1
|
Nazarian Z, Arab SS. Discovery of carboxylesterases via metagenomics: Putative enzymes that contribute to chemical kinetic resolution. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
2
|
Riziotis IG, Thornton JM. Capturing the geometry, function, and evolution of enzymes with 3D templates. Protein Sci 2022; 31:e4363. [PMID: 35762726 PMCID: PMC9207746 DOI: 10.1002/pro.4363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/06/2022] [Accepted: 05/14/2022] [Indexed: 11/05/2022]
Abstract
Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs, or catalytic sites. Here we explore methods to generate template libraries and algorithms to query structures for conserved 3D motifs. Applications of templates are discussed, as well as some exemplar cases for examining evolutionary links in enzymes. We also introduce the concept of using more than one template per structure to represent flexible sites, as an approach to better understand catalysis through snapshots captured in enzyme structures. Functional annotation from structure is an important topic that has recently resurfaced due to the new more accurate methods of protein structure prediction. Therefore, we anticipate that template‐based functional site detection will be a powerful tool in the task of characterizing a vast number of new protein models.
Collapse
|
3
|
Dou Z, Jia P, Chen X, Wu Z, Xu G, Ni Y. Structural and mechanistic insights into enantioselectivity toward near-symmetric esters of a novel carboxylesterase RoCE. Catal Sci Technol 2022. [DOI: 10.1039/d2cy01542k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A novel carboxylesterase RoCE was identified with relatively high enantioselectivity toward “hard-to-be-discriminated” oxyheterocyclic esters. Molecular basis of enantioselectivity was elucidated and applied in increasing enantioselectivity of RoCE.
Collapse
Affiliation(s)
- Zhe Dou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Peng Jia
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoyu Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zheng Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| |
Collapse
|
4
|
An integrated overview of bacterial carboxylesterase: Structure, function and biocatalytic applications. Colloids Surf B Biointerfaces 2021; 205:111882. [PMID: 34087776 DOI: 10.1016/j.colsurfb.2021.111882] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022]
Abstract
Carboxylesterases (CEs) are members of prominent esterase, and as their name imply, they catalyze the cleavage of ester linkages. By far, a considerable number of novel CEs have been identified to investigate their exquisite physiological and biochemical properties. They are abundant enzymes in nature, widely distributed in relatively broad temperature range and in various sources; both macroorganisms and microorganisms. Given the importance of these enzymes in broad industries, interest in the study of their mechanisms and structural-based engineering are greatly increasing. This review presents the current state of knowledge and understanding about the structure and functions of this ester-metabolizing enzyme, primarily from bacterial sources. In addition, the potential biotechnological applications of bacterial CEs are also encompassed. This review will be useful in understanding the molecular basis and structural protein of bacterial CEs that are significant for the advancement of enzymology field in industries.
Collapse
|
5
|
Liu X, Zhao M, Fan X, Fu Y. Reshaping the active pocket of esterase Est816 for resolution of economically important racemates. Catal Sci Technol 2021. [DOI: 10.1039/d1cy01028j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eight 2-arylpropionic acids with high E values were generated by engineered Est816, which overcomes the contradiction between the wide substrate scope and high enantioselectivity of esterases.
Collapse
Affiliation(s)
- Xiaolong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Meng Zhao
- School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Rd, Hefei, 230032, Anhui, People's Republic of China
| | - Xinjiong Fan
- School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Rd, Hefei, 230032, Anhui, People's Republic of China
| | - Yao Fu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| |
Collapse
|
6
|
Xiao Y, Lu Q, Yi X, Zhong G, Liu J. Synergistic Degradation of Pyrethroids by the Quorum Sensing-Regulated Carboxylesterase of Bacillus subtilis BSF01. Front Bioeng Biotechnol 2020; 8:889. [PMID: 32850741 PMCID: PMC7403188 DOI: 10.3389/fbioe.2020.00889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/10/2020] [Indexed: 12/31/2022] Open
Abstract
The well-studied quorum sensing (QS) mechanism has established a complex knowledge system of how microorganisms behave collectively in natural ecosystems, which contributes to bridging the gap between the ecological functions of microbial communities and the molecular mechanisms of cell-to-cell communication. In particular, the ability of agrochemical degradation has been one most attractive potential of functional bacteria, but the interaction and mutual effects of intracellular degradation and intraspecific behavior remained unclear. In this study, we establish a connection between QS regulation and biodegradation by harnessing the previously isolated Bacillus subtilis BSF01 as a template which degrades various pyrethroids. First, we characterize the genetic and transcriptional basis of comA-involved QS system in B. subtilis BSF01 since the ComQXPA circuit coordinates group behaviors in B. subtilis isolates. Second, the genetic and transcriptional details of pyrethroid-degrading carboxylesterase CesB are defined, and its catalytic capacity is evaluated under different conditions. More importantly, we adopt DNA pull-down and yeast one-hybrid techniques to reveal that the enzymatic degradation of pyrethroids is initiated through QS signal regulator ComA binding to carboxylesterase gene cesB, highlighting the synergistic effect of QS regulation and pyrethroid degradation in B. subtilis BSF01. Taken together, the elucidated mechanism provides novel details on the intercellular response of functional bacteria against xenobiotic exposure, which opens up possibilities to facilitate the in-situ contaminant bioremediation via combining the QS-mediated strategies.
