmad
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China
| | - Hongxia Li
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China
| | - Yigang Tong
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China.
| | - Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, PR China.
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6
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Li H, Gao S, Qiu Y, Liang C, Zhu S, Zheng G. Genome mining integrating semi-rational protein engineering and nanoreactor design: roadmap for a robust biocatalyst for industrial resolution of Vince lactam. Appl Microbiol Biotechnol 2019; 104:1109-1123. [PMID: 31828408 DOI: 10.1007/s00253-019-10275-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/13/2019] [Accepted: 11/23/2019] [Indexed: 11/25/2022]
Abstract
Biomanufacturing of chemicals using biocatalysts is an attractive strategy for the production of valuable pharmaceuticals since it is usually more economical and has a much-reduced environmental impact. However, there are often challenges such as their thermal instability that should be overcome before a newly discovered enzyme is eventually translated into industrial processes. In this work, we describe a roadmap for the development of a robust catalyst for industrial resolution of Vince lactam, a key intermediate for the synthesis of carbocyclic-nucleoside-related pharmaceuticals. By a genome mining strategy, a new (+)-γ-lactamase (MiteL) from Microbacterium testaceum was successfully discovered and biochemically characterized. In vitro studies showed that the enzyme exhibited high activity but poor enantioselectivity (E = 6.3 ± 0.2) toward racemic Vince lactam, and thus, it is not suitable for industrial applications. Based on structural modeling and docking studies, a semi-rational engineering strategy combined with an efficient screening method was then applied to improve the enantioselectivity of MiteL. Several mutants with significant shifting stereoselectivity toward (-)-γ-lactam were obtained by site-saturation mutagenesis. Synergy effects led to the final mutant F14D/Q114R/M117L, which enabled efficient acquisition of (-)-γ-lactam with a high E value (> 200). The mutant was biochemically characterized, and the docking studies suggested a plausible mechanism for its improved selectivity. Finally, a sunflower-like nanoreactor was successfully constructed to improve the mutant's robustness via protein supramolecular self-assembly. Thus, the synergism between semi-rational protein engineering and self-assembling immobilization enabled construction of a nanoreactor with superior properties, which can be used for resolution of Vince lactam in large scale.
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Affiliation(s)
- Hongxia Li
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shuaihua Gao
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yan Qiu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Chaoqun Liang
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China. .,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China. .,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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7
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Chen Y, Zhang X, Zheng G, Gao S. Preparation of the enantiomerically enriched precursor of lamivudine (3TC™) via asymmetric catalysis mediated by Klebsiella oxytoca. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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8
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Dynamic kinetic resolution of Vince lactam catalyzed by γ-lactamases: a mini-review. ACTA ACUST UNITED AC 2018; 45:1017-1031. [DOI: 10.1007/s10295-018-2093-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/16/2018] [Indexed: 10/28/2022]
Abstract
Abstract
γ-Lactamases are versatile enzymes used for enzymatic kinetic resolution of racemic Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) in the industry. Optically pure enantiomers and their hydrolytic products are widely employed as key chemical intermediates for developing a wide range of carbocyclic nucleoside medicines, including US FDA-approved drugs peramivir and abacavir. Owing to the broad applications in the healthcare industry, the resolution process of Vince lactam has witnessed tremendous progress during the past decades. Some of the most important advances are the enzymatic strategies involving γ-lactamases. The strong industrial demand drives the progress in various strategies for discovering novel biocatalysts. In the past few years, several new scientific breakthroughs, including the genome-mining strategy and elucidation of several crystal structures, boosted the research on γ-lactamases. So far, several families of γ-lactamases for resolution of Vince lactam have been discovered, and their number is continuously increasing. The purpose of this mini-review is to describe the discovery strategy and classification of these intriguing enzymes and to cover our current knowledge on their potential biological functions. Moreover, structural properties are described in addition to their possible catalytic mechanisms. Additionally, recent advances in the newest approaches, such as immobilization to increase stability, and other engineering efforts are introduced.
