1
|
Wirjanata G, Lin J, Dziekan JM, El Sahili A, Chung Z, Tjia S, Binte Zulkifli NE, Boentoro J, Tham R, Jia LS, Go KD, Yu H, Partridge A, Olsen D, Prabhu N, Sobota RM, Nordlund P, Lescar J, Bozdech Z. Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development. Cell Chem Biol 2024; 31:743-759.e8. [PMID: 38593807 DOI: 10.1016/j.chembiol.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/02/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Identification of new druggable protein targets remains the key challenge in the current antimalarial development efforts. Here we used mass-spectrometry-based cellular thermal shift assay (MS-CETSA) to identify potential targets of several antimalarials and drug candidates. We found that falcilysin (FLN) is a common binding partner for several drug candidates such as MK-4815, MMV000848, and MMV665806 but also interacts with quinoline drugs such as chloroquine and mefloquine. Enzymatic assays showed that these compounds can inhibit FLN proteolytic activity. Their interaction with FLN was explored systematically by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with lowered FLN expression demonstrated statistically significant increases in susceptibility toward MK-4815, MMV000848, and several quinolines. Importantly, the hydrophobic pocket of FLN appears amenable to inhibition and the structures reported here can guide the development of novel drugs against malaria.
Collapse
Affiliation(s)
- Grennady Wirjanata
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Infectious Diseases Labs & Singapore Immunology Network, Agency for Science, Technology and Research, 138648 Singapore, Singapore
| | - Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore
| | - Zara Chung
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Roy Tham
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Lai Si Jia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - David Olsen
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 637551, Singapore.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore.
| |
Collapse
|
2
|
Fernandez-Lopez L, Roda S, Robles-Martín A, Muñoz-Tafalla R, Almendral D, Ferrer M, Guallar V. Enhancing the Hydrolytic Activity of a Lipase towards Larger Triglycerides through Lid Domain Engineering. Int J Mol Sci 2023; 24:13768. [PMID: 37762071 PMCID: PMC10530837 DOI: 10.3390/ijms241813768] [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: 08/03/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Lipases have valuable potential for industrial use, particularly those mostly active against water-insoluble substrates, such as triglycerides composed of long-carbon chain fatty acids. However, in most cases, engineered variants often need to be constructed to achieve optimal performance for such substrates. Protein engineering techniques have been reported as strategies for improving lipase characteristics by introducing specific mutations in the cap domain of esterases or in the lid domain of lipases or through lid domain swapping. Here, we improved the lipase activity of a lipase (WP_075743487.1, or LipMRD) retrieved from the Marine Metagenomics MarRef Database and assigned to the Actinoalloteichus genus. The improvement was achieved through site-directed mutagenesis and by substituting its lid domain (FRGTEITQIKDWLTDA) with that of Rhizopus delemar lipase (previously R. oryzae; UniProt accession number, I1BGQ3) (FRGTNSFRSAITDIVF). The results demonstrated that the redesigned mutants gain activity against bulkier triglycerides, such as glyceryl tridecanoate and tridodecanoate, olive oil, coconut oil, and palm oil. Residue W89 (LipMRD numbering) appears to be key to the increase in lipase activity, an increase that was also achieved with lid swapping. This study reinforces the importance of the lid domains and their amino acid compositions in determining the substrate specificity of lipases, but the generalization of the lid domain swapping between lipases or the introduction of specific mutations in the lid domain to improve lipase activity may require further investigation.