Collapse
Affiliation(s)
- Ying Xiao
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.,Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China.,Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangzhou, China
| | - Qiqi Lu
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.,Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Xin Yi
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.,Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Guohua Zhong
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.,Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Jie Liu
- Key Laboratory of Integrated Pest Management of Crop in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.,Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| |
Collapse
|
7
|
Denesyuk A, Dimitriou PS, Johnson MS, Nakayama T, Denessiouk K. The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements. PLoS One 2020; 15:e0229376. [PMID: 32084230 PMCID: PMC7034887 DOI: 10.1371/journal.pone.0229376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The alpha/beta-Hydrolases (ABH) are a structural class of proteins that are found widespread in nature and includes enzymes that can catalyze various reactions in different substrates. The catalytic versatility of the ABH fold enzymes, which has been a valuable property in protein engineering applications, is based on a similar acid-base-nucleophile catalytic mechanism. In our research, we are concerned with the structure that surrounds the key units of the catalytic machinery, and we have previously found conserved structural organizations that coordinate the catalytic acid, the catalytic nucleophile and the residues of the oxyanion hole. Here, we explore the architecture that surrounds the catalytic histidine at the active sites of enzymes from 40 ABH fold families, where we have identified six conserved interactions that coordinate the catalytic histidine next to the catalytic acid and the catalytic nucleophile. Specifically, the catalytic nucleophile is coordinated next to the catalytic histidine by two weak hydrogen bonds, while the catalytic acid is directly involved in the coordination of the catalytic histidine through by two weak hydrogen bonds. The imidazole ring of the catalytic histidine is coordinated by a CH-π contact and a hydrophobic interaction. Moreover, the catalytic triad residues are connected with a residue that is located at the core of the active site of ABH fold, which is suggested to be the fourth member of a “structural catalytic tetrad”. Besides their role in the stability of the catalytic mechanism, the conserved elements of the catalytic site are actively involved in ligand binding and affect other properties of the catalytic activity, such as substrate specificity, enantioselectivity, pH optimum and thermostability of ABH fold enzymes. These properties are regularly targeted in protein engineering applications, and thus, the identified conserved structural elements can serve as potential modification sites in order to develop ABH fold enzymes with altered activities.
Collapse
Affiliation(s)
- Alexander Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Russia
- * E-mail:
| | - Polytimi S. Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| |
Collapse
|
8
|
Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application. CRYSTALS 2019. [DOI: 10.3390/cryst9110597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.
Collapse
|
9
|
Hajighasemi M, Tchigvintsev A, Nocek B, Flick R, Popovic A, Hai T, Khusnutdinova AN, Brown G, Xu X, Cui H, Anstett J, Chernikova TN, Brüls T, Le Paslier D, Yakimov MM, Joachimiak A, Golyshina OV, Savchenko A, Golyshin PN, Edwards EA, Yakunin AF. Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12388-12401. [PMID: 30284819 DOI: 10.1021/acs.est.8b04252] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The continuous growth of global plastics production, including polyesters, has resulted in increasing plastic pollution and subsequent negative environmental impacts. Therefore, enzyme-catalyzed depolymerization of synthetic polyesters as a plastics recycling approach has become a focus of research. In this study, we screened over 200 purified uncharacterized hydrolases from environmental metagenomes and sequenced microbial genomes and identified at least 10 proteins with high hydrolytic activity against synthetic polyesters. These include the metagenomic esterases MGS0156 and GEN0105, which hydrolyzed polylactic acid (PLA), polycaprolactone, as well as bis(benzoyloxyethyl)-terephthalate. With solid PLA as a substrate, both enzymes produced a mixture of lactic acid monomers, dimers, and higher oligomers as products. The crystal structure of MGS0156 was determined at 1.95 Å resolution and revealed a modified α/β hydrolase fold, with a lid domain and highly hydrophobic active site. Mutational studies of MGS0156 identified the residues critical for hydrolytic activity against both polyester and monoester substrates, with two-times higher polyesterase activity in the MGS0156 L169A mutant protein. Thus, our work identified novel, highly active polyesterases in environmental metagenomes and provided molecular insights into their activity, thereby augmenting our understanding of enzymatic polyester hydrolysis.
