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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.
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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
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2
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Fang Y, Liu F, Shi Y, Yang T, Xin Y, Gu Z, Shi G, Zhang L. N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE. Front Microbiol 2023; 14:1193955. [PMID: 37434709 PMCID: PMC10332459 DOI: 10.3389/fmicb.2023.1193955] [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: 03/26/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
TrLipE is a thermophilic lipase that has potential commercial applications because of its catalytic ability under extreme conditions. Consistent with most lipases, the lid of TrLipE is located over the catalytic pocket, controls the substrate channel to the active center, and regulates the substrate specificity, activity, and stability of the enzyme through conformational changes. TrLipE from Thermomicrobium roseum has potential industrial applications, which is hindered by its weak enzymatic activity. Here, 18 chimeras (TrL1-TrL18) were reconstructed by N-terminal lid swapping between TrLipE and structurally similar enzymes. The results showed that the chimeras had a similar pH range and optimum pH as wild TrLipE but a narrower temperature range of 40-80°C, and TrL17 and the other chimeras showed lower optimum temperatures of 70°C and 60°C, respectively. In addition, the half-lives of the chimeras were lower than those of TrLipE under optimum temperature conditions. Molecular dynamics simulations indicated that chimeras had high RMSD, RMSF, and B-factor values. When p-nitrophenol esters with different chains were used as substrates, compared with TrLipE, most of the chimeras had a low Km and high kcat value. The chimeras TrL2, TrL3, TrL17, and TrL18 could specifically catalyze the substrate 4-nitrophenyl benzoate, with TrL17 showing the highest kcat/Km value of 363.88 ± 15.83 L⋅min-1⋅mmol-1. Mutants were then designed by investigating the binding free energies of TrL17 and 4-nitrophenyl benzoate. The results indicated that single, double, and triple substitution variants (M89W and I206N; E33W/I206M and M89W/I206M; and M89W/I206M/L21I and M89W/I206N/L21I, respectively) presented approximately 2- to 3-fold faster catalysis of 4-nitrophenyl benzoate than the wild TrL17. Our observations will facilitate the development of the properties and industrial applications of TrLipE.
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Affiliation(s)
- Yakun Fang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Fan Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Yi Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Ting Yang
- Wuxi Food Safety Inspection and Test Center, Technology Innovation Center of Special Food for State Market Regulation, Wuxi, Jiangsu, China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
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Wu K, Zhai X, Chen H, Zheng J, Yu Z, Xu X, Huang J. The effect of barium and strontium on activity of glucoamylase QsGH97a from Qipengyuania seohaensis SW-135. Sci Rep 2023; 13:5840. [PMID: 37037863 PMCID: PMC10086023 DOI: 10.1038/s41598-023-32161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 03/23/2023] [Indexed: 04/12/2023] Open
Abstract
Glycoside hydrolases (GHs), the enzymes that break glycosidic bonds, are ubiquitous in the ecosystem, where they perform a range of biological functions. As an interesting glycosidase family, Glycoside hydrolase family 97 (GH97) contains α-glucosidase, α-galactosidase, and glucoamylase. Only ten members of GH97 have been characterized so far. It is critical to explore novel members to elucidate the catalytic mechanism and application potential of GH97 family. In this study, a novel glucoamylase QsGH97a from Qipengyuania seohaensis SW-135 was cloned and expressed in E. coli. Sequence analysis and NMR results show that QsGH97a is classified into GH97a, and adopts inverting mechanism. The biochemical characterization indicates that QsGH97a shows the optimal activity at 50 °C and pH 8.0. Ca2+ has little effect on the catalytic activity; however, the activity can be substantially increased by 8-13 folds in the presence of Ba2+ or Sr2+. Additionally, the metal content of QsGH97a assay showed a high proportion of Sr2+. The specific metal activity was initially revealed in glucoamylases, which is not found in other members. These results imply that QsGH97a not only is a new member of GH97, but also has potential for industrial applications. Our study reveals that Ba2+ or Sr2+ may be involved in the catalytic mechanism of glucoamylase, laying the groundwork for a more complete knowledge of GH97 and its possible industrial application.
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Affiliation(s)
- Kaijuan Wu
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - Xingyu Zhai
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
| | - Jinfeng Zheng
- Hunan Institute for Drug Control, Changsha, 410013, Hunan, China
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, 410013, Hunan, China
| | - Xuewei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China.
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, 410013, Hunan, China.
- China-Africa Research Center of Infectious Diseases, Central South University, Changsha, 410013, Hunan, China.
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4
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Son J, Choi W, Kim H, Kim M, Lee JH, Shin SC, Kim HW. Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4. IUCRJ 2023; 10:220-232. [PMID: 36862488 PMCID: PMC9980389 DOI: 10.1107/s2052252523001562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure-function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix-turn-helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases.
