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Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sánchez-Costa M, Hidalgo A, Berenguer J, González-Siso MI, Cruces J, Rúa ML, Hermoso JA. Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Comput Struct Biotechnol J 2021; 19:1214-1232. [PMID: 33680362 PMCID: PMC7905190 DOI: 10.1016/j.csbj.2021.01.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/31/2022] Open
Abstract
A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60°C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the α/β-hydrolase superfamily. The canonical α/β-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.
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Key Words
- CHCA, cyclohexane carboxylic acid
- CMC, critical micellar concentration
- CV, column volume
- Crystal structure
- DMSO, dimethyl sulfoxide
- DSF, Differential scanning fluorimetry
- Enzyme-substrate complex
- FLU, fluorescein
- HSL, hormone-sensitive lipase
- LDAO, N,N-dimethyldodecylamine N-oxide
- MNP, methyl-naproxen
- Metagenomic
- NP, naproxen
- PPL, Porcine Pancreatic Lipase
- Thermophilic esterase
- pNP, 4-nitrophenol
- α/β hydrolase fold
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Affiliation(s)
- Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Ivanna Rivera
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
| | - Jelena Rajkovic
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Kamila Knapik
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Ana Torrado
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | | | | | - Manuel Becerra
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | - Mercedes Sánchez-Costa
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - José Berenguer
- Department of Molecular Biology, Center for Molecular Biology “Severo Ochoa” (UAM-CSIC), Autonomous University of Madrid, Madrid, Spain
| | - María-Isabel González-Siso
- EXPRELA Group, University A Coruña, Science Faculty, Advanced Scientific Research Center (CICA), A Coruña, Spain
| | | | - María L. Rúa
- Biochemistry Laboratory, CITACA-Agri-Food Research and Transfer Cluster, Campus Auga, University of Vigo, Ourense, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
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Chen ZS, Wu YD, Hao JH, Liu YJ, He KP, Jiang WH, Xiong MJ, Lv YS, Cao SL, Zhu J. Molecular Dynamic Simulation of the Porcine Pancreatic Lipase in Non-aqueous Organic Solvents. Front Bioeng Biotechnol 2020; 8:676. [PMID: 32766212 PMCID: PMC7381131 DOI: 10.3389/fbioe.2020.00676] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/01/2020] [Indexed: 11/13/2022] Open
Abstract
This paper investigates the conformational stability of porcine pancreatic lipase (PPL) in three non-aqueous organic solvents, including dimethyl sulfoxide (DMSO), propylene glycol (PRG), and ethanol (EtOH) through molecular dynamic (MD) simulation. The root mean square deviations (RMSDs), radius of gyration (Rg), solution accessible surface area (SASA), radial distribution function (RDF), hydrogen bond (H-bond), Ramachandran plot analysis, secondary structure, and enzyme substrate affinity of the PPL in the various organic solvents were comparatively investigated. The results showed that the backbone and active pocket RMSD, and hydrophilic ASA of PPL in three solvents increase with the increase in the solvent LogP, while the Rg, hydrophobic ASA, and H-bond between the solvent and PPL decrease. Among the three organic solvents, DMSO acts as a better solvent, in which the PPL can be loose and extended, and retains its native backbone in DMSO compared to PRG and EtOH. Moreover, Ramachandran plot analysis indicated that the PPL structure quality in DMSO was higher than that in PRG and EtOH. Also, the molecular docking results showed that PPL in DMSO exhibited the highest enzyme-substrate affinity.
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Affiliation(s)
- Zi-Shi Chen
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Yi-Da Wu
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Jin-Heng Hao
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Yu-Jia Liu
- School of Chemical Engineering and Energy Technology, Engineering Research Center of Health Food Design and Nutrition Regulation, Dongguan University of Technology, Dongguan, China
| | - Kang-Ping He
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Wen-Hao Jiang
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Mei-Jie Xiong
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Yong-Si Lv
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China
| | - Shi-Lin Cao
- Group of Sustainable Biochemical Engineering, School of Food Science and Engineering, Foshan University, Foshan, China.,Sustainable Biochemical and Biosynthetic Engineering Center, Foshan Wu-Yuan Biotechnology Co., Ltd., Guangdong Biomedical Industrial Base, Foshan, China
| | - Jie Zhu
- School of Chemical Engineering and Energy Technology, Engineering Research Center of Health Food Design and Nutrition Regulation, Dongguan University of Technology, Dongguan, China
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Shirke AN, White C, Englaender JA, Zwarycz A, Butterfoss GL, Linhardt RJ, Gross RA. Stabilizing Leaf and Branch Compost Cutinase (LCC) with Glycosylation: Mechanism and Effect on PET Hydrolysis. Biochemistry 2018; 57:1190-1200. [PMID: 29328676 DOI: 10.1021/acs.biochem.7b01189] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cutinases are polyester hydrolases that show a remarkable capability to hydrolyze polyethylene terephthalate (PET) to its monomeric units. This revelation has stimulated research aimed at developing sustainable and green cutinase-catalyzed PET recycling methods. Leaf and branch compost cutinase (LCC) is particularly suited toward these ends given its relatively high PET hydrolysis activity and thermostability. Any practical enzymatic PET recycling application will require that the protein have kinetic stability at or above the PET glass transition temperature (Tg, i.e., 70 °C). This paper elucidates the thermodynamics and kinetics of LCC conformational and colloidal stability. Aggregation emerged as a major contributor that reduces LCC kinetic stability. In its native state, LCC is prone to aggregation owing to electrostatic interactions. Further, with increasing temperature, perturbation of LCC's tertiary structure and corresponding exposure of hydrophobic domains leads to rapid aggregation. Glycosylation was employed in an attempt to impede LCC aggregation. Owing to the presence of three putative N-glycosylation sites, expression of native LCC in Pichia pastoris resulted in the production of glycosylated LCC (LCC-G). LCC-G showed improved stability to native state aggregation while increasing the temperature for thermal induced aggregation by 10 °C. Furthermore, stabilization against thermal aggregation resulted in improved catalytic PET hydrolysis both at its optimum temperature and concentration.
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Affiliation(s)
- Abhijit N Shirke
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Christine White
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jacob A Englaender
- Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Allison Zwarycz
- Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University Abu Dhabi , Abu Dhabi, UAE
| | - Robert J Linhardt
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Richard A Gross
- Department of Chemistry and Chemiscal Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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