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Wang N, Zhang N, Sun ML, Sun Y, Dong QY, Wang Y, Gu ZT, Ding HT, Qin QL, Jiang Y, Chen XL, Zhang YZ, Gao C, Li CY. Molecular insights into the catalytic mechanism of a phthalate ester hydrolase. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135191. [PMID: 39013318 DOI: 10.1016/j.jhazmat.2024.135191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/18/2024]
Abstract
Phthalate esters (PAEs) are emerging hazardous and toxic chemicals that are extensively used as plasticizers or additives. Diethyl phthalate (DEP) and dimethyl phthalate (DMP), two kinds of PAEs, have been listed as the priority pollutants by many countries. PAE hydrolases are the most effective enzymes in PAE degradation, among which family IV esterases are predominate. However, only a few PAE hydrolases have been characterized, and as far as we know, no crystal structure of any PAE hydrolases of the family IV esterases is available to date. HylD1 is a PAE hydrolase of the family IV esterases, which can degrade DMP and DEP. Here, the recombinant HylD1 was characterized. HylD1 maintained a dimer in solution, and functioned under a relatively wide pH range. The crystal structures of HylD1 and its complex with monoethyl phthalate were solved. Residues involved in substrate binding were identified. The catalytic mechanism of HylD1 mediated by the catalytic triad Ser140-Asp231-His261 was further proposed. The hylD1 gene is widely distributed in different environments, suggesting its important role in PAEs degradation. This study provides a better understanding of PAEs hydrolysis, and lays out favorable bases for the rational design of highly-efficient PAEs degradation enzymes for industrial applications in future.
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Affiliation(s)
- Ning Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Nan Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Mei-Ling Sun
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Yan Sun
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Qing-Yu Dong
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Yu Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Zeng-Tian Gu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Hai-Tao Ding
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Yong Jiang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China.
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China.
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2
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da Silva AS, Adriani PP, de Oliveira GS, Rocha ARL, Perpétuo EA, Dias MVB, Chambergo FS. Biochemical characterization of an esterase from Thermobifida fusca YX with acetyl xylan esterase activity. Mol Biol Rep 2024; 51:767. [PMID: 38878205 DOI: 10.1007/s11033-024-09601-7] [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] [Received: 02/25/2024] [Accepted: 05/01/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Esterases (EC 3.1.1.X) are enzymes that catalyze the hydrolysis ester bonds. These enzymes have large potential for diverse applications in fine industries, particularly in pharmaceuticals, cosmetics, and bioethanol production. METHODS AND RESULTS In this study, a gene encoding an esterase from Thermobifida fusca YX (TfEst) was successfully cloned, and its product was overexpressed in Escherichia coli and purified using affinity chromatography. The TfEst kinetic assay revealed catalytic efficiencies of 0.58 s-1 mM-1, 1.09 s-1 mM-1, and 0.062 s-1 mM-1 against p-Nitrophenyl acetate, p-Nitrophenyl butyrate, and 1-naphthyl acetate substrates, respectively. Furthermore, TfEst also exhibited activity in a pH range from 6.0 to 10.0, with maximum activity at pH 8.0. The enzyme demonstrated a half-life of 20 min at 70 °C. Notably, TfEst displayed acetyl xylan esterase activity as evidenced by the acetylated xylan assay. The structural prediction of TfEst using AlphaFold indicated that has an α/β-hydrolase fold, which is consistent with other esterases. CONCLUSIONS The enzyme stability over a broad pH range and its activity at elevated temperatures make it an appealing candidate for industrial processes. Overall, TfEst emerges as a promising enzymatic tool with significant implications for the advancement of biotechnology and biofuels industries.
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Affiliation(s)
- Adriana S da Silva
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil
| | - Patricia P Adriani
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel S de Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Elen A Perpétuo
- Bio4Tec, Centro de Capacitação e Pesquisa em Meio Ambiente, CEPEMA-POLI-USP, Universidade de São Paulo, Cubatão, Brazil
- Institute of Marine Sciences (IMar), Federal University of Sao Paulo, Santos, Brazil
| | - Marcio V B Dias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe S Chambergo
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil.
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3
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Fruhauf S, Pühringer D, Thamhesl M, Fajtl P, Kunz-Vekiru E, Höbartner-Gussl A, Schatzmayr G, Adam G, Damborsky J, Djinovic-Carugo K, Prokop Z, Moll WD. Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone. ACS Catal 2024; 14:3392-3410. [PMID: 38449531 PMCID: PMC10913051 DOI: 10.1021/acscatal.4c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Zearalenone (ZEN) is a mycoestrogenic polyketide produced by Fusarium graminearum and other phytopathogenic members of the genus Fusarium. Contamination of cereals with ZEN is frequent, and hydrolytic detoxification with fungal lactonases has been explored. Here, we report the isolation of a bacterial strain, Rhodococcus erythropolis PFA D8-1, with ZEN hydrolyzing activity, cloning of the gene encoding α/β hydrolase ZenA encoded on the linear megaplasmid pSFRL1, and biochemical characterization of nine homologues. Furthermore, we report site-directed mutagenesis as well as structural analysis of the dimeric ZenARe of R. erythropolis and the more thermostable, tetrameric ZenAScfl of Streptomyces coelicoflavus with and without bound ligands. The X-ray crystal structures not only revealed canonical features of α/β hydrolases with a cap domain including a Ser-His-Asp catalytic triad but also unusual features including an uncommon oxyanion hole motif and a peripheral, short antiparallel β-sheet involved in tetramer interactions. Presteady-state kinetic analyses for ZenARe and ZenAScfl identified balanced rate-limiting steps of the reaction cycle, which can change depending on temperature. Some new bacterial ZEN lactonases have lower KM and higher kcat than the known fungal ZEN lactonases and may lend themselves to enzyme technology development for the degradation of ZEN in feed or food.
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Affiliation(s)
- Sebastian Fruhauf
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Dominic Pühringer
- Department
for Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria
| | - Michaela Thamhesl
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Patricia Fajtl
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Elisavet Kunz-Vekiru
- Institute
of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology
IFA-Tulln, University of Natural Resources
and Life Sciences Vienna (BOKU), Konrad-Lorenz-Straße 20, Tulln 3430, Austria
| | - Andreas Höbartner-Gussl
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Gerd Schatzmayr
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
| | - Gerhard Adam
- Institute
of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences
Vienna (BOKU), Konrad-Lorenz-Straße
24, Tulln 3430, Austria
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Bld. A13, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Kristina Djinovic-Carugo
- Department
for Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna 1030, Austria
- Department
of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia
- European
Molecular Biology Laboratory (EMBL) Grenoble, Grenoble 38000, France
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5, Bld. A13, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital Brno, Pekarska 53, Brno 656
91, Czech Republic
| | - Wulf-Dieter Moll
- dsm-firmenich
Animal Nutrition and Health R&D Center Tulln, Technopark 1, Tulln 3430, Austria
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4
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Zhang X, Li L, Zheng Q. Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics. J Chem Inf Model 2023; 63:4762-4771. [PMID: 37452749 DOI: 10.1021/acs.jcim.3c00415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Pf2001 esterase (Pf2001) from Pyrococcus furiosus has hyperthermophilic properties and exerts a biocatalytic function in a dimeric state. Crystal structures revealed that the structural rearrangement of the cap domain is responsible for the Pf2001 dimer formation. However, the details of the cap domain remodeling and the effects of temperature on the dimerization process remain elusive at the molecular level, taking into account that experimental methods are difficult to capture the dynamic process of dimerization to some extent. Herein, four dimer models based on the monomeric crystal structure (PDB ID: 5G59) were constructed to investigate the conformational transition details and temperature effects in the dimerization by conventional molecular dynamics and accelerated molecular dynamics simulations. Our simulation results indicate that the monomer undergoes a conformational change into a "preparatory state" at high temperatures, which is more favorable for its transformation into a stable dimer. The subsequent free energy landscape analysis further identifies four intermediate states (from separated state to dimeric state) and discloses that a more accessible α-helix driven by stronger hydrophobic interactions induces a rearrangement of the cap domain, displaying a "tic-tac-toe" activation feature that is important for stabilizing the dimer interface and facilitating the formation of hydrophobic pockets. In addition, the electrostatic potential surface analysis illustrates that the weaker electrostatic repulsion (Lys and Arg) in the dimer interface at high temperatures is also a key factor for dimer stabilization. Altogether, our results can provide molecular-level insight into the dimer formation process of hyperthermophilic esterase and would be useful to understand the enzymatic specificity of α/β-hydrolase.
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Affiliation(s)
- Xue Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Lei Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
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5
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Role of N-Terminal Extensional Long α-Helix in the Arylesterase from Lacticaseibacillus rhamnosus GG on Catalysis and Stability. Catalysts 2023. [DOI: 10.3390/catal13020441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
In the α/β hydrolases superfamily, the extra module modulated enzymatic activity, substrate specificity, and stability. The functional role of N-terminal extensional long α-helix (Ala2-Glu29, designated as NEL-helix) acting as the extra module in the arylesterase LggEst from Lacticaseibacillus rhamnosus GG had been systemically investigated by deletion mutagenesis, biochemical characterization, and biophysical methods. The deletion of the NEL-helix did not change the overall structure of this arylesterase. The deletion of the NEL-helix led to the shifting of optimal pH into the acidity and the loss of thermophilic activity. The deletion of the NEL-helix produced a 10.6-fold drop in catalytic activity towards the best substrate pNPC10. NEL-Helix was crucial for the thermostability, chemical resistance, and organic solvents tolerance. The deletion of the NEL-helix did not change the overall rigidity of enzyme structure and only reduced the local rigidity of the active site. Sodium deoxycholate might partially replenish the loss of activity caused by the deletion of the NEL-helix. Our research further enriched the functional role of the extra module on catalysis and stability in the α/β hydrolase fold superfamily.