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Affiliation(s)
- Jonghyeon Son
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- New Drug Development Center, Daegu–Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Woong Choi
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hyun Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Minseo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
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5
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Nagaroor V, Gummadi SN. An overview of mammalian and microbial hormone-sensitive lipases (lipolytic family IV): biochemical properties and industrial applications. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36154870 DOI: 10.1080/02648725.2022.2127071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/13/2022] [Indexed: 11/02/2022]
Abstract
In mammals, hormone-sensitive lipase (EC 3.1.1.79) is an intracellular lipase that significantly regulates lipid metabolism. Mammalian HSL is more active towards diacylglycerol but lacks a lid covering the active site. Dyslipidemia, hepatic steatosis, cancer, and cancer-associated cachexia are symptoms of HSL pathophysiology. Certain microbial proteins show a sequence homologous to the catalytic domain of mammalian HSL, hence called microbial HSL. They possess a funnel-shaped substrate-binding pocket and restricted length of acyl chain esters, thus known as esterases. These enzymes have broad substrate specificities and are capable of stereo, regio, and enantioselective, making them attractive biocatalysts in a wide range of industrial applications in the production of flavors, pharmaceuticals, biosensors, and fine chemicals. This review will provide insight into mammalian and microbial HSLs, their sources, structural features related to substrate specificity, thermal stability, and their applications.
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Affiliation(s)
- Vijayalakshmi Nagaroor
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology laboratory (AIM lab), Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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Zhai X, Wu K, Ji R, Zhao Y, Lu J, Yu Z, Xu X, Huang J. Structure and Function Insight of the α-Glucosidase QsGH13 From Qipengyuania seohaensis sp. SW-135. Front Microbiol 2022; 13:849585. [PMID: 35308395 PMCID: PMC8928221 DOI: 10.3389/fmicb.2022.849585] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
Abstract
The α-glucosidases play indispensable roles in the metabolic mechanism of organism, prevention, and treatment of the disease, and sugar hydrolysis, and are widely used in chemical synthesis, clinical diagnosis, and other fields. However, improving their catalytic efficiency and production to meet commercial demand remains a huge challenge. Here we detected a novel GH13 family α-glucosidase, QsGH13, from the deep-sea bacterium Qipengyuania seohaensis sp. SW-135. QsGH13 is highly substrate specific and only hydrolyzes sugars containing alpha-1,4 glucoside bonds. For example, its enzymatic activity for p-nitrophenyl-α-D-glucopyranoside was 25.41 U/mg, and the Km value was 0.2952 ± 0.0322 mM. The biochemical results showed that the optimum temperature of QsGH13 is 45°C, the optimum pH is 10.0, and it has excellent biological characteristics such as alkali resistance and salt resistance. The crystal structure of QsGH13 was resolved with a resolution of 2.2 Å, where QsGH13 is composed of a typical TIM barrel catalytic domain A, a loop-rich domain B, and a conserved domain C. QsGH13 crystal belonged to the monoclinic space group P212121, with unit-cell parameters a = 58.816 Å, b = 129.920 Å, c = 161.307 Å, α = γ = β = 90°, which contains two monomers per asymmetric unit. The β → α loop 4 of QsGH13 was located above catalytic pocket. Typical catalytic triad residues Glu202, Asp266, and Glu329 were found in QsGH13. The biochemical properties and structural analysis of QsGH13 have greatly improved our understanding of the catalytic mechanism of GH13 family. This study provides new ideas to broaden the application of α-glucosidase in alcohol fermentation, glycolysis, and other industries.
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Affiliation(s)
- Xingyu Zhai
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China.,Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Kaijuan Wu
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiming Zhao
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Zheng Yu
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Xuewei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, China
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Kumar NG, Contaifer D, Wijesinghe DS, Jefferson KK. Staphylococcus aureus Lipase 3 (SAL3) is a surface-associated lipase that hydrolyzes short chain fatty acids. PLoS One 2021; 16:e0258106. [PMID: 34618844 PMCID: PMC8496776 DOI: 10.1371/journal.pone.0258106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial lipases play important roles during infection. The Staphylococcus aureus genome contains several genes that encode well-characterized lipases and several genes predicted to encode lipases or esterases for which the function has not yet been established. In this study, we sought to define the function of an uncharacterized S. aureus protein, and we propose the annotation S. aureus lipase 3 (SAL3) (SAUSA300_0641). We confirmed that SAL3 is a lipase and that it is surface associated and secreted through an unknown mechanism. We determined that SAL3 specifically hydrolyzes short chain (4-carbon and fewer) fatty acids and specifically binds negatively charged lipids including phosphatidic acid, phosphatidylinositol phosphate, and phosphatidylglycerol, which is the most abundant lipid in the staphylococcal cell membrane. Mutating the catalytic triad S66-A, D167-A, S168-A, and H301-A in the recombinant protein abolished lipase activity without altering binding to host lipid substrates. Taken together we report the discovery of a novel lipase from S. aureus specific to short chain fatty acids with yet to be determined roles in host pathogen interactions.
