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Yoo W, Kim B, Jeon S, Kim KK, Kim TD. Identification, characterization, and immobilization of a novel YbfF esterase from Halomonas elongata. Int J Biol Macromol 2020; 165:1139-1148. [PMID: 33031847 DOI: 10.1016/j.ijbiomac.2020.09.247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022]
Abstract
The YbfF esterase family, which has a bifurcated binding pocket for diverse ligands, could serve as excellent biocatalysts in industrial and biotechnological applications. Here, the identification, characterization, and immobilization of a novel YbfF esterase (YbfFHalomonas elongata) from Halomonas elongata DSM 2581 is reported. Biochemical characterization of YbfF was carried out using activity staining, chromatographic analysis, kinetic analysis, activity assay, acetic acid release, and pH-indicator-based hydrolysis. YbfFH.elongata displayed broad substrate specificity, including that for p-nitrophenyl esters, glucose pentaacetate, tert-butyl acetate, and β-lactam-containing compounds, with high efficiency. Based on a homology model of YbfFH.elongata, Trp237 in the substrate-binding pocket, a critical residue for catalytic activity and substrate specificity was identified and characterized. Furthermore, crosslinked enzyme aggregates and nanoflower formation were explored to enhance the chemical stability and recyclability of YbfFH.elongata. The present study is the first report of a YbfF esterase from extremophiles, and explains its protein stability, catalytic activity, substrate specificities and diversities, kinetics, functional residues, amyloid formation, and immobilization.
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Affiliation(s)
- Wanki Yoo
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Precision Medicine, School of Medicine, SungKyunKwan University, Suwon 16419, Republic of Korea
| | - Booyoung Kim
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sangeun Jeon
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, School of Medicine, SungKyunKwan University, Suwon 16419, Republic of Korea
| | - T Doohun Kim
- Department of Chemistry, Graduate School of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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Le LTHL, Yoo W, Jeon S, Lee C, Kim KK, Lee JH, Kim TD. Biodiesel and flavor compound production using a novel promiscuous cold-adapted SGNH-type lipase ( HaSGNH1) from the psychrophilic bacterium Halocynthiibacter arcticus. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:55. [PMID: 32190120 PMCID: PMC7074997 DOI: 10.1186/s13068-020-01696-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Biodiesel and flavor compound production using enzymatic transesterification by microbial lipases provides mild reaction conditions and low energy cost compared to the chemical process. SGNH-type lipases are very effective catalysts for enzymatic transesterification due to their high reaction rate, great stability, relatively small size for convenient genetic manipulations, and ease of immobilization. Hence, it is highly important to identify novel SGNH-type lipases with high catalytic efficiencies and good stabilities. RESULTS A promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from Halocynthiibacter arcticus was catalytically characterized and functionally explored. HaSGNH1 displayed broad substrate specificity that included tert-butyl acetate, glucose pentaacetate, and p-nitrophenyl esters with excellent stability and high efficiency. Important amino acids (N83, M86, R87, F131, and I173F) around the substrate-binding pocket were shown to be responsible for catalytic activity, substrate specificity, and reaction kinetics. Moreover, immobilized HaSGNH1 was used to produce high yields of butyl and oleic esters. CONCLUSIONS This work provides a molecular understanding of substrate specificities, catalytic regulation, immobilization, and industrial applications of a promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from H. arcticus. This is the first analysis on biodiesel and flavor synthesis using a cold-adapted halophilic SGNH-type lipase from a Halocynthiibacter species.
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Affiliation(s)
- Ly Thi Huong Luu Le
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, 04310 South Korea
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, 04310 South Korea
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Sangeun Jeon
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, 04310 South Korea
| | - Changwoo Lee
- Department of Polar Sciences, University of Science and Technology (UST), Incheon, 21990 South Korea
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, 21990 South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Jun Hyuck Lee
- Department of Polar Sciences, University of Science and Technology (UST), Incheon, 21990 South Korea
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, 21990 South Korea
| | - T. Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul, 04310 South Korea
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Le LTHL, Yoo W, Jeon S, Kim KK, Kim TD. Characterization and Immobilization of a Novel SGNH Family Esterase ( LaSGNH1) from Lactobacillus acidophilus NCFM. Int J Mol Sci 2019; 21:ijms21010091. [PMID: 31877740 PMCID: PMC6981805 DOI: 10.3390/ijms21010091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/10/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022] Open
Abstract
The SGNH family esterases are highly effective biocatalysts due to their strong catalytic efficiencies, great stabilities, relatively small sizes, and ease of immobilization. Here, a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus NCFM, which has homologues in many Lactobacillus species, was identified, characterized, and immobilized. LaSGNH1 is highly active towards acetate- or butyrate-containing compounds, such as p-nitrophenyl acetate or 1-naphthyl acetate. Enzymatic properties of LaSGNH1, including thermal stability, optimum pH, chemical stability, and urea stability, were investigated. Interestingly, LaSGNH1 displayed a wide range of substrate specificity that included glyceryl tributyrate, tert-butyl acetate, and glucose pentaacetate. Furthermore, immobilization of LaSGNH1 by crosslinked enzyme aggregates (CLEAs) showed enhanced thermal stability and efficient recycling property. In summary, this work paves the way for molecular understandings and industrial applications of a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus.