Collapse
Affiliation(s)
- Laura Fernandez-Lopez
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
| | - Ana Robles-Martín
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- PhD Programme, Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Rubén Muñoz-Tafalla
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- PhD Programme, Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Kuan JE, Tsai CH, Chou CC, Wu C, Wu WF. Enzymatic Characterization of a Novel HSL Family IV Esterase EstD04 from Pseudomonas sp. D01 in Mealworm Gut Microbiota. Molecules 2023; 28:5410. [PMID: 37513282 PMCID: PMC10385968 DOI: 10.3390/molecules28145410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Pseudomonas sp. D01, capable of growing in tributyrin medium, was isolated from the gut microbiota of yellow mealworm. By using in silico analyses, we discovered a hypothesized esterase encoding gene in the D01 bacterium, and its encoded protein, EstD04, was classified as a bacterial hormone-sensitive lipase (bHSL) of the type IV lipase family. The study revealed that the recombinant EstD04-His(6x) protein exhibited esterase activity and broad substrate specificity, as it was capable of hydrolyzing p-nitrophenyl derivatives with different acyl chain lengths. By using the most favorable substrate p-nitrophenyl butyrate (C4), we defined the optimal temperature and pH value for EstD04 esterase activity as 40 °C and pH 8, respectively, with a catalytic efficiency (kcat/Km) of 6.17 × 103 mM-1 s-1 at 40 °C. EstD04 demonstrated high stability between pH 8 and 10, and thus, it might be capably used as an alkaline esterase in industrial applications. The addition of Mg2+ and NH4+, as well as DMSO, could stimulate EstD04 enzyme activity. Based on bioinformatic motif analyses and tertiary structural simulation, we determined EstD04 to be a typical bHSL protein with highly conserved motifs, including a triad catalytic center (Ser160, Glu253, and His283), two cap regions, hinge sites, and an oxyanion hole, which are important for the type IV enzyme activity. Moreover, the sequence analysis suggested that the two unique discrete cap regions of EstD04 may contribute to its alkali mesophilic nature, allowing EstD04 to exhibit extremely distinct physiological properties from its evolutionarily closest esterase.
Collapse
Affiliation(s)
- Jung-En Kuan
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Chih-Hsuan Tsai
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701401, Taiwan
| | - Chun-Chi Chou
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Cindy Wu
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Whei-Fen Wu
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
5
|
Luo C, Hu Y, Xing S, Xie W, Li C, He L, Wang X, Zeng X. Adsorption-precipitation-cross-linking immobilization of GDSL-type esterase from Aspergillus niger GZUF36 by polydopamine-modified magnetic clarity tetroxide nanocouplings and its enzymatic characterization. Int J Biol Macromol 2023:125533. [PMID: 37355062 DOI: 10.1016/j.ijbiomac.2023.125533] [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: 04/30/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Recombinant INANE1 (rINANE1), a recombinant intracellular GDSL-type esterase from Aspergillus niger GZUF36, has high acetate substrate specificity. Here, rINANE1 was successfully immobilized on polydopamine (PDA)-modified magnetic ferric oxide nanoparticles (Fe3O4NPs) by adsorption-precipitation-cross-linking to obtain cross-linked enzyme aggregate (CLEA)-rINANE1-Fe3O4@PDA. Fe3O4, Fe3O4@PDA, and CLEA-rINANE1-Fe3O4@PDA were characterized by scanning electron microscopy, X-ray diffraction, vibrating-sample magnetometry, Fourier transform infrared (FTIR) spectroscopy, and zeta potential analysis. Upon immobilization, CLEA-rINANE1-Fe3O4@PDA, with a protein loading of 72.72 ± 1.01 mg/g, reached optimal activity recovery of 104.40 % ± 1.14 %. FTIR analysis showed that immobilization increased the relative content of β-folding in rINANE1 by 12.25 % and reduced irregular curl by 4.16 %, rendering the structure more orderly. Specifically, under an alkaline condition (pH 10), CLEA-rINANE1-Fe3O4@PDA performed over 100 % of initial activity. The optimum temperature increased by 5 °C, and over 55 % of the initial activity was observed after 12 h at 55 °C. CLEA-rINANE1-Fe3O4@PDA showed over 40 % of its relative activity, whereas free rINANE1 showed <10 % in acetonitrile. In addition, the relative activity of CLEA-rINANE1-Fe3O4@PDA was retained at about 80 % after eight cycles and maintained at 109 % after 45 days. The PDA-modified magnetic ferrite nanoparticles exhibited excellent stability and recyclability, providing a new avenue for developing industrial biocatalysts.
Collapse
Affiliation(s)
- Chaocheng Luo
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China
| | - Yuedan Hu
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China
| | - Shuqi Xing
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China
| | - Wei Xie
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China
| | - Cuiqin Li
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China; School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, PR China; Key Lab of Fermentation Engineering and Biopharmacy, Guizhou University, Guiyang 550025, PR China
| | - Laping He
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China; Key Lab of Fermentation Engineering and Biopharmacy, Guizhou University, Guiyang 550025, PR China.