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Affiliation(s)
- Naren Gajenthra Kumar
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel Contaifer
- Department of Pharmacotherapy and Outcomes Sciences, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dayanjan S. Wijesinghe
- Department of Pharmacotherapy and Outcomes Sciences, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kimberly K. Jefferson
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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Park JE, Jeong GS, Lee HW, Kim H. Molecular Characterization of Novel Family IV and VIII Esterases from a Compost Metagenomic Library. Microorganisms 2021; 9:microorganisms9081614. [PMID: 34442693 PMCID: PMC8399190 DOI: 10.3390/microorganisms9081614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
Two novel esterase genes, est8L and est13L, were isolated and identified from a compost metagenomic library. The encoded Est8L and Est13L had molecular masses of 33,181 and 44,913 Da consisting of 314 and 411 amino acids, respectively, without signal peptides. Est8L showed the highest identity (32.9%) to a hyper-thermophilic carboxylesterase AFEST from Archaeoglobus fulgidus compared to other esterases reported and was classified to be a novel member of family IV esterases with conserved regions such as HGGG, DY, GXSXG, DPL, and GXIH. Est13L showed the highest identity (98.5%) to the family VIII esterase Est7K from the metagenome library. Est8L and Est13L had the highest activities for p-nitrophenyl butyrate (C4) and p-nitrophenyl caproate (C6), respectively, and Est13L showed a broad substrate specificity for p-nitrophenyl substrates. Est8L and Est13L effectively hydrolyzed glyceryl tributyrate. The optimum temperatures for activities of Est8L and Est13L were identical (40 °C), and the optimum pH values were 9.0 and 10.0, respectively. Est13L showed higher thermostability than Est8L. Sephacryl S-200 HR chromatography showed that the native form of Est8L was a dimer. Interestingly, Est13L was found to be a tetramer, contrary to other family VIII esterases reported. Est8L was inhibited by 30% isopropanol, methanol, and acetonitrile; however, Est13L was activated to 182.9% and 356.1%, respectively, by 30% isopropanol and methanol. Est8L showed enantioselectivity for the S-form, but Est13L showed no enantioselectivity. These results show that intracellular Est8L and/or Est13L are oligomeric in terms of native forms and can be used for pharmaceutical and industrial applications with organic solvents under alkaline conditions.
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Affiliation(s)
| | | | | | - Hoon Kim
- Correspondence: ; Tel.: +82-617503751
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Characterization of a Novel Family IV Esterase Containing a Predicted CzcO Domain and a Family V Esterase with Broad Substrate Specificity from an Oil-Polluted Mud Flat Metagenomic Library. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11135905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two novel esterase genes, est2L and est4L, were identified from a previously constructed metagenomic library derived from an oil-polluted mud flat sample. The encoded Est2L and Est4L were composed of 839 and 267 amino acids, respectively, without signal peptides. Est2L was a unique fusion type of protein composed of two domains: a domain of the CzcO superfamily, associated with a cationic diffusion promoter with CzcD, and a domain of the acetylesterase superfamily, belonging to family IV with conserved motifs, such as HGG, GXSAG, and GXPP. Est2L was the first fused esterase with a CzcO domain. Est4L belonged to family V with GXS, GXSMGG, and PTL motifs. Native Est2L and Est4L were found to be in dimeric and tetrameric forms, respectively. Est2L and Est4L showed the highest activities at 60 °C and 50 °C, respectively, and at a pH of 10.0. Est2L preferred short length substrates, especially p-nitrophenyl (pNP)-acetate, with moderate butyrylcholinesterase activity, whereas Est4L showed the highest activity with pNP-decanoate and had broad specificity. Significant effects were not observed in Est2L from Co2+ and Zn2+, although Est2L contains the domain CzcD. Est2L and Est4L showed high stabilities in 30% methanol and 1% Triton X-100. These enzymes could be used for a variety of applications, such as detergent and mining processing under alkaline conditions.
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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.
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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
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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] [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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12
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Boyko KM, Kryukova MV, Petrovskaya LE, Kryukova EA, Nikolaeva AY, Korzhenevsky DA, Lomakina GY, Novototskaya-Vlasova KA, Rivkina EM, Dolgikh DA, Kirpichnikov MP, Popov VO. Structural and Biochemical Characterization of a Cold-Active PMGL3 Esterase with Unusual Oligomeric Structure. Biomolecules 2021; 11:biom11010057. [PMID: 33466452 PMCID: PMC7824956 DOI: 10.3390/biom11010057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 11/23/2022] Open
Abstract
The gene coding for a novel cold-active esterase PMGL3 was previously obtained from a Siberian permafrost metagenomic DNA library and expressed in Escherichia coli. We elucidated the 3D structure of the enzyme which belongs to the hormone-sensitive lipase (HSL) family. Similar to other bacterial HSLs, PMGL3 shares a canonical α/β hydrolase fold and is presumably a dimer in solution but, in addition to the dimer, it forms a tetrameric structure in a crystal and upon prolonged incubation at 4 °C. Detailed analysis demonstrated that the crystal tetramer of PMGL3 has a unique architecture compared to other known tetramers of the bacterial HSLs. To study the role of the specific residues comprising the tetramerization interface of PMGL3, several mutant variants were constructed. Size exclusion chromatography (SEC) analysis of D7N, E47Q, and K67A mutants demonstrated that they still contained a portion of tetrameric form after heat treatment, although its amount was significantly lower in D7N and K67A compared to the wild type. Moreover, the D7N and K67A mutants demonstrated a 40 and 60% increase in the half-life at 40 °C in comparison with the wild type protein. Km values of these mutants were similar to that of the wt PMGL3. However, the catalytic constants of the E47Q and K67A mutants were reduced by ~40%.