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6
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China H, Ogino H. Effect of attaching hydrophilic oligopeptides to the C-terminus of organic solvent-tolerant metal-free bromoperoxidase BPO-A1 from Streptomyces aureofaciens on organic solvent-stability. Biochem Biophys Res Commun 2023; 640:142-149. [PMID: 36508927 DOI: 10.1016/j.bbrc.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Metal-free bromoperoxidase BPO-A1 from Streptomyces aureofacience was selected among several similar enzymes exhibiting brominating activity as the most stable haloperoxidase against 70%(v/v) methanol. A comparison of the BPO-A1 and octahistidine-tagged BPO-A1 at the C-terminus (BPO-A1-His8) revealed that the His-tag enhanced the organic solvent-stability of BPO-A1 with pH- and heat-stabilities. Additionally, the contribution of the hydrophilicity at the C-terminal of BPO-A1 to the organic solvent-stability was confirmed employing several mutants bearing hydrophilic oligopeptides. Fortunately, two excellent mutants, BPO-A1-Lys8 and BPO-A1-Arg8, with high stabilities against various water-miscible organic solvents were obtained. In conclusion, the enhancing effect of the hydrophilic oligopeptides on the organic solvent-stability was associated with a decrease in the hydrophobic surface area near the C-terminus.
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Affiliation(s)
- Hideyasu China
- Department of Medical Bioscience, Nagahama Institute of Bio-Science and Technology, 1266, Tamuracho Nagahama-shi, Shiga, 526-0829, Japan.
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka, 599-8531, Japan.
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7
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Khairul Anuar NFS, Huyop F, Ur-Rehman G, Abdullah F, Normi YM, Sabullah MK, Abdul Wahab R. An Overview into Polyethylene Terephthalate (PET) Hydrolases and Efforts in Tailoring Enzymes for Improved Plastic Degradation. Int J Mol Sci 2022; 23:12644. [PMID: 36293501 PMCID: PMC9603852 DOI: 10.3390/ijms232012644] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Plastic or microplastic pollution is a global threat affecting ecosystems, with the current generation reaching as much as 400 metric tons per/year. Soil ecosystems comprising agricultural lands act as microplastics sinks, though the impact could be unexpectedly more far-reaching. This is troubling as most plastic forms, such as polyethylene terephthalate (PET), formed from polymerized terephthalic acid (TPA) and ethylene glycol (EG) monomers, are non-biodegradable environmental pollutants. The current approach to use mechanical, thermal, and chemical-based treatments to reduce PET waste remains cost-prohibitive and could potentially produce toxic secondary pollutants. Thus, better remediation methods must be developed to deal with plastic pollutants in marine and terrestrial environments. Enzymatic treatments could be a plausible avenue to overcome plastic pollutants, given the near-ambient conditions under which enzymes function without the need for chemicals. The discovery of several PET hydrolases, along with further modification of the enzymes, has considerably aided efforts to improve their ability to degrade the ester bond of PET. Hence, this review emphasizes PET-degrading microbial hydrolases and their contribution to alleviating environmental microplastics. Information on the molecular and degradation mechanisms of PET is also highlighted in this review, which might be useful in the future rational engineering of PET-hydrolyzing enzymes.
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Affiliation(s)
- Nurul Fatin Syamimi Khairul Anuar
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
| | - Ghani Ur-Rehman
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
- Advanced Membrane Technology Research Centre (AMTEC), Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
| | - Faizuan Abdullah
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
| | - Yahaya M. Normi
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Mohd Khalizan Sabullah
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
- Advanced Membrane Technology Research Centre (AMTEC), Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
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8
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Nagaroor V, Gummadi SN. An overview of mammalian and microbial hormone-sensitive lipases (lipolytic family IV): biochemical properties and industrial applications. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36154870 DOI: 10.1080/02648725.2022.2127071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/13/2022] [Indexed: 11/02/2022]
Abstract
In mammals, hormone-sensitive lipase (EC 3.1.1.79) is an intracellular lipase that significantly regulates lipid metabolism. Mammalian HSL is more active towards diacylglycerol but lacks a lid covering the active site. Dyslipidemia, hepatic steatosis, cancer, and cancer-associated cachexia are symptoms of HSL pathophysiology. Certain microbial proteins show a sequence homologous to the catalytic domain of mammalian HSL, hence called microbial HSL. They possess a funnel-shaped substrate-binding pocket and restricted length of acyl chain esters, thus known as esterases. These enzymes have broad substrate specificities and are capable of stereo, regio, and enantioselective, making them attractive biocatalysts in a wide range of industrial applications in the production of flavors, pharmaceuticals, biosensors, and fine chemicals. This review will provide insight into mammalian and microbial HSLs, their sources, structural features related to substrate specificity, thermal stability, and their applications.
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Affiliation(s)
- Vijayalakshmi Nagaroor
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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9
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Yan Z, Ding L, Zou D, Qiu J, Shao Y, Sun S, Li L, Xin Z. Characterization of a novel carboxylesterase with catalytic activity toward di(2-ethylhexyl) phthalate from a soil metagenomic library. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147260. [PMID: 33957585 DOI: 10.1016/j.scitotenv.2021.147260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
A novel carboxylesterase gene estyz5 was isolated from a soil metagenomic library. The recombinant enzyme EstYZ5 is 298 amino acids in length with a predicted molecular weight of 32 kDa. Sequence alignment and phylogenetic analysis revealed that EstYZ5 belongs to the hormone-sensitive lipase (HSL) family with a deduced catalytic triad of Ser144-Glu238-His268. EstYZ5 contains two conserved motifs, a pentapeptide motif GDSAG and a HGGG motif, which are typically found in members of the HSL family. Esterolytic activity of the recombinant enzyme was optimal at 30 °C and pH 8.0, and the kcat/Km value of the enzyme for the optimum substrate p-nitrophenyl butyrate was as high as 1272 mM-1·s-1. Importantly, EstYZ5 showed activity toward di(2-ethylhexyl) phthalate with complex side chains, which is rare for HSLs. Molecular docking simulations revealed that the catalytic triad and an oxyanion hole likely play vital roles in enzymatic activity and specificity. The phthalate-degrading activity of EstYZ5, combined with its high levels of esterolytic activity, render this new enzyme a candidate for biotechnological applications.
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Affiliation(s)
- Zhenzhen Yan
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Liping Ding
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Dandan Zou
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiarong Qiu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Longxiang Li
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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10
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Park JE, Jeong GS, Lee HW, Kim H. Molecular Characterization of Novel Family IV and VIII Esterases from a Compost Metagenomic Library. Microorganisms 2021; 9:microorganisms9081614. [PMID: 34442693 PMCID: PMC8399190 DOI: 10.3390/microorganisms9081614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
Two novel esterase genes, est8L and est13L, were isolated and identified from a compost metagenomic library. The encoded Est8L and Est13L had molecular masses of 33,181 and 44,913 Da consisting of 314 and 411 amino acids, respectively, without signal peptides. Est8L showed the highest identity (32.9%) to a hyper-thermophilic carboxylesterase AFEST from Archaeoglobus fulgidus compared to other esterases reported and was classified to be a novel member of family IV esterases with conserved regions such as HGGG, DY, GXSXG, DPL, and GXIH. Est13L showed the highest identity (98.5%) to the family VIII esterase Est7K from the metagenome library. Est8L and Est13L had the highest activities for p-nitrophenyl butyrate (C4) and p-nitrophenyl caproate (C6), respectively, and Est13L showed a broad substrate specificity for p-nitrophenyl substrates. Est8L and Est13L effectively hydrolyzed glyceryl tributyrate. The optimum temperatures for activities of Est8L and Est13L were identical (40 °C), and the optimum pH values were 9.0 and 10.0, respectively. Est13L showed higher thermostability than Est8L. Sephacryl S-200 HR chromatography showed that the native form of Est8L was a dimer. Interestingly, Est13L was found to be a tetramer, contrary to other family VIII esterases reported. Est8L was inhibited by 30% isopropanol, methanol, and acetonitrile; however, Est13L was activated to 182.9% and 356.1%, respectively, by 30% isopropanol and methanol. Est8L showed enantioselectivity for the S-form, but Est13L showed no enantioselectivity. These results show that intracellular Est8L and/or Est13L are oligomeric in terms of native forms and can be used for pharmaceutical and industrial applications with organic solvents under alkaline conditions.