Collapse
Affiliation(s)
- Mahbod Hajighasemi
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Anatoli Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Tran Hai
- School of Biological Sciences , Bangor University , Gwynedd LL57 2UW , U.K
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Julia Anstett
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | | | - Thomas Brüls
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale, Institut de Génomique , Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS), UMR8030, Génomique métabolique , Evry , France
| | - Denis Le Paslier
- Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS) , UMR8030, Génomique métabolique, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale, Institut de Génomique , Evry , France
| | - Michail M Yakimov
- Institute for Coastal Marine Environment , CNR , 98122 Messina , Italy
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Olga V Golyshina
- School of Biological Sciences , Bangor University , Gwynedd LL57 2UW , U.K
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Peter N Golyshin
- School of Biological Sciences , Bangor University , Gwynedd LL57 2UW , U.K
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , ON M5S 3E5 , Canada
| |
Collapse
|
10
|
Riegler-Berket L, Leitmeier A, Aschauer P, Dreveny I, Oberer M. Identification of lipases with activity towards monoacylglycerol by criterion of conserved cap architectures. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:679-687. [PMID: 29627382 DOI: 10.1016/j.bbalip.2018.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/09/2018] [Accepted: 03/27/2018] [Indexed: 11/26/2022]
Abstract
Monoacylglycerol lipases (MGL) are a subclass of lipases that predominantly hydrolyze monoacylglycerol (MG) into glycerol and fatty acid. MGLs are ubiquitous enzymes across species and play a role in lipid metabolism, affecting energy homeostasis and signaling processes. Structurally, MGLs belong to the α/β hydrolase fold family with a cap covering the substrate binding pocket. Analysis of the known 3D structures of human, yeast and bacterial MGLs revealed striking similarity of the cap architecture. Since MGLs from different organisms share very low sequence similarity, it is difficult to identify MGLs based on the amino acid sequence alone. Here, we investigated whether the cap architecture could be a characteristic feature of this subclass of lipases with activity towards MG and whether it is possible to identify MGLs based on the cap shape. Through database searches, we identified the structures of five different candidate α/β hydrolase fold proteins with unknown or reported esterase activity. These proteins exhibit cap architecture similarities to known human, yeast and bacterial MGL structures. Out of these candidates we confirmed MGL activity for the protein LipS, which displayed the highest structural similarity to known MGLs. Two further enzymes, Avi_0199 and VC1974, displayed low level MGL activities. These findings corroborate our hypothesis that this conserved cap architecture can be used as criterion to identify lipases with activity towards MGs.
Collapse
Affiliation(s)
- Lina Riegler-Berket
- Institute of Molecular Biosciences, University of Graz, Austria; BioTechMed-Graz, Austria
| | - Andrea Leitmeier
- Institute of Molecular Biosciences, University of Graz, Austria; BioTechMed-Graz, Austria
| | - Philipp Aschauer
- Institute of Molecular Biosciences, University of Graz, Austria; BioTechMed-Graz, Austria
| | - Ingrid Dreveny
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, Austria; BioTechMed-Graz, Austria.
| |
Collapse
|
11
|
De Vitis V, Nakhnoukh C, Pinto A, Contente ML, Barbiroli A, Milani M, Bolognesi M, Molinari F, Gourlay LJ, Romano D. A stereospecific carboxyl esterase from Bacillus coagulans hosting nonlipase activity within a lipase-like fold. FEBS J 2018; 285:903-914. [PMID: 29278448 DOI: 10.1111/febs.14368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/30/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022]
Abstract
Microbial carboxylesterases are important biocatalysts that selectively hydrolyze an extensive range of esters. Here, we report the biochemical and structural characterization of an atypical carboxylesterase from Bacillus coagulans (BCE), endowed with high enantioselectivity toward different 1,2-O-isopropylideneglycerol (IPG or solketal) esters. BCE efficiently catalyzes the production of enantiopure (S)-IPG, a chiral building block for the synthesis of β-blockers, glycerophospholipids, and prostaglandins; efficient hydrolysis was observed up to 65 °C. To gain insight into the mechanistic bases of such enantioselectivity, we solved the crystal structures of BCE in apo- and glycerol-bound forms at resolutions of 1.9 and 1.8 Å, respectively. In silico docking studies on the BCE structure confirmed that IPG esters with small acyl chains (≤ C6) were easily accommodated in the active site pocket, indicating that small conformational changes are necessary to accept longer substrates. Furthermore, docking studies suggested that enantioselectivity may be due to an improved stabilization of the tetrahedral reaction intermediate for the S-enantiomer. Contrary to the above functional data implying nonlipolytic functions, BCE displays a lipase-like 3D structure that hosts a "lid" domain capping the main entrance to the active site. In lipases the lid mediates catalysis through interfacial activation, a process that we did not observe for BCE. Overall, we present the functional-structural properties of an atypical carboxyl esterase that has nonlipase-like functions, yet possesses a lipase-like 3D fold. Our data provide original enzymatic information in view of BCE applications as an inexpensive, efficient biocatalyst for the production of enantiopure (S)-IPG. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank (www.rcsb.org) under accession numbers 5O7G (apo-BCE) and 5OLU (glycerol-bound BCE).