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Affiliation(s)
- Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Correspondence: (K.M.B.); (L.E.P.)
| | - Mariya V. Kryukova
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Lada E. Petrovskaya
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Correspondence: (K.M.B.); (L.E.P.)
| | - Elena A. Kryukova
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
| | - Alena Y. Nikolaeva
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Dmitry A. Korzhenevsky
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Galina Yu. Lomakina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Department of Fundamental Sciences, Bauman Moscow State Technical University, 105005 Moscow, Russia
| | - Ksenia A. Novototskaya-Vlasova
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Elizaveta M. Rivkina
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Dmitry A. Dolgikh
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
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13
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Recazens E, Mouisel E, Langin D. Hormone-sensitive lipase: sixty years later. Prog Lipid Res 2020; 82:101084. [PMID: 33387571 DOI: 10.1016/j.plipres.2020.101084] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 12/24/2020] [Indexed: 12/19/2022]
Abstract
Hormone-sensitive lipase (HSL) was initially characterized as the hormonally regulated neutral lipase activity responsible for the breakdown of triacylglycerols into fatty acids in adipose tissue. This review aims at providing up-to-date information on structural properties, regulation of expression, activity and function as well as therapeutic potential. The lipase is expressed as different isoforms produced from tissue-specific alternative promoters. All isoforms are composed of an N-terminal domain and a C-terminal catalytic domain within which a regulatory domain containing the phosphorylation sites is embedded. Some isoforms possess additional N-terminal regions. The catalytic domain shares similarities with bacteria, fungus and vascular plant proteins but not with other mammalian lipases. HSL singularity is provided by regulatory and N-terminal domains sharing no homology with other proteins. HSL has a broad substrate specificity compared to other neutral lipases. It hydrolyzes acylglycerols, cholesteryl and retinyl esters among other substrates. A novel role of HSL, independent of its enzymatic function, has recently been described in adipocytes. Clinical studies revealed dysregulations of HSL expression and activity in disorders, such as lipodystrophy, obesity, type 2 diabetes and cancer-associated cachexia. Development of specific inhibitors positions HSL as a pharmacological target for the treatment of metabolic complications.
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Affiliation(s)
- Emeline Recazens
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France
| | - Etienne Mouisel
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France
| | - Dominique Langin
- Institute of Metabolic and Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, 31432 Toulouse, France; University of Toulouse, Paul Sabatier University, UMR1297, Toulouse, France; Franco-Czech Laboratory for Clinical Research on Obesity, Third Faculty of Medicine, Prague and Paul Sabatier University, Toulouse, France; Toulouse University Hospitals, Laboratory of Clinical Biochemistry, Toulouse, France.
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14
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Expression, Characterisation and Homology Modelling of a Novel Hormone-Sensitive Lipase (HSL)-Like Esterase from Glaciozyma antarctica. Catalysts 2020. [DOI: 10.3390/catal10010058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Microorganisms, especially those that survive in extremely cold places such as Antarctica, have gained research attention since they produce a unique feature of the protein, such as being able to withstand at extreme temperature, salinity, and pressure, that make them desired for biotechnological application. Here, we report the first hormone-sensitive lipase (HSL)-like esterase from a Glaciozyma species, a psychrophilic yeast designated as GlaEst12-like esterase. In this study, the putative lipolytic enzyme was cloned, expressed in E. coli, purified, and characterised for its biochemical properties. Protein sequences analysis showed that GlaEst12 shared about 30% sequence identity with chain A of the bacterial hormone-sensitive lipase of E40. It belongs to the H group since it has the conserved motifs of Histidine-Glycine-Glycine-Glycine (HGGG)and Glycine-Aspartate-Serine-Alanine-Glycine (GDSAG) at the amino acid sequences. The recombinant GlaEst12 was successfully purified via one-step Ni-Sepharose affinity chromatography. Interestingly, GlaEst12 showed unusual properties with other enzymes from psychrophilic origin since it showed an optimal temperature ranged between 50–60 °C and was stable at alkaline pH conditions. Unlike other HSL-like esterase, this esterase showed higher activity towards medium-chain ester substrates rather than shorter chain ester. The 3D structure of GlaEst12, predicted by homology modelling using Robetta software, showed a secondary structure composed of mainly α/β hydrolase fold, with the catalytic residues being found at Ser232, Glu341, and His371.