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Affiliation(s)
| | | | | | - Hoon Kim
- Correspondence: ; Tel.: +82-617503751
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11
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Characterization of a Novel Family IV Esterase Containing a Predicted CzcO Domain and a Family V Esterase with Broad Substrate Specificity from an Oil-Polluted Mud Flat Metagenomic Library. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11135905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two novel esterase genes, est2L and est4L, were identified from a previously constructed metagenomic library derived from an oil-polluted mud flat sample. The encoded Est2L and Est4L were composed of 839 and 267 amino acids, respectively, without signal peptides. Est2L was a unique fusion type of protein composed of two domains: a domain of the CzcO superfamily, associated with a cationic diffusion promoter with CzcD, and a domain of the acetylesterase superfamily, belonging to family IV with conserved motifs, such as HGG, GXSAG, and GXPP. Est2L was the first fused esterase with a CzcO domain. Est4L belonged to family V with GXS, GXSMGG, and PTL motifs. Native Est2L and Est4L were found to be in dimeric and tetrameric forms, respectively. Est2L and Est4L showed the highest activities at 60 °C and 50 °C, respectively, and at a pH of 10.0. Est2L preferred short length substrates, especially p-nitrophenyl (pNP)-acetate, with moderate butyrylcholinesterase activity, whereas Est4L showed the highest activity with pNP-decanoate and had broad specificity. Significant effects were not observed in Est2L from Co2+ and Zn2+, although Est2L contains the domain CzcD. Est2L and Est4L showed high stabilities in 30% methanol and 1% Triton X-100. These enzymes could be used for a variety of applications, such as detergent and mining processing under alkaline conditions.
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12
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Identification and characterization of a novel carboxylesterase EstQ7 from a soil metagenomic library. Arch Microbiol 2021; 203:4113-4125. [PMID: 34057548 DOI: 10.1007/s00203-021-02398-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
A novel lipolytic gene, estq7, was identified from a fosmid metagenomic library. The recombinant enzyme EstQ7 consists of 370 amino acids with an anticipated molecular mass of 42 kDa. Multiple sequence alignments showed that EstQ7 contained a pentapeptide motif GHSMG, and a putative catalytic triad Ser174-Asp306-His344. Interestingly, EstQ7 was found to have very little similarity to the characterized lipolytic enzymes. Phylogenetic analysis revealed that EstQ7 may be a member of a novel family of lipolytic enzymes. Biochemical characterization of the recombinant enzyme revealed that it constitutes a slightly alkalophilic, moderate thermophilic and highly active carboxylesterase against short-chain fatty acid esters with optimum temperature 50 ℃ and pH 8.2. The Km and kcat values toward p-nitrophenyl acetate were determined to be 0.17 mM and 1910s-1, respectively. Moreover, EstQ7 was demonstrated to have acyltransferase activity by GC-MS analysis. Structural modeling of the three-dimensional structure of this new enzyme showed that it exhibits a typical α/β hydrolase fold, and the catalytic triad residues are spatially close. Molecular docking revealed the interactions between the enzyme and the ligand. The high levels of lipolytic activity of EstQ7, combined with its moderate thermophilic property and acyltransferase activity, render this novel enzyme a promising candidate biocatalyst for food, pharmaceutical and biotechnological applications.
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Boyko KM, Kryukova MV, Petrovskaya LE, Kryukova EA, Nikolaeva AY, Korzhenevsky DA, Lomakina GY, Novototskaya-Vlasova KA, Rivkina EM, Dolgikh DA, Kirpichnikov MP, Popov VO. Structural and Biochemical Characterization of a Cold-Active PMGL3 Esterase with Unusual Oligomeric Structure. Biomolecules 2021; 11:biom11010057. [PMID: 33466452 PMCID: PMC7824956 DOI: 10.3390/biom11010057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 11/23/2022] Open
Abstract
The gene coding for a novel cold-active esterase PMGL3 was previously obtained from a Siberian permafrost metagenomic DNA library and expressed in Escherichia coli. We elucidated the 3D structure of the enzyme which belongs to the hormone-sensitive lipase (HSL) family. Similar to other bacterial HSLs, PMGL3 shares a canonical α/β hydrolase fold and is presumably a dimer in solution but, in addition to the dimer, it forms a tetrameric structure in a crystal and upon prolonged incubation at 4 °C. Detailed analysis demonstrated that the crystal tetramer of PMGL3 has a unique architecture compared to other known tetramers of the bacterial HSLs. To study the role of the specific residues comprising the tetramerization interface of PMGL3, several mutant variants were constructed. Size exclusion chromatography (SEC) analysis of D7N, E47Q, and K67A mutants demonstrated that they still contained a portion of tetrameric form after heat treatment, although its amount was significantly lower in D7N and K67A compared to the wild type. Moreover, the D7N and K67A mutants demonstrated a 40 and 60% increase in the half-life at 40 °C in comparison with the wild type protein. Km values of these mutants were similar to that of the wt PMGL3. However, the catalytic constants of the E47Q and K67A mutants were reduced by ~40%.
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Affiliation(s)
- Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Correspondence: (K.M.B.); (L.E.P.)
| | - Mariya V. Kryukova
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Lada E. Petrovskaya
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Correspondence: (K.M.B.); (L.E.P.)
| | - Elena A. Kryukova
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
| | - Alena Y. Nikolaeva
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Dmitry A. Korzhenevsky
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Galina Yu. Lomakina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Department of Fundamental Sciences, Bauman Moscow State Technical University, 105005 Moscow, Russia
| | - Ksenia A. Novototskaya-Vlasova
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Elizaveta M. Rivkina
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Dmitry A. Dolgikh
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
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Recazens E, Mouisel E, Langin D. Hormone-sensitive lipase: sixty years later. Prog Lipid Res 2020; 82:101084. [PMID: 33387571 DOI: 10.1016/j.plipres.2020.101084] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 12/24/2020] [Indexed: 12/19/2022]
Abstract
Hormone-sensitive lipase (HSL) was initially characterized as the hormonally regulated neutral lipase activity responsible for the breakdown of triacylglycerols into fatty acids in adipose tissue. This review aims at providing up-to-date information on structural properties, regulation of expression, activity and function as well as therapeutic potential. The lipase is expressed as different isoforms produced from tissue-specific alternative promoters. All isoforms are composed of an N-terminal domain and a C-terminal catalytic domain within which a regulatory domain containing the phosphorylation sites is embedded. Some isoforms possess additional N-terminal regions. The catalytic domain shares similarities with bacteria, fungus and vascular plant proteins but not with other mammalian lipases. HSL singularity is provided by regulatory and N-terminal domains sharing no homology with other proteins. HSL has a broad substrate specificity compared to other neutral lipases. It hydrolyzes acylglycerols, cholesteryl and retinyl esters among other substrates. A novel role of HSL, independent of its enzymatic function, has recently been described in adipocytes. Clinical studies revealed dysregulations of HSL expression and activity in disorders, such as lipodystrophy, obesity, type 2 diabetes and cancer-associated cachexia. Development of specific inhibitors positions HSL as a pharmacological target for the treatment of metabolic complications.
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Affiliation(s)
- Emeline Recazens
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France
| | - Etienne Mouisel
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France
| | - Dominique Langin
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France; Franco-Czech Laboratory for Clinical Research on Obesity, Third Faculty of Medicine, Prague and Paul Sabatier University, Toulouse, France; Toulouse University Hospitals, Laboratory of Clinical Biochemistry, Toulouse, France.
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15
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Sharma P, Tomar R, Yadav SS, Badmalia MD, Nath SK, Ashish, Kundu B. Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property. Sci Rep 2020; 10:21702. [PMID: 33303914 PMCID: PMC7728782 DOI: 10.1038/s41598-020-78877-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
It remains undeciphered how thermophilic enzymes display enhanced stability at elevated temperatures. Taking l-asparaginase from P. furiosus (PfA) as an example, we combined scattering shapes deduced from small-angle X-ray scattering (SAXS) data at increased temperatures with symmetry mates from crystallographic structures to find that heating caused end-to-end association. The small contact point of self-binding appeared to be enabled by a terminal short β-strand in N-terminal domain, Leu179-Val-Val-Asn182 (LVVN). Interestingly, deletion of this strand led to a defunct enzyme, whereas suplementation of the peptide LVVN to the defunct enzyme restored structural frameworkwith mesophile-type functionality. Crystal structure of the peptide-bound defunct enzyme showed that one peptide ispresent in the same coordinates as in original enzyme, explaining gain-of lost function. A second peptide was seen bound to the protein at a different location suggesting its possible role in substrate-free molecular-association. Overall, we show that the heating induced self-assembly of native shapes of PfA led to an apparent super-stable assembly.
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Affiliation(s)
- Pankaj Sharma
- CSIR-Institute of Microbial Technology, Sec 39 A, Chandigarh, 160036, India
| | - Rachana Tomar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | | | - Maulik D Badmalia
- CSIR-Institute of Microbial Technology, Sec 39 A, Chandigarh, 160036, India
| | - Samir Kumar Nath
- CSIR-Institute of Microbial Technology, Sec 39 A, Chandigarh, 160036, India
| | - Ashish
- CSIR-Institute of Microbial Technology, Sec 39 A, Chandigarh, 160036, India.