| | - Xiao Wang
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China
| | - Xuefeng Zeng
- Key Laboratory of Agricultural and Animal Products Store & Processing of Guizhou Province, Guizhou University, Guiyang 550025, PR China; College of Liquor and Food Engineering, Guizhou University, Guiyang 550025, PR China; Key Lab of Fermentation Engineering and Biopharmacy, Guizhou University, Guiyang 550025, PR China
| |
Collapse
|
6
|
The Mobility of the Cap Domain Is Essential for the Substrate Promiscuity of a Family IV Esterase from Sorghum Rhizosphere Microbiome. Appl Environ Microbiol 2023; 89:e0180722. [PMID: 36602332 PMCID: PMC9888213 DOI: 10.1128/aem.01807-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Metagenomics offers the possibility to screen for versatile biocatalysts. In this study, the microbial community of the Sorghum bicolor rhizosphere was spiked with technical cashew nut shell liquid, and after incubation, the environmental DNA (eDNA) was extracted and subsequently used to build a metagenomic library. We report the biochemical features and crystal structure of a novel esterase from the family IV, EH0, retrieved from an uncultured sphingomonad after a functional screen in tributyrin agar plates. EH0 (optimum temperature [Topt], 50°C; melting temperature [Tm], 55.7°C; optimum pH [pHopt], 9.5) was stable in the presence of 10 to 20% (vol/vol) organic solvents and exhibited hydrolytic activity against p-nitrophenyl esters from acetate to palmitate, preferably butyrate (496 U mg-1), and a large battery of 69 structurally different esters (up to 30.2 U mg-1), including bis(2-hydroxyethyl)-terephthalate (0.16 ± 0.06 U mg-1). This broad substrate specificity contrasts with the fact that EH0 showed a long and narrow catalytic tunnel, whose access appears to be hindered by a tight folding of its cap domain. We propose that this cap domain is a highly flexible structure whose opening is mediated by unique structural elements, one of which is the presence of two contiguous proline residues likely acting as possible hinges, which together allow for the entrance of the substrates. Therefore, this work provides a new role for the cap domain, which until now was thought to be an immobile element that contained hydrophobic patches involved in substrate prerecognition and in turn substrate specificity within family IV esterases. IMPORTANCE A better understanding of structure-function relationships of enzymes allows revelation of key structural motifs or elements. Here, we studied the structural basis of the substrate promiscuity of EH0, a family IV esterase, isolated from a sample of the Sorghum bicolor rhizosphere microbiome exposed to technical cashew nut shell liquid. The analysis of EH0 revealed the potential of the sorghum rhizosphere microbiome as a source of enzymes with interesting properties, such as pH and solvent tolerance and remarkably broad substrate promiscuity. Its structure resembled those of homologous proteins from mesophilic Parvibaculum and Erythrobacter spp. and hyperthermophilic Pyrobaculum and Sulfolobus spp. and had a very narrow, single-entry access tunnel to the active site, with access controlled by a capping domain that includes a number of nonconserved proline residues. These structural markers, distinct from those of other substrate-promiscuous esterases, can help in tuning substrate profiles beyond tunnel and active site engineering.
Collapse
|
7
|
Cea‐Rama I, Coscolín C, Gonzalez‐Alfonso JL, Raj J, Vasiljević M, Plou FJ, Ferrer M, Sanz‐Aparicio J. Crystal structure of a family VIII β-lactamase fold hydrolase reveals the molecular mechanism for its broad substrate scope. FEBS J 2022; 289:6714-6730. [PMID: 35694902 PMCID: PMC9795927 DOI: 10.1111/febs.16554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/10/2022] [Accepted: 06/10/2022] [Indexed: 12/30/2022]
Abstract
Family VIII esterases present similarities to class C β-lactamases, which show nucleophilic serines located at the S-X-X-K motif instead of the G-X-S-X-G or G-D-S-(L) motif shown by other carboxylesterase families. Here, we report the crystal structure of a novel family VIII (subfamily VIII. I) esterase (EH7 ; denaturing temperature, 52.6 ± 0.3 °C; pH optimum 7.0-9.0) to deepen its broad substrate range. Indeed, the analysis of the substrate specificity revealed its capacity to hydrolyse nitrocefin as a model chromogenic cephalosporin substrate (40.4 ± 11.4 units·g-1 ), and a large battery of 66 structurally different esters (up to 1730 min-1 ), including bis(2-hydroxyethyl)-terephthalate (241.7 ± 8.5 units·g-1 ) and the mycotoxin T-2 (1220 ± 52 units·g-1 ). It also showed acyltransferase activity through the synthesis of benzyl 3-oxobutanoate (40.4 ± 11.4 units·g-1 ) from benzyl alcohol and vinyl acetoacetate. Such a broad substrate scope is rare among family VIII esterases and lipolytic enzymes. Structural analyses of free and substrate-bound forms of this homooctamer esterase suggest that EH7 presents a more opened and exposed S1 site having no steric hindrance for the entrance of substrates to the active site, more flexible R1, R2 and R3 regions allowing for the binding of a wide spectrum of substrates into the active site, and small residues in the conserved motif Y-X-X containing the catalytic Tyr enabling the entrance of large substrates. These unique structural elements in combination with docking experiments allowed us to gain valuable insights into the substrate specificity of this esterase and possible others belonging to family VIII.