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15
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Li Z, Li L, Huo Y, Chen Z, Zhao Y, Huang J, Jian S, Rong Z, Wu D, Gan J, Hu X, Li J, Xu XW. Structure-guided protein engineering increases enzymatic activities of the SGNH family esterases. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:107. [PMID: 32549911 PMCID: PMC7294632 DOI: 10.1186/s13068-020-01742-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/30/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Esterases and lipases hydrolyze short-chain esters and long-chain triglycerides, respectively, and therefore play essential roles in the synthesis and decomposition of ester bonds in the pharmaceutical and food industries. Many SGNH family esterases share high similarity in sequences. However, they have distinct enzymatic activities toward the same substrates. Due to a lack of structural information, the detailed catalytic mechanisms of these esterases remain barely investigated. RESULTS In this study, we identified two SGNH family esterases, CrmE10 and AlinE4, from marine bacteria with significantly different preferences for pH, temperature, metal ion, and organic solvent tolerance despite high sequence similarity. The crystal structures of these two esterases, including wild type and mutants, were determined to high resolutions ranging from 1.18 Å to 2.24 Å. Both CrmE10 and AlinE4 were composed of five β-strands and nine α-helices, which formed one compact N-terminal α/β globular domain and one extended C-terminal domain. The aspartic residues (D178 in CrmE10/D162 in AlinE4) destabilized the conformations of the catalytic triad (Ser-Asp-His) in both esterases, and the metal ion Cd2+ might reduce enzymatic activity by blocking proton transfer or substrate binding. CrmE10 and AlinE4 showed distinctly different electrostatic surface potentials, despite the similar atomic architectures and a similar swap catalytic mechanism. When five negatively charged residues (Asp or Glu) were mutated to residue Lys, CrmE10 obtained elevated alkaline adaptability and significantly increased the enzymatic activity from 0 to 20% at pH 10.5. Also, CrmE10 mutants exhibited dramatic change for enzymatic properties when compared with the wide-type enzyme. CONCLUSIONS These findings offer a perspective for understanding the catalytic mechanism of different esterases and might facilitate the industrial biocatalytic applications.
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Affiliation(s)
- Zhengyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Long Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Yingyi Huo
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
| | - Zijun Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Yu Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jing Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Shuling Jian
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
| | - Zhen Rong
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
| | - Di Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Xiaojian Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438 China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources, Ministry of Natural Resources & Second Institute of Oceanography, Hangzhou, 310012 China
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16
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Shen Y, Li Z, Huo YY, Bao L, Gao B, Xiao P, Hu X, Xu XW, Li J. Structural and Functional Insights Into CmGH1, a Novel GH39 Family β-Glucosidase From Deep-Sea Bacterium. Front Microbiol 2019; 10:2922. [PMID: 31921083 PMCID: PMC6933502 DOI: 10.3389/fmicb.2019.02922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/04/2019] [Indexed: 01/07/2023] Open
Abstract
Glucosidases play key roles in many diseases and are limiting enzymes during cellulose degradation, which is an important part of global carbon cycle. Here, we identified a novel β-glucosidase, CmGH1, isolated from marine bacterium Croceicoccus marinus E4A9T. In spite of its high sequence and structural similarity with β-xylosidase family members, CmGH1 had enzymatic activity toward p-nitrophenyl-β-D-glucopyranoside (p-NPG) and cellobiose. The Km and Kcat values of CmGH1 toward p-NPG were 0.332 ± 0.038 mM and 2.15 ± 0.081 min–1, respectively. CmGH1 was tolerant to high concentration salts, detergents, as well as many kinds of organic solvents. The crystal structure of CmGH1 was resolved with a 1.8 Å resolution, which showed that CmGH1 was composed of a canonical (α/β)8-barrel catalytic domain and an auxiliary β-sandwich domain. Although no canonical catalytic triad residues were found in CmGH1, structural comparison and mutagenesis analysis suggested that residues Gln157 and Tyr264 of CmGH1 were the active sites. Mutant Q157E significantly increased its hydrolase activity up to 15-fold, whereas Y264E totally abolished its enzymatic activity. These results might provide new insights into understanding the different catalytic mechanism during evolution for β-glucosidases and β-xylosidases.
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Affiliation(s)
- Yanfang Shen
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Luyao Bao
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Baocai Gao
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Peng Xiao
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Xiaojian Hu
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Department of Neurology, School of Life Sciences, Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
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17
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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.