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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16
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Boyko KM, Kryukova MV, Petrovskaya LE, Nikolaeva AY, Korzhenevsky DA, Novototskaya-Vlasova KA, Rivkina EM, Dolgikh DA, Kirpichnikov MP, Popov VO. Crystal structure of PMGL2 esterase from the hormone-sensitive lipase family with GCSAG motif around the catalytic serine. PLoS One 2020; 15:e0226838. [PMID: 31990908 PMCID: PMC6986724 DOI: 10.1371/journal.pone.0226838] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022] Open
Abstract
Lipases comprise a large class of hydrolytic enzymes which catalyze the cleavage of the ester bonds in triacylglycerols and find numerous biotechnological applications. Previously, we have cloned the gene coding for a novel esterase PMGL2 from a Siberian permafrost metagenomic DNA library. We have determined the 3D structure of PMGL2 which belongs to the hormone-sensitive lipase (HSL) family and contains a new variant of the active site motif, GCSAG. Similar to many other HSLs, PMGL2 forms dimers in solution and in the crystal. Our results demonstrated that PMGL2 and structurally characterized members of the GTSAG motif subfamily possess a common dimerization interface that significantly differs from that of members of the GDSAG subfamily of known structure. Moreover, PMGL2 had a unique organization of the active site cavity with significantly different topology compared to the other lipolytic enzymes from the HSL family with known structure including the distinct orientation of the active site entrances within the dimer and about four times larger size of the active site cavity. To study the role of the cysteine residue in GCSAG motif of PMGL2, the catalytic properties and structure of its double C173T/C202S mutant were examined and found to be very similar to the wild type protein. The presence of the bound PEG molecule in the active site of the mutant form allowed for precise mapping of the amino acid residues forming the substrate cavity.
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Affiliation(s)
- Konstantin M. Boyko
- Department of Enzyme Engineering, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marya V. Kryukova
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Lada E. Petrovskaya
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena Y. Nikolaeva
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dmitry A. Korzhenevsky
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ksenia A. Novototskaya-Vlasova
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Elizaveta M. Rivkina
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Dmitry A. Dolgikh
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir O. Popov
- Department of Enzyme Engineering, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
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Biochemical characterization of an esterase from Clostridium acetobutylicum with novel GYSMG pentapeptide motif at the catalytic domain. J Ind Microbiol Biotechnol 2019; 47:169-181. [PMID: 31807968 DOI: 10.1007/s10295-019-02253-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
Gene CA_C0816 codes for a serine hydrolase protein from Clostridium acetobutylicum (ATCC 824) a member of hormone-sensitive lipase of lipolytic family IV. This gene was overexpressed in E. coli strain BL21and purified using Ni2+-NTA affinity chromatography. Size exclusion chromatography revealed that the protein is a dimer in solution. Optimum pH and temperature for recombinant Clostridium acetobutylicum esterase (Ca-Est) were found to be 7.0 and 60 °C, respectively. This enzyme exhibited high preference for p-nitrophenyl butyrate. KM and kcat/KM of the enzyme were 24.90 µM and 25.13 s-1 µM-1, respectively. Sequence analysis of Ca-Est predicts the presence of catalytic amino acids Ser 89, His 224, and Glu 196, presence of novel GYSMG conserved sequence (instead of GDSAG and GTSAG motif), and undescribed variation of HGSG motif. Site-directed mutagenesis confirmed that Ser 89 and His 224 play a major role in catalysis. This study reports that Ca-Est is hormone-sensitive lipase with novel GYSMG pentapeptide motif at a catalytic domain.
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18
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Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability. N Biotechnol 2019; 53:65-72. [DOI: 10.1016/j.nbt.2019.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/24/2019] [Accepted: 07/07/2019] [Indexed: 01/05/2023]
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19
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Screening, Isolation and Identification of Thermophilic Esterase Enzyme Isolated from Rhodococcus SP: LKE-021. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.3.63] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Dachuri V, Truongvan N, DangThu Q, Jang SH, Lee C. Distinct roles of an ionic interaction holding an alpha-helix with catalytic Asp and a beta-strand with catalytic His in a hyperthermophilic esterase EstE1 and a mesophilic esterase rPPE. Extremophiles 2019; 23:649-657. [PMID: 31332517 DOI: 10.1007/s00792-019-01115-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
Abstract
An ionic interaction that holds an α-helix and a β-strand on which catalytic Asp and His residues are located, respectively, is conserved in a hyperthermophilic esterase EstE1 (optimum temperature 70 °C) and a mesophilic esterase rPPE (optimum temperature 50 °C). We investigated the role of an ionic interaction between E258 and R275 in EstE1 and that between E263 and R280 in rPPE in active-site stability of serine esterases adapted to different temperatures. Ala substitutions caused a 5-10 °C decrease in the optimum temperature of both EstE1 and rPPE mutants. Surprisingly, disruption of the ionic interaction caused larger effects on the conformational flexibility of EstE1 mutants despite their rigid structures, whereas the disruption had fewer effects on the thermal stability of EstE1 mutants at 60-70 °C, as the structure of EstE1 was adapted to high temperatures. In contrast, mesophilic rPPE mutants showed dramatic decreases in thermal stability at 40-50 °C, but less changes in conformational flexibility because of their inherently flexible structures. The results of this study suggest that the ionic interaction between the α-helix with catalytic Asp and the β-strand with catalytic His plays an important role in the active-site conformation of EstE1 and rPPE, with larger effects on the conformational flexibility of hyperthermophilic EstE1 and the thermal stability of mesophilic rPPE.
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Affiliation(s)
- VinayKumar Dachuri
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, 38453, South Korea
- Research Center for Herbal Convergence on Liver Disease, Daegu Haany University, Gyeongsan, 38578, South Korea
| | - Ngoc Truongvan
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, 38453, South Korea
| | - Quynh DangThu
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, 38453, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, 38453, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, 38453, South Korea.
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Two Novel Acetylesterases from Pantoea dispersa: Recombinant Expression, Purification, and Characterization. Appl Biochem Biotechnol 2019; 189:834-854. [PMID: 31127451 DOI: 10.1007/s12010-019-03024-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022]
Abstract
Two novel acetylesterases from Pantoea dispersa, with low amino acid sequence identity between them, were expressed in Escherichia coli with a carboxyl-His6 tail given by the expression plasmid, purified, and characterized. The purified proteins, named Est-1 and Est-2, had a molecular mass of 33 kDa and 37 kDa, respectively. Both proteins presented a modeled structure of homodimers with monomers presenting the α/β-hydrolase fold, with the catalytic triad Ser-Asp-His present in the active site. The KM for p-nitrophenyl acetate and Vmax values found for Est-1 were of 1.4 ± 0.2 mM and 8.66 ± 0.59 μmol/min and for Est-2 were of 0.36 ± 0.077 mM and 6.13 ± 0.56 μmol/min, respectively. Both enzymes presented an optimum pH of 7.0. The optimum temperature for Est-1 was 40 °C and for Est-2 was 50 °C. The temperatures in which the enzymes Est-1 and Est-2 lost half of their activity (T50) were 44.1 and 58.9 °C, respectively. SDS, EDTA, and PMSF significantly inhibited the enzymes. The two purified enzymes also presented activity against triacetin and were able to deacetylate the carbohydrates pectin and xylan, with higher activity against pectin. Thus, they could be considered as carbohydrate esterases.
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Characterization and mutation anaylsis of a cold-active bacterial hormone-sensitive lipase from Salinisphaera sp. P7-4. Arch Biochem Biophys 2019; 663:132-142. [DOI: 10.1016/j.abb.2019.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 11/18/2022]
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23
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Mo HM, Xu Y, Yu XW. Improved Soluble Expression and Catalytic Activity of a Thermostable Esterase Using a High-Throughput Screening System Based on a Split-GFP Assembly. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12756-12764. [PMID: 30411620 DOI: 10.1021/acs.jafc.8b04646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The thermostable esterase Aaeo1 displays a low expression level and forms a great amount of inclusion bodies in E. coli. Herein, a split-GFP system was established in which the fluorescence intensity exhibited a good linear correlation with the soluble protein expression level and the esterase activity. In the primary high-throughput screening, the mutant library was screened by flow cytometry via detection of a split-GFP reporter. Then, through a secondary screening against esterase activity, two mutants with improved soluble expression and catalytic activity were obtained. The soluble expression of the mutant enzymes in E. coli was improved by 2-fold. The kcat/ Km values of the mutant enzymes were 2-fold higher than that of the parent. We explored the relationship between the amino acid mutations in the two mutants and the enzyme activity. The enzyme activity of mutant I51V-E170D was 4.5 times higher than that of the parent.