Collapse
Affiliation(s)
| | | | | | - Jog Raj
- PATENT CO, DOOMišićevoSerbia
| | | | | | | | | |
Collapse
|
8
|
Johan UUM, Rahman RNZRA, Kamarudin NHA, Latip W, Ali MSM. A new hyper-thermostable carboxylesterase from Anoxybacillus geothermalis D9. Int J Biol Macromol 2022; 222:2486-2497. [DOI: 10.1016/j.ijbiomac.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
|
9
|
Roda S, Fernandez-Lopez L, Benedens M, Bollinger A, Thies S, Schumacher J, Coscolín C, Kazemi M, Santiago G, Gertzen CGW, Gonzalez-Alfonso JL, Plou FJ, Jaeger KE, Smits SHJ, Ferrer M, Guallar V. A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions. Angew Chem Int Ed Engl 2022; 61:e202207344. [PMID: 35734849 PMCID: PMC9540564 DOI: 10.1002/anie.202207344] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 01/01/2023]
Abstract
Engineering dual‐function single polypeptide catalysts with two abiotic or biotic catalytic entities (or combinations of both) supporting cascade reactions is becoming an important area of enzyme engineering and catalysis. Herein we present the development of a PluriZyme, TR2E2, with efficient native transaminase (kcat: 69.49±1.77 min−1) and artificial esterase (kcat: 3908–0.41 min−1) activities integrated into a single scaffold, and evaluate its utility in a cascade reaction. TR2E2 (pHopt: 8.0–9.5; Topt: 60–65 °C) efficiently converts methyl 3‐oxo‐4‐(2,4,5‐trifluorophenyl)butanoate into 3‐(R)‐amino‐4‐(2,4,5‐trifluorophenyl)butanoic acid, a crucial intermediate for the synthesis of antidiabetic drugs. The reaction proceeds through the conversion of the β‐keto ester into the β‐keto acid at the hydrolytic site and subsequently into the β‐amino acid (e.e. >99 %) at the transaminase site. The catalytic power of the TR2E2PluriZyme was proven with a set of β‐keto esters, demonstrating the potential of such designs to address bioinspired cascade reactions.
Collapse
Affiliation(s)
- Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | | | - Marius Benedens
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Alexander Bollinger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Julia Schumacher
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Cristina Coscolín
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Masoud Kazemi
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | - Gerard Santiago
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | - Christoph G W Gertzen
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | | | - Francisco J Plou
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Manuel Ferrer
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| |
Collapse
|
10
|
Roda S, Fernandez-Lopez L, Benedens M, Bollinger A, Thies S, Schumacher J, Coscolín C, Kazemi M, Santiago G, Gertzen CGW, Gonzalez-Alfonso JL, Plou FJ, Jaeger KE, Smits SHJ, Ferrer M, Guallar V. A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Laura Fernandez-Lopez
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Marius Benedens
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies Wilhelm Johnen Straße, Bldg 15.8, 01/303 40228 Düsseldorf GERMANY
| | - Alexander Bollinger
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Stephan Thies
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Julia Schumacher
- Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies Building 26.44.01.62, Universitaetsstr 1 40228 Düsseldorf GERMANY
| | - Cristina Coscolín
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 28049 Madrid SPAIN
| | - Masoud Kazemi
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Gerard Santiago
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Christoph G. W. Gertzen
- Heinrich Heine University Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Institute for Pharmaceutical and Medicinal Chemistry 40228 Düsseldorf GERMANY
| | - Jose L. Gonzalez-Alfonso
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Francisco J. Plou
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Karl-Erich Jaeger
- Forschungszentrum Julich ICG: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Sander H. J. Smits
- Heinrich Heine University Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies 40228 Düsseldorf GERMANY
| | - Manuel Ferrer
- Institute of Catalysis CSIC Department of Biocatalysis Marie Curie 2Campus Cantoblanco 28049 Madrid SPAIN
| | - Víctor Guallar
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| |
Collapse
|
11
|