Collapse
Affiliation(s)
- Valerio De Vitis
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | | | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Martina L Contente
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy.,School of Chemistry, University of Nottingham, UK
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Mario Milani
- Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Italy.,Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy.,Pediatric Research Center "Romeo e Enrica Invernizzi", Cryo Electron Microscopy Laboratory, University of Milano, Italy
| | - Francesco Molinari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Louise J Gourlay
- Department of Biosciences, Università degli Studi di Milano, Italy
| | - Diego Romano
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| |
Collapse
|
12
|
Sánchez-Carbente MDR, Batista-García RA, Sánchez-Reyes A, Escudero-Garcia A, Morales-Herrera C, Cuervo-Soto LI, French-Pacheco L, Fernández-Silva A, Amero C, Castillo E, Folch-Mallol JL. The first description of a hormone-sensitive lipase from a basidiomycete: Structural insights and biochemical characterization revealed Bjerkandera adusta BaEstB as a novel esterase. Microbiologyopen 2017; 6. [PMID: 28251842 PMCID: PMC5552909 DOI: 10.1002/mbo3.463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/25/2017] [Accepted: 02/02/2017] [Indexed: 11/06/2022] Open
Abstract
The heterologous expression and characterization of a Hormone-Sensitive Lipases (HSL) esterase (BaEstB) from the Basidiomycete fungus Bjerkandera adusta is reported for the first time. According to structural analysis, amino acid similarities and conservation of particular motifs, it was established that this enzyme belongs to the (HSL) family. The cDNA sequence consisted of 969 nucleotides, while the gene comprised 1133, including three introns of 57, 50, and 57 nucleotides. Through three-dimensional modeling and phylogenetic analysis, we conclude that BaEstB is an ortholog of the previously described RmEstB-HSL from the phylogenetically distant fungus Rhizomucor miehei. The purified BaEstB was characterized in terms of its specificity for the hydrolysis of different acyl substrates confirming its low lipolytic activity and a noticeable esterase activity. The biochemical characterization of BaEstB, the DLS analysis and the kinetic parameters determination revealed this enzyme as a true esterase, preferentially found in a dimeric state, displaying activity under alkaline conditions and relative low temperature (pH = 10, 20°C). Our data suggest that BaEstB is more active on substrates with short acyl chains and bulky aromatic moieties. Phylogenetic data allow us to suggest that a number of fungal hypothetical proteins could belong to the HSL family.
Collapse
Affiliation(s)
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Ayixón Sánchez-Reyes
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Angela Escudero-Garcia
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Catalina Morales-Herrera
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Laura I Cuervo-Soto
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Departamento de Biología, Facultad de Ciencias, Universidad Antonio Nariño, Bogota, Colombia
| | - Leidys French-Pacheco
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Arline Fernández-Silva
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Carlos Amero
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Edmundo Castillo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| |
Collapse
|
13
|
Lee CW, Kwon S, Park SH, Kim BY, Yoo W, Ryu BH, Kim HW, Shin SC, Kim S, Park H, Kim TD, Lee JH. Crystal Structure and Functional Characterization of an Esterase (EaEST) from Exiguobacterium antarcticum. PLoS One 2017; 12:e0169540. [PMID: 28125606 PMCID: PMC5268438 DOI: 10.1371/journal.pone.0169540] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/19/2016] [Indexed: 11/19/2022] Open
Abstract
A novel microbial esterase, EaEST, from a psychrophilic bacterium Exiguobacterium antarcticum B7, was identified and characterized. To our knowledge, this is the first report describing structural analysis and biochemical characterization of an esterase isolated from the genus Exiguobacterium. Crystal structure of EaEST, determined at a resolution of 1.9 Å, showed that the enzyme has a canonical α/β hydrolase fold with an α-helical cap domain and a catalytic triad consisting of Ser96, Asp220, and His248. Interestingly, the active site of the structure of EaEST is occupied by a peracetate molecule, which is the product of perhydrolysis of acetate. This result suggests that EaEST may have perhydrolase activity. The activity assay showed that EaEST has significant perhydrolase and esterase activity with respect to short-chain p-nitrophenyl esters (≤C8), naphthyl derivatives, phenyl acetate, and glyceryl tributyrate. However, the S96A single mutant had low esterase and perhydrolase activity. Moreover, the L27A mutant showed low levels of protein expression and solubility as well as preference for different substrates. On conducting an enantioselectivity analysis using R- and S-methyl-3-hydroxy-2-methylpropionate, a preference for R-enantiomers was observed. Surprisingly, immobilized EaEST was found to not only retain 200% of its initial activity after incubation for 1 h at 80°C, but also retained more than 60% of its initial activity after 20 cycles of reutilization. This research will serve as basis for future engineering of this esterase for biotechnological and industrial applications.