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Affiliation(s)
- Hong-Mei Mo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , PR China
- Suqian Industrial Technology Research Institute of Jiangnan University , Suqian 223814 , PR China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , PR China
- Suqian Industrial Technology Research Institute of Jiangnan University , Suqian 223814 , PR China
| | - Xiao-Wei Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi 214122 , PR China
- Suqian Industrial Technology Research Institute of Jiangnan University , Suqian 223814 , PR China
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Álvarez-Cao ME, González R, Pernas MA, Rúa ML. Contribution of the Oligomeric State to the Thermostability of Isoenzyme 3 from Candida rugosa. Microorganisms 2018; 6:E108. [PMID: 30347699 PMCID: PMC6313406 DOI: 10.3390/microorganisms6040108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
Thermophilic proteins have evolved different strategies to maintain structure and function at high temperatures; they have large, hydrophobic cores, and feature increased electrostatic interactions, with disulfide bonds, salt-bridging, and surface charges. Oligomerization is also recognized as a mechanism for protein stabilization to confer a thermophilic adaptation. Mesophilic proteins are less thermostable than their thermophilic homologs, but oligomerization plays an important role in biological processes on a wide variety of mesophilic enzymes, including thermostabilization. The mesophilic yeast Candida rugosa contains a complex family of highly related lipase isoenzymes. Lip3 has been purified and characterized in two oligomeric states, monomer (mLip3) and dimer (dLip3), and crystallized in a dimeric conformation, providing a perfect model for studying the effects of homodimerization on mesophilic enzymes. We studied kinetics and stability at different pHs and temperatures, using the response surface methodology to compare both forms. At the kinetic level, homodimerization expanded Lip3 specificity (serving as a better catalyst on soluble substrates). Indeed, dimerization increased its thermostability by more than 15 °C (maximum temperature for dLip3 was out of the experimental range; >50 °C), and increased the pH stability by nearly one pH unit, demonstrating that oligomerization is a viable strategy for the stabilization of mesophilic enzymes.
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Affiliation(s)
- María-Efigenia Álvarez-Cao
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
| | - Roberto González
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
| | - María A Pernas
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
| | - María Luisa Rúa
- Department of Food and Analytical Chemistry, Sciences Faculty of Ourense, University of Vigo, As Lagoas s/n, 32004 Ourense, Spain.
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25
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Ke M, Ramesh B, Hang Y, Liu Z. Engineering and characterization of a novel low temperature active and thermo stable esterase from marine Enterobacter cloacae. Int J Biol Macromol 2018; 118:304-310. [DOI: 10.1016/j.ijbiomac.2018.05.193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/23/2018] [Accepted: 05/26/2018] [Indexed: 10/16/2022]
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26
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Noby N, Saeed H, Embaby AM, Pavlidis IV, Hussein A. Cloning, expression and characterization of cold active esterase (EstN7) from Bacillus cohnii strain N1: A novel member of family IV. Int J Biol Macromol 2018; 120:1247-1255. [PMID: 30063933 DOI: 10.1016/j.ijbiomac.2018.07.169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 01/11/2023]
Abstract
Esterases and lipases from extremophiles have attracted great attention due to their unique characteristics and wide applications. In the present study, an open reading frame (ORF) encoding a novel cold active esterase (EstN7) from Bacillus cohnii strain N1 was cloned and expressed in Escherichia coli. The full-length esterase gene encoding a protein of 320 amino acids with estimated molecular weight of 37.0 kDa. Amino acid sequence analysis revealed that the EstN7 belongs to family IV lipases with a characteristic penta-peptide motif (GXSXG), the catalytic triad Ser, Asp, His and the conserved HGGG motif of the family IV. The recombinant enzyme was purified to apparent homogeneity using nickel-affinity chromatography with a purification fold of 5 and recovery 94.5%. The specific activity of the purified enzyme was 336.89 U/mg. The recombinant EstN7 showed optimal activity at 5 °C moreover, EstN7 displayed full robust stability in the presence of wide range of organic solvents. The purified enzyme had Km and Vmax of 45 ± 0.019 μM and 1113 μmol min-1 mg-1, respectively on p-NP-acetate. These promising characteristics of the recombinant EstN7 would underpin its possible usage with high potential in the synthesis of fragile compounds in pharmaceutical industries.
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Affiliation(s)
- Nehad Noby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt.
| | - Hesham Saeed
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt.
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | | | - Ahmed Hussein
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
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27
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De Waele S, Vandenberghe I, Laukens B, Planckaert S, Verweire S, Van Bogaert I, Soetaert W, Devreese B, Ciesielska K. Optimized expression of the Starmerella bombicola lactone esterase in Pichia pastoris through temperature adaptation, codon-optimization and co-expression with HAC1. Protein Expr Purif 2018; 143:62-70. [DOI: 10.1016/j.pep.2017.10.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/18/2017] [Accepted: 10/30/2017] [Indexed: 12/27/2022]
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28
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Varejão N, De-Andrade RA, Almeida RV, Anobom CD, Foguel D, Reverter D. Structural Mechanism for the Temperature-Dependent Activation of the Hyperthermophilic Pf2001 Esterase. Structure 2018; 26:199-208.e3. [PMID: 29307486 DOI: 10.1016/j.str.2017.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 09/28/2017] [Accepted: 12/06/2017] [Indexed: 10/18/2022]
Abstract
Lipases and esterases constitute a group of enzymes that catalyze the hydrolysis or synthesis of ester bonds. A major biotechnological interest corresponds to thermophilic esterases, due to their intrinsic stability at high temperatures. The Pf2001 esterase from Pyrococcus furiosus reaches its optimal activity between 70°C and 80°C. The crystal structure of the Pf2001 esterase shows two different conformations: monomer and dimer. The structures reveal important rearrangements in the "cap" subdomain between monomer and dimer, by the formation of an extensive intertwined helical interface. Moreover, the dimer interface is essential for the formation of the hydrophobic channel for substrate selectivity, as confirmed by mutagenesis and kinetic analysis. We also provide evidence for dimer formation at high temperatures, a process that correlates with its enzymatic activation. Thus, we propose a temperature-dependent activation mechanism of the Pf2001 esterase via dimerization that is necessary for the substrate channel formation in the active-site cleft.
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Affiliation(s)
- Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina and Departamento de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain; Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Rafael A De-Andrade
- Instituto de Química, Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil
| | - Rodrigo V Almeida
- Instituto de Química, Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil
| | - Cristiane D Anobom
- Instituto de Química, Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio de Janeiro, 21941-909 Rio de Janeiro, Brazil
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, RJ, Brazil.
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Departamento de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain.
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Kashif A, Tran LH, Jang SH, Lee C. Roles of Active-Site Aromatic Residues in Cold Adaptation of Sphingomonas glacialis Esterase EstSP1. ACS OMEGA 2017; 2:8760-8769. [PMID: 31457406 PMCID: PMC6645578 DOI: 10.1021/acsomega.7b01435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/23/2017] [Indexed: 06/10/2023]
Abstract
The aromatic amino acids, Tyr or Trp, which line the active-site walls of esterases, stabilize the catalytic His loop via hydrogen bonding. A Tyr residue is preferred in extremophilic esterases (psychrophilic or hyperthermophilic esterases), whereas a Trp residue is preferred in moderate-temperature esterases. Here, we provide evidence that Tyr and Trp play distinct roles in cold adaptation of the psychrophilic esterase EstSP1 isolated from an Arctic bacterium Sphingomonas glacialis PAMC 26605. Stern-Volmer plots showed that the mutation of Tyr191 to Ala, Phe, Trp, and His resulted in reduced conformational flexibility of the overall protein structure. Interestingly, the Y191W and Y191H mutants showed increased thermal stability at moderate temperatures. All Tyr191 mutants showed reduced catalytic activity relative to wild-type EstSP1. Our results indicate that Tyr with its phenyl hydroxyl group is favored for increased conformational flexibility and high catalytic activity of EstSP1 at low temperatures at the expense of thermal stability. The results of this study suggest that, in the permanently cold Arctic zone, enzyme activity has been selected for psychrophilic enzymes over thermal stability. The results presented herein provide novel insight into the roles of Tyr and Trp residues for temperature adaptation of enzymes that function at low, moderate, and high temperatures.
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Affiliation(s)
| | | | | | - ChangWoo Lee
- E-mail: . Tel: +82-53-850-6464. Fax: +82-53-850-6469
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Murakami M, Saito M, Yokobori H, Nishimura K, Tanigawa M, Nagata Y. Involvement of C-terminal amino acids of a hyperthermophilic serine racemase in its thermostability. Extremophiles 2017; 22:99-107. [PMID: 29124361 DOI: 10.1007/s00792-017-0980-9] [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: 06/29/2017] [Accepted: 11/03/2017] [Indexed: 11/27/2022]
Abstract
Pyrobaculum islandicum is a hyperthermophilic archaeon that grows optimally at 95-100 °C. In the previous study, we extensively purified a serine racemase from this organism and cloned the gene for overexpression in Escherichia coli (Ohnishi et al. 2008). This enzyme also exhibits highly thermostable L-serine/L-threonine dehydratase activity. In the present study, we aimed to elucidate the molecular mechanisms underlying the high thermostability of this enzyme. A recombinant variant of this enzyme, PiSRvt, constructed by truncating the C-terminal 72 amino acids, was compared with the native enzyme, PiSR. The dehydratase activity of PiSR and PiSRvt was found to owe to a homotrimer and a monomer, respectively, that demonstrated high and moderate thermostability, respectively. These observations reveal that the C-terminal region contributes to monomer trimerization that provides the extreme thermostability.
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Affiliation(s)
- Masahito Murakami
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Chiyoda-Ward, Tokyo, 101-8308, Japan
| | - Makoto Saito
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Chiyoda-Ward, Tokyo, 101-8308, Japan
| | - Hirokazu Yokobori
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Chiyoda-Ward, Tokyo, 101-8308, Japan
| | - Katsushi Nishimura
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Chiyoda-Ward, Tokyo, 101-8308, Japan
| | - Minoru Tanigawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Chiyoda-Ward, Tokyo, 101-8308, Japan
| | - Yoko Nagata
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, Chiyoda-Ward, Tokyo, 101-8308, Japan.