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18
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Molecular Characterization of a Novel Cold-Active Hormone-Sensitive Lipase ( HaHSL) from Halocynthiibacter Arcticus. Biomolecules 2019; 9:biom9110704. [PMID: 31694309 PMCID: PMC6921082 DOI: 10.3390/biom9110704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 01/31/2023] Open
Abstract
Bacterial hormone-sensitive lipases (bHSLs), which are homologous to the catalytic domains of human HSLs, have received great interest due to their uses in the preparation of highly valuable biochemicals, such as drug intermediates or chiral building blocks. Here, a novel cold-active HSL from Halocynthiibacter arcticus (HaHSL) was examined and its enzymatic properties were investigated using several biochemical and biophysical methods. Interestingly, HaHSL acted on a large variety of substrates including tertiary alcohol esters and fish oils. Additionally, this enzyme was highly tolerant to high concentrations of salt, detergents, and glycerol. Furthermore, immobilized HaHSL retained its activity for up to six cycles of use. Homology modeling suggested that aromatic amino acids (Trp23, Tyr74, Phe78, Trp83, and Phe245) in close proximity to the substrate-binding pocket were important for enzyme activity. Mutational analysis revealed that Tyr74 played an important role in substrate specificity, thermostability, and enantioselectivity. In summary, the current study provides an invaluable insight into the novel cold-active HaHSL from H. arcticus, which can be efficiently and sustainably used in a wide range of biotechnological applications.
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19
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Duan S, Chen Z, Li Z, Ji R, Gan J, Li J. Purification and enzymatic characterization of the RNA ligase RTCB from Thermus thermophilus. Biotechnol Lett 2019; 41:1051-1057. [PMID: 31280403 DOI: 10.1007/s10529-019-02707-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/04/2019] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To identify the key residues of Thermus thermophilus (T. thermophilus) RTCB in RNA ligation and DNA activation. RESULTS The biochemical activities of RTCB from T. thermophilus were purified, characterized, and compared. Structure and sequence alignment between T. thermophilus RTCB and Pyrococcus horikoshii (P. horikoshii) RTCB identified six conserved residues (D64, D95, N203, H204, E207, H399) that were essential for RNA ligation. Mutation analysis showed that the expression levels of mutants D95A, N203A, H204A, E207A and H399A were relatively low. Compared to wide-type RTCB, variant D64A protein had no RNA ligation and DNA activation activity. In addition, T. thermophilus RTCB showed acceptable catalytic activity of 3'-phosphate DNA activation at 37 °C. CONCLUSION D64 was proved to be essential for RTCB-catalyzed RNA ligation and DNA activation (from 37 to 70 °C) in T. thermophilus.
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Affiliation(s)
- Shuyan Duan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, 200438, Shanghai, China
| | - Zijun Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, 200438, Shanghai, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, 200438, Shanghai, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, 200438, Shanghai, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, 200438, Shanghai, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, 200438, Shanghai, China.
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20
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Gavin DP, Murphy EJ, Foley AM, Castilla IA, Reen FJ, Woods DF, Collins SG, O'Gara F, Maguire AR. Identification of an Esterase Isolated Using Metagenomic Technology which Displays an Unusual Substrate Scope and its Characterisation as an Enantioselective Biocatalyst. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Declan P. Gavin
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Edel J. Murphy
- School of Chemistry; Analytical and Biological Chemistry Research Facility; University College Cork; T12 K8AF Cork Ireland
| | - Aoife M. Foley
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Ignacio Abreu Castilla
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - F. Jerry Reen
- School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - David F. Woods
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
| | - Stuart G. Collins
- School of Chemistry; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre; School of Microbiology; University College Cork; T12 K8AF Cork Ireland
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute; Curtin University; Perth WA 6102 Australia
- Telethon Kids Institute; Perth WA 6008 Australia
| | - Anita R. Maguire
- School of Chemistry; School of Pharmacy; Analytical and Biological Chemistry Research Facility; Synthesis and Solid State Pharmaceutical Centre; University College Cork; T12 K8AF Cork Ireland
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21
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Gricajeva A, Bikutė I, Kalėdienė L. Atypical organic-solvent tolerant bacterial hormone sensitive lipase-like homologue EstAG1 from Staphylococcus saprophyticus AG1: Synthesis and characterization. Int J Biol Macromol 2019; 130:253-265. [PMID: 30797006 DOI: 10.1016/j.ijbiomac.2019.02.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022]
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Some of the most industrially relevant enzymes of this type are lipolytic and their market is predicted to uphold leadership up till 2024. In this study, a novel bacterial hormone-sensitive lipase-like (bHSL) family homologue, designated EstAG1, was discovered by mining gDNA of bacteria isolated from fat contaminated soil in Lithuania. Putative lipolytic enzyme was cloned, overexpressed in E. coli, purified and characterized determining its biochemical properties. While the true physiological role of the discovered leaderless, ~36 kDa enzyme is unknown, metal-activated EstAG1 possessed optima at 45-47.5 °C, pH 7.5-8, with a generally intermediate activity profile between esterases and lipases. Furthermore, EstAG1 was hyperactivated by ethanol, dioxane and DMSO, implicating that it could be industrially applicable enzyme for the synthesis of valuable products such as biodiesel, flavor esters, etc. Sequence analysis and structure modeling revealed that the highest sequence homology of EstAG1 with the closest structurally and functionally described protein makes up only 26%. It was also revealed that EstAG1 has some differences in the bHSL family-characteristic conserved sequence motives. Therefore, EstAG1 presents interest both in terms of biotechnological applications and basic research.