Collapse
Affiliation(s)
- Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Sena Kwon
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Boo-Young Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
| | - Han-Woo Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Seung Chul Shin
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Sunghwan Kim
- New Drug Development Center, Daegu-Gyeongpuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - T. Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, Korea
- * E-mail: (JHL); (TDK)
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
- * E-mail: (JHL); (TDK)
| |
Collapse
|
14
|
Enantioselective Resolution of (±)-1-Phenylethanol and (±)-1-Phenylethyl Acetate by a Novel Esterase from Bacillus sp. SCSIO 15121. Appl Biochem Biotechnol 2015; 178:558-75. [DOI: 10.1007/s12010-015-1894-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/08/2015] [Indexed: 11/29/2022]
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Romano D, Bonomi F, de Mattos MC, de Sousa Fonseca T, de Oliveira MDCF, Molinari F. Esterases as stereoselective biocatalysts. Biotechnol Adv 2015; 33:547-65. [PMID: 25677731 DOI: 10.1016/j.biotechadv.2015.01.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 12/23/2022]
Abstract
Non-lypolitic esterases are carboxylester hydrolases with preference for the hydrolysis of water-soluble esters bearing short-chain acyl residues. The potential of esterases as enantioselective biocatalysts has enlarged in the last few years due to the progresses achieved in different areas, such as screening methodologies, overproduction of recombinant esterases, structural information useful for understanding the rational behind enantioselectivity, and efficient methods in protein engineering. Contributions of these complementary know-hows to the development of new robust enantioselective esterases are critically discussed in this review.
Collapse
Affiliation(s)
- Diego Romano
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Francesco Bonomi
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Marcos Carlos de Mattos
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Campus do Pici, Postal Box 6044, 60455-970 Fortaleza, Ceará, Brazil
| | - Thiago de Sousa Fonseca
- Department of Organic and Inorganic Chemistry, Federal University of Ceará, Campus do Pici, Postal Box 6044, 60455-970 Fortaleza, Ceará, Brazil
| | | | - Francesco Molinari
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| |
Collapse
|
17
|
Sattler JH, Fuchs M, Mutti FG, Grischek B, Engel P, Pfeffer J, Woodley JM, Kroutil W. Introducing an in situ capping strategy in systems biocatalysis to access 6-aminohexanoic acid. Angew Chem Int Ed Engl 2014; 53:14153-7. [PMID: 25366462 DOI: 10.1002/anie.201409227] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 12/29/2022]
Abstract
The combination of two cofactor self-sufficient biocatalytic cascade modules allowed the successful transformation of cyclohexanol into the nylon-6 monomer 6-aminohexanoic acid at the expense of only oxygen and ammonia. A hitherto unprecedented carboxylic acid capping strategy was introduced to minimize the formation of the dead-end intermediate 6-hydroxyhexanoic acid. For this purpose, the precursor ε-caprolactone was converted in aqueous medium in the presence of methanol into the corresponding methyl ester instead of the acid. Hence, it was shown for the first time that esterases--specifically horse liver esterase--can perform the selective ring-opening of ε-caprolactone with a clear preference for methanol over water as the nucleophile.
Collapse
Affiliation(s)
- Johann H Sattler
- Institut für Chemie, Organische und Bioorganische Chemie, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria); Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz (Austria)
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Sattler JH, Fuchs M, Mutti FG, Grischek B, Engel P, Pfeffer J, Woodley JM, Kroutil W. Introducing an In Situ Capping Strategy in Systems Biocatalysis To Access 6-Aminohexanoic acid. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409227] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|