You S, Zhang YX, Shi F, Zhang WX, Li J, Zhang S, Chen ZL, Zhao WG, Wang J. Lowering energy consumption for fermentable sugar production from Ramulus mori: Engineered xylanase synergy and improved pretreatment strategy. BIORESOURCE TECHNOLOGY 2022; 344:126368. [PMID: 34808317 DOI: 10.1016/j.biortech.2021.126368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Biorefinery of Ramulus mori with lower energy consumption through improved enzyme and pretreatment strategies was reported. Directed evolution and saturation mutagenesis were used for the modification of xylanase, the yield of fermentable sugars and the degree of synergy (DS) were determined for different pretreatment (seawater/non-seawater) and enzyme treatment groups (xylanase/cellulase/co-treatment). The dominant mutant I133A/Q143Y of Bispora sp. xylanase XYL10C_ΔN was obtained with improved specific activity (1860 U/mg), catalytic efficiency (1150 mL/s∙mg) at 40 °C, and thermostability (T50 increased by 7 °C). With the pretreatment of seawater immersion, the highest yield of fermentable sugars for Ramulus mori at 40 °C reached 199 μmol/g when hydrolyzed with cellulase and I133A/Q143Y, with the highest DS of 2.6; this was 4.5-fold that of the group hydrolyzed by cellulase alone with non-seawater pretreatment. Thus, bioconversion of reducing sugar from Ramulus mori was improved significantly at lower temperatures, which provides an efficient and energy-saving wayfor biofuel production.
Collapse
Affiliation(s)
- Shuai You
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Gene tic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China
| | - Yi-Xin Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Fan Shi
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Wen-Xin Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Jing Li
- Department of Nephrology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, PR China
| | - Sheng Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China
| | - Zhong-Li Chen
- Xinyuan Cocoon Silk Group Co., Ltd., Nantong 226600, PR China
| | - Wei-Guo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Gene tic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, PR China; Key Laboratory of Silkworm and Mulberry Gene tic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, PR China.
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
| | | | | | - Hoon Kim
- Correspondence: ; Tel.: +82-617503751
| |
Collapse
|
13
|
Cea-Rama I, Coscolín C, Katsonis P, Bargiela R, Golyshin PN, Lichtarge O, Ferrer M, Sanz-Aparicio J. Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase. Comput Struct Biotechnol J 2021; 19:2307-2317. [PMID: 33995922 PMCID: PMC8105184 DOI: 10.1016/j.csbj.2021.04.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 01/02/2023] Open
Abstract
Our understanding of enzymes with high substrate ambiguity remains limited because their large active sites allow substrate docking freedom to an extent that seems incompatible with stereospecificity. One possibility is that some of these enzymes evolved a set of evolutionarily fitted sequence positions that stringently allow switching substrate ambiguity and chiral specificity. To explore this hypothesis, we targeted for mutation a serine ester hydrolase (EH3) that exhibits an impressive 71-substrate repertoire but is not stereospecific (e.e. 50%). We used structural actions and the computational evolutionary trace method to explore specificity-swapping sequence positions and hypothesized that position I244 was critical. Driven by evolutionary action analysis, this position was substituted to leucine, which together with isoleucine appears to be the amino acid most commonly present in the closest homologous sequences (max. identity, ca. 67.1%), and to phenylalanine, which appears in distant homologues. While the I244L mutation did not have any functional consequences, the I244F mutation allowed the esterase to maintain a remarkable 53-substrate range while gaining stereospecificity properties (e.e. 99.99%). These data support the possibility that some enzymes evolve sequence positions that control the substrate scope and stereospecificity. Such residues, which can be evolutionarily screened, may serve as starting points for further designing substrate-ambiguous, yet chiral-specific, enzymes that are greatly appreciated in biotechnology and synthetic chemistry.
Collapse
Affiliation(s)
- Isabel Cea-Rama
- Institute of Physical Chemistry “Rocasolano”, CSIC, 28006 Madrid, Spain
| | | | | | - Rafael Bargiela
- Centre for Environmental Biotechnology, Bangor University, LL57 2UW Bangor, UK
| | - Peter N. Golyshin
- Centre for Environmental Biotechnology, Bangor University, LL57 2UW Bangor, UK
- School of Natural Sciences, Bangor University, LL57 2UW Bangor, UK
| | | | | | | |
Collapse
|