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Affiliation(s)
- Alisa Gricajeva
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Ingrida Bikutė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Lilija Kalėdienė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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22
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Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K. Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. Protein Sci 2018; 28:344-364. [PMID: 30311984 DOI: 10.1002/pro.3527] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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Affiliation(s)
- Polytimi S Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Toru Nakayama
- Tohoku University, Biomolecular Engineering, Sendai, Miyagi, 980-8579, Japan
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
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23
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Rong Z, Huo YY, Jian SL, Wu YH, Xu XW. Characterization of a novel alkaline esterase from Altererythrobacter epoxidivorans CGMCC 1.7731 T. Prep Biochem Biotechnol 2018; 48:113-120. [PMID: 29099313 DOI: 10.1080/10826068.2017.1387559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A novel esterase gene (e25) was identified from Altererythrobacter epoxidivorans CGMCC 1.7731T by genome sequence screening. The e25 gene is 948 nucleotides in length and encodes a 315 amino acid protein (E25) with a predicted molecular mass of 33,683 Da. A phylogenetic tree revealed that E25 belongs to the hormone-sensitive lipase (HSL) family of lipolytic enzymes. An activity assay of E25 showed that it exhibited the highest catalytic efficiency when using p-nitrophenyl caproate (C6) as a substrate. The optimum pH and temperature were determined to be approximately pH 9 and 45°C, and the Km and Vmax values were 0.12 mM and 1,772 µmol/min/mg, respectively. After an incubation at 40°C for 80 min, E25 retained 75% of its basal activity. The enzyme exhibited good tolerance to metal cations, such as Ba2+, Ca2+, and Cu2+ (10 mM), but its activity was strongly inhibited by Co2+, Ni2+, Mn2+, and Zn2+. The E25 enzyme was stimulated by glycerol and retained over 60% of its basal activity in the presence of 1% Tween-80 and Triton X-100. Overall, the activity of E25 under alkaline conditions and its organic solvent and detergent tolerance indicate that E25 could be useful as a novel industrial catalyst in biotechnological applications.
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Affiliation(s)
- Zhen Rong
- a Key Laboratory of Marine Ecosystem and Biogeochemistry , Second Institute of Oceanography, State Oceanic Administration , Hangzhou , China
| | - Ying-Yi Huo
- a Key Laboratory of Marine Ecosystem and Biogeochemistry , Second Institute of Oceanography, State Oceanic Administration , Hangzhou , China
| | - Shu-Ling Jian
- a Key Laboratory of Marine Ecosystem and Biogeochemistry , Second Institute of Oceanography, State Oceanic Administration , Hangzhou , China
| | - Yue-Hong Wu
- a Key Laboratory of Marine Ecosystem and Biogeochemistry , Second Institute of Oceanography, State Oceanic Administration , Hangzhou , China
| | - Xue-Wei Xu
- a Key Laboratory of Marine Ecosystem and Biogeochemistry , Second Institute of Oceanography, State Oceanic Administration , Hangzhou , China
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24
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Huo YY, Rong Z, Jian SL, Xu CD, Li J, Xu XW. A Novel Halotolerant Thermoalkaliphilic Esterase from Marine Bacterium Erythrobacter seohaensis SW-135. Front Microbiol 2017; 8:2315. [PMID: 29213264 PMCID: PMC5702849 DOI: 10.3389/fmicb.2017.02315] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/09/2017] [Indexed: 01/08/2023] Open
Abstract
A novel esterase gene, e69, was cloned from Erythrobacter seohaensis SW-135, which was isolated from a tidal flat sediment of the Yellow Sea in Korea. This gene is 825 bp in length and codes for a 29.54 kDa protein containing 274 amino acids. Phylogenetic analysis showed that E69 is a new member of the bacterial lipolytic enzyme family IV. This enzyme exhibited the highest level of activity toward p-nitrophenyl (NP) butyrate but little or no activity toward the other p-NP esters tested. The optimum temperature and pH of the catalytic activity of E69 were 60°C and pH 10.5, respectively. The enzyme exhibited stable activity over a wide range of alkaline pH values (7.5-9.5). In addition, E69 was found to be a halotolerant esterase as it exhibited the highest hydrolytic activity in the presence of 0.5 M NaCl and was still active in the presence of 3 M NaCl. Moreover, it possessed some degree of tolerance to Triton X-100 and several organic solvents. Through homology modeling and comparison with other esterases, it was suggested that the absence of the cap domain and its narrow substrate-binding pocket might be responsible for its narrow substrate specificity. Sequence and structural analysis results suggested that its high ratio of negatively to positively charged residues, large hydrophobic surface area, and negative electrostatic potential on the surface may be responsible for its alkaline adaptation. The results of this study provide insight into marine alkaliphilic esterases, and the unique properties of E69 make it a promising candidate as a biocatalyst for industrial applications.