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9
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Gao S, Lu Y, Li Y, Huang R, Zheng G. Enhancement in the catalytic activity of Sulfolobus solfataricus P2 (+)-γ-lactamase by semi-rational design with the aid of a newly established high-throughput screening method. Appl Microbiol Biotechnol 2018; 103:251-263. [DOI: 10.1007/s00253-018-9428-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/26/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
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10
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Su Y, Gao S, Li H, Zheng G. Enantioselective resolution of γ-lactam utilizing a novel (+)-γ-lactamase from Bacillus thuringiensis. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.06.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Biocatalysis for the synthesis of pharmaceuticals and pharmaceutical intermediates. Bioorg Med Chem 2018; 26:1275-1284. [DOI: 10.1016/j.bmc.2017.06.043] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/12/2017] [Accepted: 06/27/2017] [Indexed: 12/31/2022]
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12
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Li H, Zhu S, Zheng G. Promiscuous (+)-γ-lactamase activity of an amidase from nitrile hydratase pathway for efficient synthesis of carbocyclic nucleosides intermediate. Bioorg Med Chem Lett 2018; 28:1071-1076. [DOI: 10.1016/j.bmcl.2018.02.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/04/2018] [Accepted: 02/09/2018] [Indexed: 11/17/2022]
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13
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Li H, Zheng G, Zhu S. Construction of an organelle-like nanodevice via supramolecular self-assembly for robust biocatalysts. Microb Cell Fact 2018; 17:26. [PMID: 29458431 PMCID: PMC5819227 DOI: 10.1186/s12934-018-0873-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/09/2018] [Indexed: 11/13/2022] Open
Abstract
Background When using the microbial cell factories for green manufacturing, several important issues need to be addressed such as how to maintain the stability of biocatalysts used in the bioprocess and how to improve the synthetic efficiency of the biological system. One strategy widely used during natural evolution is the creation of organelles which can be used for regional control. This kind of compartmentalization strategy has inspired the design of artificial organelle-like nanodevice for synthetic biology and “green chemistry”. Results Mimicking the natural concept of functional compartments, here we show that the engineered thermostable ketohydroxyglutarate aldolase from Thermotoga maritima could be developed as a general platform for nanoreactor design via supramolecular self-assembly. An industrial biocatalyst-(+)-γ-lactamase was selected as a model catalyst and successful encapsulated in the nanoreactor with high copies. These nanomaterials could easily be synthesized by Escherichia coli by heterologous expression and subsequently self-assembles into the target organelle-like nanoreactors both in vivo and in vitro. By probing their structural characteristics via transmission electronic microscopy and their catalytic activity under diverse conditions, we proved that these nanoreactors could confer a significant benefit to the cargo proteins. The encapsulated protein exhibits significantly improved stability under conditions such as in the presence of organic solvent or proteases, and shows better substrate tolerance than free enzyme. Conclusions Our biodesign strategy provides new methods to develop new catalytically active protein-nanoreactors and could easily be applied into other biocatalysts. These artificial organelles could have widely application in sustainable catalysis, synthetic biology and could significantly improve the performance of microbial cell factories. Graphical Abstract ![]()
Electronic supplementary material The online version of this article (10.1186/s12934-018-0873-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongxia Li
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, 100029, Beijing, People's Republic of China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, 100029, Beijing, People's Republic of China.
| | - Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, 100029, Beijing, People's Republic of China.
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Engineering the Enantioselectivity and Thermostability of a (+)-γ-Lactamase from Microbacterium hydrocarbonoxydans for Kinetic Resolution of Vince Lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one). Appl Environ Microbiol 2017; 84:AEM.01780-17. [PMID: 29054871 DOI: 10.1128/aem.01780-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs, such as carbovir and abacavir, which are used to fight against HIV and hepatitis B virus. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme. The approach resulted in two mutants, Val54Ser and Val54Leu, which catalyzed the hydrolysis of Vince lactam to give (-)-Vince lactam, with 99.2% (enantiomeric ratio [E] > 200) enantiomeric excess (ee) and 99.5% ee (E > 200), respectively. To improve the thermostability of the enzyme, 11 residues with high temperature factors (B-factors) calculated by B-FITTER or high root mean square fluctuation (RMSF) values from the molecular dynamics simulation were selected. Six mutants with increased thermostability were obtained. Finally, the mutants generated with improved enantioselectivity and mutants evolved for enhanced thermostability were combined. Several variants showing (+)-selectivity (E value > 200) and improved thermostability were observed. These engineered enzymes are good candidates to serve as enantioselective catalysts for the preparation of enantiomerically pure Vince lactam.IMPORTANCE Enzymatic kinetic resolution of the racemic Vince lactam using (+)-γ-lactamase is the most often utilized means of resolving the enantiomers for the preparation of carbocyclic nucleoside compounds. The efficiency of the native enzymes could be improved by using protein engineering methods, such as directed evolution and rational design. In our study, two properties (enantioselectivity and thermostability) of a γ-lactamase identified from Microbacterium hydrocarbonoxydans were tackled using a semirational design. The protein engineering was initialized by combinatorial active-site saturation test to improve the enantioselectivity. At the same time, two strategies were applied to identify mutation candidates to enhance the thermostability based on calculations from both a static (B-FITTER based on the crystal structure) and a dynamic (root mean square fluctuation [RMSF] values based on molecular dynamics simulations) way. After combining the mutants, we successfully obtained the final mutants showing better properties in both properties. The engineered (+)-lactamase could be a candidate for the preparation of (-)-Vince lactam.