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Structural and Mechanistic Insights into the Improvement of the Halotolerance of a Marine Microbial Esterase by Increasing Intra- and Interdomain Hydrophobic Interactions. Appl Environ Microbiol 2017; 83:AEM.01286-17. [PMID: 28733281 DOI: 10.1128/aem.01286-17] [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: 06/08/2017] [Accepted: 07/12/2017] [Indexed: 11/20/2022] Open
Abstract
Halotolerant enzymes are beneficial for industrial processes requiring high salt concentrations and low water activity. Most halophilic proteins are evolved to have reduced hydrophobic interactions on the surface and in the hydrophobic cores for their haloadaptation. However, in this study, we improved the halotolerance of a thermolabile esterase, E40, by increasing intraprotein hydrophobic interactions. E40 was quite unstable in buffers containing more than 0.3 M NaCl, and its kcat and substrate affinity were both significantly reduced in 0.5 M NaCl. By introducing hydrophobic residues in loop 1 of the CAP domain and/or α7 of the catalytic domain in E40, we obtained several mutants with improved halotolerance, and the M3 S202W I203F mutant was the most halotolerant. ("M3" represents a mutation in loop 1 of the CAP domain in which residues R22-K23-T24 of E40 are replaced by residues Y22-K23-H24-L25-S26 of Est2.) Then we solved the crystal structures of the S202W I203F and M3 S202W I203F mutants to reveal the structural basis for their improved halotolerance. Structural analysis revealed that the introduction of hydrophobic residues W202 and F203 in α7 significantly improved E40 halotolerance by strengthening intradomain hydrophobic interactions of F203 with W202 and other residues in the catalytic domain. By further introducing hydrophobic residues in loop 1, the M3 S202W I203F mutant became more rigid and halotolerant due to the formation of additional interdomain hydrophobic interactions between the introduced Y22 in loop 1 and W204 in α7. These results indicate that increasing intraprotein hydrophobic interactions is also a way to improve the halotolerance of enzymes with industrial potential under high-salt conditions.IMPORTANCE Esterases and lipases for industrial application are often subjected to harsh conditions such as high salt concentrations, low water activity, and the presence of organic solvents. However, reports on halotolerant esterases and lipases are limited, and the underlying mechanism for their halotolerance is still unclear due to the lack of structures. In this study, we focused on the improvement of the halotolerance of a salt-sensitive esterase, E40, and the underlying mechanism. The halotolerance of E40 was significantly improved by introducing hydrophobic residues. Comparative structural analysis of E40 and its halotolerant mutants revealed that increased intraprotein hydrophobic interactions make these mutants more rigid and more stable than the wild type against high concentrations of salts. This study shows a new way to improve enzyme halotolerance, which is helpful for protein engineering of salt-sensitive enzymes.
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A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mychorrizal fungus Tuber melanosporum. Sci Rep 2017; 7:7628. [PMID: 28794466 PMCID: PMC5550427 DOI: 10.1038/s41598-017-08007-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
An increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative “lipases/esterases” preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum (“black truffle”), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters. TmelEST2 was the most active (kcat = 2302 s−1 for p-nitrophenyl-butyrate) and thermally stable (T50 = 68.3 °C), while TmelEST3 was the only one displaying some activity on tertiary alcohol esters. X-ray diffraction analysis of TmelEST2 revealed a classical α/β hydrolase-fold structure, with a network of dimer-stabilizing intermolecular interactions typical of archaea esterases. The predicted structures of TmelEST1 and 3 are overall quite similar to that of TmelEST2 but with some important differences. Most notably, the much smaller volume of the substrate-binding pocket and the more acidic electrostatic surface profile of TmelEST1. This was also the only TmelEST capable of hydrolyzing feruloyl-esters, suggestinng a possible role in root cell-wall deconstruction during symbiosis establishment. In addition to their potential biotechnological interest, TmelESTs raise important questions regarding the evolutionary recruitment of archaea-like enzymes into mesophilic subterranean fungi such as truffles.
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33
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Pereira MR, Maester TC, Mercaldi GF, de Macedo Lemos EG, Hyvönen M, Balan A. From a metagenomic source to a high-resolution structure of a novel alkaline esterase. Appl Microbiol Biotechnol 2017; 101:4935-4949. [PMID: 28331945 DOI: 10.1007/s00253-017-8226-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 02/27/2017] [Accepted: 03/05/2017] [Indexed: 10/19/2022]
Abstract
Esterases catalyze the cleavage and formation of ester bonds and are members of the diverse family of α/β hydrolase fold. They are useful in industries from different sectors, such as food, detergent, fine chemicals, and biofuel production. In a previous work, 30 positive clones for lipolytic activity were identified from a metagenomic library of a microbial consortium specialized in diesel oil degradation. In this study, a putative gene encoding an esterase/lipase, denominated est8, has been cloned and the corresponding protein expressed recombinantly, purified to homogeneity and characterized functional and structurally. We show that the protein codified by est8 gene, denominated Est8, is an alkaline esterase with high catalytic efficiency against p-nitrophenyl acetate and stable in the presence of up to 10% dimethyl sulfoxide. The three-dimensional structure of Est8 was determined at 1.85-Ǻ resolution, allowing the characterization of the substrate-binding pocket and features that rationalize the preference of Est8 for short-chain substrates. In an attempt to increase the size of ligand-binding pocket and enzyme activity against distinct substrates of long chain, we mutated two residues (Met213 and Phe217) that block the substrate channel. A small increase in the reaction velocity for p-nitrophenyl butyrate and p-nitrophenyl valerate hydrolysis was observed. Activity against p-nitrophenyl acetate was reduced. The functional and structural characterization of Est8 is explored in comparison with orthologues.
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Affiliation(s)
- Mariana Rangel Pereira
- National Laboratory of Biosciences (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo State, Brazil.,University of São Paulo (USP), São Paulo, São Paulo State, Brazil.,Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State, Brazil
| | - Thaís Carvalho Maester
- University of São Paulo (USP), São Paulo, São Paulo State, Brazil.,Department of Technology, São Paulo State University (UNESP), Jaboticabal, São Paulo State, Brazil
| | - Gustavo Fernando Mercaldi
- National Laboratory of Biosciences (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo State, Brazil.,Institute of Biology, University of Campinas, Campinas, São Paulo State, Brazil
| | | | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Balan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Choi YH, Lee YN, Park YJ, Yoon SJ, Lee HB. Identification of amino acids related to catalytic function of Sulfolobus solfataricus P1 carboxylesterase by site-directed mutagenesis and molecular modeling. BMB Rep 2017; 49:349-54. [PMID: 27222124 PMCID: PMC5070724 DOI: 10.5483/bmbrep.2016.49.6.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Indexed: 11/21/2022] Open
Abstract
The archaeon Sulfolobus solfataricus P1 carboxylesterase is a thermostable enzyme with a molecular mass of 33.5 kDa belonging to the mammalian hormone-sensitive lipase (HSL) family. In our previous study, we purified the enzyme and suggested the expected amino acids related to its catalysis by chemical modification and a sequence homology search. For further validating these amino acids in this study, we modified them using site-directed mutagenesis and examined the activity of the mutant enzymes using spectrophotometric analysis and then estimated by homology modeling and fluorescence analysis. As a result, it was identified that Ser151, Asp244, and His274 consist of a catalytic triad, and Gly80, Gly81, and Ala152 compose an oxyanion hole of the enzyme. In addition, it was also determined that the cysteine residues are located near the active site or at the positions inducing any conformational changes of the enzyme by their replacement with serine residues. [BMB Reports 2016; 49(6): 349-354]
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Affiliation(s)
- Yun-Ho Choi
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Ye-Na Lee
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Young-Jun Park
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Sung-Jin Yoon
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Hee-Bong Lee
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Korea
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35
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A novel, versatile family IV carboxylesterase exhibits high stability and activity in a broad pH spectrum. Biotechnol Lett 2017; 39:577-587. [DOI: 10.1007/s10529-016-2282-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
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36
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Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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McKary MG, Abendroth J, Edwards TE, Johnson RJ. Structural Basis for the Strict Substrate Selectivity of the Mycobacterial Hydrolase LipW. Biochemistry 2016; 55:7099-7111. [PMID: 27936614 DOI: 10.1021/acs.biochem.6b01057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex life cycle of Mycobacterium tuberculosis requires diverse energy mobilization and utilization strategies facilitated by a battery of lipid metabolism enzymes. Among lipid metabolism enzymes, the Lip family of mycobacterial serine hydrolases is essential to lipid scavenging, metabolic cycles, and reactivation from dormancy. On the basis of the homologous rescue strategy for mycobacterial drug targets, we have characterized the three-dimensional structure of full length LipW from Mycobacterium marinum, the first structure of a catalytically active Lip family member. LipW contains a deep, expansive substrate-binding pocket with only a narrow, restrictive active site, suggesting tight substrate selectivity for short, unbranched esters. Structural alignment reinforced this strict substrate selectivity of LipW, as the binding pocket of LipW aligned most closely with the bacterial acyl esterase superfamily. Detailed kinetic analysis of two different LipW homologues confirmed this strict substrate selectivity, as each homologue selected for unbranched propionyl ester substrates, irrespective of the alcohol portion of the ester. Using comprehensive substitutional analysis across the binding pocket, the strict substrate selectivity of LipW for propionyl esters was assigned to a narrow funnel in the acyl-binding pocket capped by a key hydrophobic valine residue. The polar, negatively charged alcohol-binding pocket also contributed to substrate orientation and stabilization of rotameric states in the catalytic serine. Together, the structural, enzymatic, and substitutional analyses of LipW provide a connection between the structure and metabolic properties of a Lip family hydrolase that refines its biological function in active and dormant tuberculosis infection.