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Affiliation(s)
- Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Zhen Rong
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Shu-Ling Jian
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Cao-Di Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, China
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25
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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26
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A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mychorrizal fungus Tuber melanosporum. Sci Rep 2017; 7:7628. [PMID: 28794466 PMCID: PMC5550427 DOI: 10.1038/s41598-017-08007-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
An increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative “lipases/esterases” preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum (“black truffle”), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters. TmelEST2 was the most active (kcat = 2302 s−1 for p-nitrophenyl-butyrate) and thermally stable (T50 = 68.3 °C), while TmelEST3 was the only one displaying some activity on tertiary alcohol esters. X-ray diffraction analysis of TmelEST2 revealed a classical α/β hydrolase-fold structure, with a network of dimer-stabilizing intermolecular interactions typical of archaea esterases. The predicted structures of TmelEST1 and 3 are overall quite similar to that of TmelEST2 but with some important differences. Most notably, the much smaller volume of the substrate-binding pocket and the more acidic electrostatic surface profile of TmelEST1. This was also the only TmelEST capable of hydrolyzing feruloyl-esters, suggestinng a possible role in root cell-wall deconstruction during symbiosis establishment. In addition to their potential biotechnological interest, TmelESTs raise important questions regarding the evolutionary recruitment of archaea-like enzymes into mesophilic subterranean fungi such as truffles.
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27
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Characterization and enzymatic properties of protein kinase ACR4 from Arabidopsis thaliana. Biochem Biophys Res Commun 2017; 489:270-274. [PMID: 28571742 DOI: 10.1016/j.bbrc.2017.05.163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/28/2017] [Indexed: 01/04/2023]
Abstract
Serine/threonine-protein kinase-like protein ARABIDOPSIS CRINKLY4 (ACR4), a transmembrane protein of Arabidopsis thaliana, plays important roles in cell division and differentiation. Although accumulating studies shed light on the function of ACR4, the structure and catalytic mechanism of ACR4 remain to be elucidated. Here, we report the purification and enzymatic properties of the intracellular kinase domain (residues 464-799) of ACR4 (ACR4IKD). Through Ni-affinity chromatography and gel filter chromatography methods, we successfully obtain high-purity ACR4IKD protein from Escherichia coli. Dynamic light scattering and gel-filtration methods reveal that ACR4IKD distributes with high homogeneity and exists as a monomer in solution. In addition, the ACR4IKD protein has typical kinase activity with myelin basic protein (MBP) as the substrate. Our study may lay the foundation for structure determination of ACR4IKD and further functional research, for example, screening significant substrates of ACR4 in Arabidopsis thaliana.
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28
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Functional characterization of hormone sensitive-like lipase from Bacillus halodurans: synthesis and recovery of pNP-laurate with high yields. Extremophiles 2017; 21:871-889. [DOI: 10.1007/s00792-017-0949-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/23/2017] [Indexed: 12/13/2022]
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29
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Huo YY, Li S, Huang J, Rong Z, Wang Z, Li Z, Ji R, Kuang S, Cui HL, Li J, Xu XW. Crystal structure of Pelagibacterium halotolerans PE8: New insight into its substrate-binding pattern. Sci Rep 2017; 7:4422. [PMID: 28667306 PMCID: PMC5493697 DOI: 10.1038/s41598-017-04550-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/17/2017] [Indexed: 11/16/2022] Open
Abstract
Lysophospholipase_carboxylesterase (LPCE) has highly conserved homologs in many diverse species ranging from bacteria to humans, as well as substantial biological significance and potential therapeutic implications. However, its biological function and catalytic mechanism remain minimally investigated because of the lack of structural information. Here, we report the crystal structure of a bacterial esterase PE8 belonging to the LPCE family. The crystal structure of PE8 was solved with a high resolution of 1.66 Å. Compared with other homologs in the family, significant differences were observed in the amino acid sequence, three-dimensional structure, and substrate-binding pattern. Residue Arg79 undergoes configuration switching when binding to the substrate and forms a unique wall, leading to a relatively closed cavity in the substrate-binding pocket compared with the relatively more open and longer clefts in other homologs. Moreover, the mutant Met122Ala showed much stronger substrate affinity and higher catalytic efficiency because less steric repulsion acted on the substrates. Taken together, these results showed that, in PE8, Arg79 and Met122 play important roles in substrate binding and the binding pocket shaping, respectively. Our study provides new insight into the catalytic mechanism of LPCE, which may facilitate the development of structure-based therapeutics and other biocatalytic applications.
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Affiliation(s)
- Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China
| | - Suhua Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Jing Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Zhen Rong
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China
| | - Zhao Wang
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Siyun Kuang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Heng-Lin Cui
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China.
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China.
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30
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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.
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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
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