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Microindolinone A, a Novel 4,5,6,7-Tetrahydroindole, from the Deep-Sea-Derived Actinomycete Microbacterium sp. MCCC 1A11207. Mar Drugs 2017. [DOI: 10.3390/md15070230 pmid: 287539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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16
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Niu S, Zhou TT, Xie CL, Zhang GY, Yang XW. Microindolinone A, a Novel 4,5,6,7-Tetrahydroindole, from the Deep-Sea-Derived Actinomycete Microbacterium sp. MCCC 1A11207. Mar Drugs 2017; 15:md15070230. [PMID: 28753937 PMCID: PMC5532672 DOI: 10.3390/md15070230] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/30/2017] [Accepted: 07/14/2017] [Indexed: 11/16/2022] Open
Abstract
A novel indole, microindolinone A (1), was isolated from a deep-sea-derived actinomycete Microbacterium sp. MCCC 1A11207, together with 18 known compounds (2-19). By detailed analysis of the ¹H, 13C, HSQC, COSY, HMBC, high resolution electron spray ionization mass spectrum (HRESIMS), and circular dichroism (CD) data, the absolute configuration of 1 was elucidated as 5R-hydroxy-4,5,6,7-tetrahydroindole-4-one. It is noteworthy that 1 is the second example of a saturated indole isolated from nature.
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Affiliation(s)
- Siwen Niu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
| | - Ting-Ting Zhou
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
| | - Chun-Lan Xie
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
| | - Gai-Yun Zhang
- Fujian Key Laboratory of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
| | - Xian-Wen Yang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
- Fujian Key Laboratory of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen 361005, China.
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18
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Structural insights into the γ-lactamase activity and substrate enantioselectivity of an isochorismatase-like hydrolase from Microbacterium hydrocarbonoxydans. Sci Rep 2017; 7:44542. [PMID: 28295028 PMCID: PMC5353710 DOI: 10.1038/srep44542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/24/2017] [Indexed: 11/29/2022] Open
Abstract
(+)-γ-lactamase catalyzes the specific hydrolysis of (+)-γ-lactam out of the racemic γ-lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one) to leave optically pure (−)-γ-lactam, which is the key building block of antiviral drugs such as carbovir and abacavir. However, no structural data has been reported on how the enzymes bind the γ-lactams and achieve their enantioselectivities. We previously identified an isochorismatase-like hydrolase (IHL, Mh33H4-5540) with (+)-γ-lactamase activity, which constitutes a novel family of γ-lactamase. Here, we first discovered that this enzyme actually hydrolyzed both (+)- and (−)-γ-lactam, but with apparently different specificities. We determined the crystal structures of the apo-form, (+)-γ-lactam bound, and (−)-γ-lactam bound forms of the enzyme. The structures showed that the binding sites of both (+) and (−)-γ-lactam resemble those of IHLs, but the “cover” loop conserved in IHLs is lacking in the enzyme, probably resulting in its incomplete enantioselectivity. Structural, biochemical, and molecular dynamics simulation studies demonstrated that the steric clash caused by the binding-site residues, especially the side-chain of Cys111 would reduce the binding affinity of (−)-γ-lactam and possibly the catalytic efficiency, which might explain the different catalytic specificities of the enantiomers of γ-lactam. Our results would facilitate the directed evolution and application of Mh33H4-5540 in antiviral drug synthesis.
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