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Affiliation(s)
- Magy G McKary
- Department of Chemistry, Butler University , 4600 Sunset Avenue, Indianapolis, Indiana 46208, United States
| | - Jan Abendroth
- Beryllium Discovery Corporation, Seattle Structural Genomics Center for Infectious Disease (SSGCID) , 7869 Northeast Day Road West, Bainbridge Island, Washington 98110, United States
| | - Thomas E Edwards
- Beryllium Discovery Corporation, Seattle Structural Genomics Center for Infectious Disease (SSGCID) , 7869 Northeast Day Road West, Bainbridge Island, Washington 98110, United States
| | - R Jeremy Johnson
- Department of Chemistry, Butler University , 4600 Sunset Avenue, Indianapolis, Indiana 46208, United States
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Hong DK, Jang SH, Lee C. Gene cloning and characterization of a psychrophilic phthalate esterase with organic solvent tolerance from an Arctic bacterium Sphingomonas glacialis PAMC 26605. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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39
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Huang J, Huo YY, Ji R, Kuang S, Ji C, Xu XW, Li J. Structural insights of a hormone sensitive lipase homologue Est22. Sci Rep 2016; 6:28550. [PMID: 27328716 PMCID: PMC4916508 DOI: 10.1038/srep28550] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Hormone sensitive lipase (HSL) catalyzes the hydrolysis of triacylglycerols into fatty acids and glycerol, thus playing key roles in energy homeostasis. However, the application of HSL serving as a pharmaceutical target and an industrial biocatalyst is largely hampered due to the lack of high-resolution structural information. Here we report biochemical properties and crystal structures of a novel HSL homologue esterase Est22 from a deep-sea metagenomic library. Est22 prefers short acyl chain esters and has a very high activity with substrate p-nitrophenyl butyrate. The crystal structures of wild type and mutated Est22 with its product p-nitrophenol are solved with resolutions ranging from 1.4 Å to 2.43 Å. The Est22 exhibits a α/β-hydrolase fold consisting with a catalytic domain and a substrate-recognizing cap domain. Residues Ser188, Asp287, and His317 comprise the catalytic triad in the catalytic domain. The p-nitrophenol molecule occupies the substrate binding pocket and forms hydrogen bonds with adjacent residues Gly108, Gly109, and Gly189. Est22 exhibits a dimeric form in solution, whereas mutants D287A and H317A change to polymeric form, which totally abolished its enzymatic activities. Our study provides insights into the catalytic mechanism of HSL family esterase and facilitates the understanding for further industrial and biotechnological applications of esterases.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Siyun Kuang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China,
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China,
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40
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Conserved tyrosine 182 residue in hyperthermophilic esterase EstE1 plays a critical role in stabilizing the active site. Extremophiles 2016; 20:187-93. [DOI: 10.1007/s00792-016-0812-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/15/2016] [Indexed: 12/12/2022]
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41
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Trading off stability against activity in extremophilic aldolases. Sci Rep 2016; 6:17908. [PMID: 26783049 PMCID: PMC4725968 DOI: 10.1038/srep17908] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/06/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms. We present the first crystal structures of psychrophilic DERAs, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts. Conversion into monomeric proteins showed that the native dimer interface contributes to stability only in the hyperthermophilic enzymes. Nevertheless, introduction of a disulfide bridge in the interface of a psychrophilic DERA did confer increased thermostability, suggesting a strategy for rational design of more durable enzyme variants. Constraint network analysis revealed particularly sparse interactions between the substrate pocket and its surrounding α-helices in psychrophilic DERAs, which indicates that a more flexible active center underlies their high turnover numbers.
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42
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Sayer C, Szabo Z, Isupov MN, Ingham C, Littlechild JA. The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta terrifontis Reveals an Open Active Site Due to a Minimal 'Cap' Domain. Front Microbiol 2015; 6:1294. [PMID: 26635762 PMCID: PMC4655241 DOI: 10.3389/fmicb.2015.01294] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 11/29/2022] Open
Abstract
A carboxyl esterase (TtEst2) has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterized biochemically and shown to have activity toward small p-nitrophenyl (pNP) carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 min at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate, and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalized based upon the properties of their active site pockets.
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Affiliation(s)
- Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | | | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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43
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Cao LC, Chen R, Xie W, Liu YH. Enhancing the Thermostability of Feruloyl Esterase EstF27 by Directed Evolution and the Underlying Structural Basis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:8225-33. [PMID: 26329893 DOI: 10.1021/acs.jafc.5b03424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
To improve the thermostability of EstF27, two rounds of random mutagenesis were performed. A thermostable mutant, M6, with six amino acid substitutions was obtained. The half-life of M6 at 55 °C is 1680 h, while that of EstF27 is 0.5 h. The Kcat/Km value of M6 is 1.9-fold higher than that of EstF27. The concentrations of ferulic acid released from destarched wheat bran by EstF27 and M6 at their respective optimal temperatures were 223.2 ± 6.8 and 464.8 ± 11.9 μM, respectively. To further understand the structural basis of the enhanced thermostability, the crystal structure of M6 is determined at 2.0 Å. Structural analysis shows that a new disulfide bond and hydrophobic interactions formed by the mutations may play an important role in stabilizing the protein. This study not only provides us with a robust catalyst, but also enriches our knowledge about the structure-function relationship of feruloyl esterase.
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Affiliation(s)
- Li-chuang Cao
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
| | - Ran Chen
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
| | - Wei Xie
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
| | - Yu-huan Liu
- School of Life Sciences, ‡State Key Laboratory for Biocontrol, School of Life Sciences, and §South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou 510275, People's Republic of China
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44
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Yang S, Qin Z, Duan X, Yan Q, Jiang Z. Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei. J Lipid Res 2015; 56:1616-24. [PMID: 26108223 PMCID: PMC4514002 DOI: 10.1194/jlr.m060673] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 01/19/2023] Open
Abstract
Two hormone-sensitive lipase (HSL) family esterases (RmEstA and RmEstB) from the thermophilic fungus Rhizomucor miehei, exhibiting distinct substrate specificity, have been recently reported to show great potential in industrial applications. In this study, the crystal structures of RmEstA and RmEstB were determined at 2.15 Å and 2.43 Å resolutions, respectively. The structures of RmEstA and RmEstB showed two distinctive domains, a catalytic domain and a cap domain, with the classical α/β-hydrolase fold. Catalytic triads consisting of residues Ser161, Asp262, and His292 in RmEstA, and Ser164, Asp261, and His291 in RmEstB were found in the respective canonical positions. Structural comparison of RmEstA and RmEstB revealed that their distinct substrate specificity might be attributed to their different substrate-binding pockets. The aromatic amino acids Phe222 and Trp92, located in the center of the substrate-binding pocket of RmEstB, blocked this pocket, thus narrowing its catalytic range for substrates (C2–C8). Two mutants (F222A and W92F in RmEstB) showing higher catalytic activity toward long-chain substrates further confirmed the hypothesized interference. This is the first report of HSL family esterase structures from filamentous fungi.jlr The information on structure-function relationships could open important avenues of exploration for further industrial applications of esterases.
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Affiliation(s)
- Shaoqing Yang
- College of Food Science and Nutritional Engineering, The Research and Innovation Center of Food Nutrition and Human Health (Beijing), China Agricultural University, Beijing 100083, China
| | - Zhen Qin
- College of Food Science and Nutritional Engineering, The Research and Innovation Center of Food Nutrition and Human Health (Beijing), China Agricultural University, Beijing 100083, China
| | - Xiaojie Duan
- College of Food Science and Nutritional Engineering, The Research and Innovation Center of Food Nutrition and Human Health (Beijing), China Agricultural University, Beijing 100083, China
| | - Qiaojuan Yan
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, The Research and Innovation Center of Food Nutrition and Human Health (Beijing), China Agricultural University, Beijing 100083, China
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45
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Li PY, Chen XL, Ji P, Li CY, Wang P, Zhang Y, Xie BB, Qin QL, Su HN, Zhou BC, Zhang YZ, Zhang XY. Interdomain hydrophobic interactions modulate the thermostability of microbial esterases from the hormone-sensitive lipase family. J Biol Chem 2015; 290:11188-98. [PMID: 25771540 DOI: 10.1074/jbc.m115.646182] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 12/11/2022] Open
Abstract
Microbial hormone-sensitive lipases (HSLs) contain a CAP domain and a catalytic domain. However, it remains unclear how the CAP domain interacts with the catalytic domain to maintain the stability of microbial HSLs. Here, we isolated an HSL esterase, E40, from a marine sedimental metagenomic library. E40 exhibited the maximal activity at 45 °C and was quite thermolabile, with a half-life of only 2 min at 40 °C, which may be an adaptation of E40 to the permanently cold sediment environment. The structure of E40 was solved to study its thermolability. Structural analysis showed that E40 lacks the interdomain hydrophobic interactions between loop 1 of the CAP domain and α7 of the catalytic domain compared with its thermostable homologs. Mutational analysis showed that the introduction of hydrophobic residues Trp(202) and Phe(203) in α7 significantly improved E40 stability and that a further introduction of hydrophobic residues in loop 1 made E40 more thermostable because of the formation of interdomain hydrophobic interactions. Altogether, the results indicate that the absence of interdomain hydrophobic interactions between loop 1 and α7 leads to the thermolability of E40. In addition, a comparative analysis of the structures of E40 and other thermolabile and thermostable HSLs suggests that the interdomain hydrophobic interactions between loop 1 and α7 are a key element for the thermostability of microbial HSLs. Therefore, this study not only illustrates the structural element leading to the thermolability of E40 but also reveals a structural determinant for HSL thermostability.
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Affiliation(s)
- Ping-Yi Li
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Peng Ji
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Chun-Yang Li
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Peng Wang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Yi Zhang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Bin-Bin Xie
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Qi-Long Qin
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Hai-Nan Su
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Bai-Cheng Zhou
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Yu-Zhong Zhang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
| | - Xi-Ying Zhang
- From the State Key Laboratory of Microbial Technology and the Marine Biotechnology Research Center, Shandong University, Jinan 250100, China
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46
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Boyineni J, Kim J, Kang BS, Lee C, Jang SH. Enhanced catalytic site thermal stability of cold-adapted esterase EstK by a W208Y mutation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1076-82. [DOI: 10.1016/j.bbapap.2014.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/10/2014] [Accepted: 03/17/2014] [Indexed: 12/12/2022]
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47
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Li PY, Ji P, Li CY, Zhang Y, Wang GL, Zhang XY, Xie BB, Qin QL, Chen XL, Zhou BC, Zhang YZ. Structural basis for dimerization and catalysis of a novel esterase from the GTSAG motif subfamily of the bacterial hormone-sensitive lipase family. J Biol Chem 2014; 289:19031-41. [PMID: 24867954 DOI: 10.1074/jbc.m114.574913] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Hormone-sensitive lipases (HSLs) are widely distributed in microorganisms, plants, and animals. Microbial HSLs are classified into two subfamilies, an unnamed new subfamily and the GDSAG motif subfamily. Due to the lack of structural information, the detailed catalytic mechanism of the new subfamily is not yet clarified. Based on sequence analysis, we propose to name the new subfamily as the GTSAG motif subfamily. We identified a novel HSL esterase E25, a member of the GTSAG motif subfamily, by functional metagenomic screening, and resolved its structure at 2.05 Å. E25 is mesophilic (optimum temperature at 50 °C), salt-tolerant, slightly alkaline (optimum pH at 8.5) for its activity, and capable of hydrolyzing short chain monoesters (C2-C10). E25 tends to form dimers both in the crystal and in solution. An E25 monomer contains an N-terminal CAP domain, and a classical α/β hydrolase-fold domain. Residues Ser(186), Asp(282), and His(312) comprise the catalytic triad. Structural and mutational analyses indicated that E25 adopts a dimerization pattern distinct from other HSLs. E25 dimer is mainly stabilized by an N-terminal loop intersection from the CAP domains and hydrogen bonds and salt bridges involving seven highly conserved hydrophilic residues from the catalytic domains. Further analysis indicated that E25 also has some catalytic profiles different from other HSLs. Dimerization is essential for E25 to exert its catalytic activity by keeping the accurate orientation of the catalytic Asp(282) within the catalytic triad. Our results reveal the structural basis for dimerization and catalysis of an esterase from the GTSAG motif subfamily of the HSL family.
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Affiliation(s)
- Ping-Yi Li
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Peng Ji
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Chun-Yang Li
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Yi Zhang
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Guang-Long Wang
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Xi-Ying Zhang
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, China
| | - Bin-Bin Xie
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, China
| | - Qi-Long Qin
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, China
| | - Xiu-Lan Chen
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, China
| | - Bai-Cheng Zhou
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center
| | - Yu-Zhong Zhang
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan 250100, China
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48
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Alvarez Y, Esteban-Torres M, Cortés-Cabrera Á, Gago F, Acebrón I, Benavente R, Mardo K, de las Rivas B, Muñoz R, Mancheño JM. Esterase LpEst1 from Lactobacillus plantarum: a novel and atypical member of the αβ hydrolase superfamily of enzymes. PLoS One 2014; 9:e92257. [PMID: 24663330 PMCID: PMC3963902 DOI: 10.1371/journal.pone.0092257] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/19/2014] [Indexed: 02/05/2023] Open
Abstract
The genome of the lactic acid bacterium Lactobacillus plantarum WCFS1 reveals the presence of a rich repertoire of esterases and lipases highlighting their important role in cellular metabolism. Among them is the carboxylesterase LpEst1 a bacterial enzyme related to the mammalian hormone-sensitive lipase, which is known to play a central role in energy homeostasis. In this study, the crystal structure of LpEst1 has been determined at 2.05 Å resolution; it exhibits an αβ-hydrolase fold, consisting of a central β-sheet surrounded by α-helices, endowed with novel topological features. The structure reveals a dimeric assembly not comparable with any other enzyme from the bacterial hormone-sensitive lipase family, probably echoing the specific structural features of the participating subunits. Biophysical studies including analytical gel filtration and ultracentrifugation support the dimeric nature of LpEst1. Structural and mutational analyses of the substrate-binding pocket and active site together with biochemical studies provided insights for understanding the substrate profile of LpEst1 and suggested for the first time the conserved Asp173, which is adjacent to the nucleophile, as a key element in the stabilization of the loop where the oxyanion hole resides.
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Affiliation(s)
- Yanaisis Alvarez
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Madrid, Spain
- Center of Advanced Studies of Cuba, CITMA, Havana, Cuba
| | - María Esteban-Torres
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Madrid, Spain
| | - Álvaro Cortés-Cabrera
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Madrid, Spain
| | - Rocío Benavente
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Madrid, Spain
| | - Karin Mardo
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Blanca de las Rivas
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Madrid, Spain
| | - Rosario Muñoz
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Madrid, Spain
| | - José M. Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Madrid, Spain
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49
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Benavente R, Esteban-Torres M, Acebrón I, de Las Rivas B, Muñoz R, Alvarez Y, Mancheño JM. Structure, biochemical characterization and analysis of the pleomorphism of carboxylesterase Cest-2923 from Lactobacillus plantarum WCFS1. FEBS J 2013; 280:6658-71. [PMID: 24127688 DOI: 10.1111/febs.12569] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/10/2013] [Accepted: 10/11/2013] [Indexed: 11/30/2022]
Abstract
The hydrolase fold is one of the most versatile structures in the protein realm according to the diversity of sequences adopting such a three-dimensional architecture. In the present study, we clarified the crystal structure of the carboxylesterase Cest-2923 from the lactic acid bacterium Lactobacillus plantarum WCFS1 refined to 2.1 Å resolution, determined its main biochemical characteristics and also carried out an analysis of its associative behaviour in solution. We found that the versatility of a canonical α/β hydrolase fold, the basic framework of the crystal structure of Cest-2923, also extends to its oligomeric behaviour in solution. Thus, we discovered that Cest-2923 exhibits a pH-dependent pleomorphic behaviour in solution involving monomers, canonical dimers and tetramers. Although, at neutral pH, the system is mainly shifted to dimeric species, under acidic conditions, tetrameric species predominate. Despite these tetramers resulting from the association of canonical dimers, as is commonly found in many other carboxylesterases from the hormone-sensitive lipase family, they can be defined as 'noncanonical' because they represent a different association mode. We identified this same type of tetramer in the closest relative of Cest-2923 that has been structurally characterized: the sugar hydrolase YeeB from Lactococcus lactis. The observed associative behaviour is consistent with the different crystallographic results for Cest-2923 from structural genomics consortia. Finally, the presence of sulfate or acetate molecules (depending on the crystal form analysed) in the close vicinity of the nucleophile Ser116 allows us to identify interactions with the putative oxyanion hole and deduce the existence of hydrolytic activity within Cest-2923 crystals.
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Affiliation(s)
- Rocío Benavente
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Madrid, Spain
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50
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Schiefner A, Gerber K, Brosig A, Boos W. Structural and mutational analyses of Aes, an inhibitor of MalT in Escherichia coli. Proteins 2013; 82:268-77. [DOI: 10.1002/prot.24383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/16/2013] [Accepted: 07/25/2013] [Indexed: 11/09/2022]
Affiliation(s)
- André Schiefner
- Lehrstuhl für Biologische Chemie; Technische Universität München; 85350 Freising-Weihenstephan Germany
| | - Kinga Gerber
- Fachbereich Biologie; Universität Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Alexander Brosig
- Fachbereich Biologie; Universität Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Winfried Boos
- Fachbereich Biologie; Universität Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
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