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Affiliation(s)
- Ly Thi Huong Luu Le
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
- Department of Precision Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea;
| | - Sangeun Jeon
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea;
| | - T. Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women’s University, Seoul 04310, Korea; (L.T.H.L.L.); (W.Y.); (S.J.)
- Correspondence: ; Tel.: +82-10-2739-6479
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A novel enantioselective SGNH family esterase (NmSGNH1) from Neisseria meningitides: Characterization, mutational analysis, and ester synthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1438-1448. [DOI: 10.1016/j.bbalip.2019.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 11/18/2022]
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Nair AR, Chellapan G. Improving operational stability of thermostable Pythium myriotylum secretory serine protease by preparation of cross-linked enzyme aggregates (CLEAs). Prep Biochem Biotechnol 2019; 50:107-115. [DOI: 10.1080/10826068.2019.1663537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Aswati R. Nair
- Department of Biochemistry and Molecular Biology, Central University of Kerala (CUK), Kasaragod, Kerala, India
| | - Geethu Chellapan
- School of Biotechnology, National Institute of Technology Calicut, Calicut, India
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Razeq FM, Jurak E, Stogios PJ, Yan R, Tenkanen M, Kabel MA, Wang W, Master ER. A novel acetyl xylan esterase enabling complete deacetylation of substituted xylans. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:74. [PMID: 29588659 PMCID: PMC5863359 DOI: 10.1186/s13068-018-1074-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/09/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Acetylated 4-O-(methyl)glucuronoxylan (GX) is the main hemicellulose in deciduous hardwood, and comprises a β-(1→4)-linked xylopyranosyl (Xylp) backbone substituted by both acetyl groups and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Whereas enzymes that target singly acetylated Xylp or doubly 2,3-O-acetyl-Xylp have been well characterized, those targeting (2-O-MeGlcpA)3-O-acetyl-Xylp structures in glucuronoxylan have remained elusive. RESULTS An unclassified carbohydrate esterase (FjoAcXE) was identified as a protein of unknown function from a polysaccharide utilization locus (PUL) otherwise comprising carbohydrate-active enzyme families known to target xylan. FjoAcXE was shown to efficiently release acetyl groups from internal (2-O-MeGlcpA)3-O-acetyl-Xylp structures, an activity that has been sought after but lacking in known carbohydrate esterases. FjoAcXE action boosted the activity of α-glucuronidases from families GH67 and GH115 by five and nine times, respectively. Moreover, FjoAcXE activity was not only restricted to GX, but also deacetylated (3-O-Araf)2-O-acetyl-Xylp of feruloylated xylooligomers, confirming the broad substrate range of this new carbohydrate esterase. CONCLUSION This study reports the discovery and characterization of the novel carbohydrate esterase, FjoAcXE. In addition to cleaving singly acetylated Xylp, and doubly 2,3-O-acetyl-Xylp, FjoAcXE efficiently cleaves internal 3-O-acetyl-Xylp linkages in (2-O-MeGlcpA)3-O-acetyl-Xylp residues along with densely substituted and branched xylooligomers; activities that until now were missing from the arsenal of enzymes required for xylan conversion.
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Affiliation(s)
- Fakhria M. Razeq
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Edita Jurak
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 00076 Aalto Espoo, Finland
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
| | - Emma R. Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5 Canada
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 00076 Aalto Espoo, Finland
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Wang Y, Ryu BH, Yoo W, Lee CW, Kim KK, Lee JH, Kim TD. Identification, characterization, immobilization, and mutational analysis of a novel acetylesterase with industrial potential (LaAcE) from Lactobacillus acidophilus. Biochim Biophys Acta Gen Subj 2017; 1862:197-210. [PMID: 29051067 DOI: 10.1016/j.bbagen.2017.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/25/2017] [Accepted: 10/10/2017] [Indexed: 11/29/2022]
Abstract
Lactic acid bacteria, which are involved in the fermentation of vegetables, meats, and dairy products, are widely used for the productions of small organic molecules and bioactive peptides. Here, a novel acetylesterase (LaAcE) from Lactobacillus acidophilus NCFM was identified, functionally characterized, immobilized, and subjected to site-directed mutagenesis for biotechnological applications. The enzymatic properties of LaAcE were investigated using biochemical and biophysical methods including native polyacrylamide gel electrophoresis, acetic acid release, biochemical assays, enzyme kinetics, and spectroscopic methods. Interestingly, LaAcE exhibited the ability to act on a broad range of substrates including glucose pentaacetate, glyceryl tributyrate, fish oil, and fermentation-related compounds. Furthermore, immobilization of LaAcE showed good recycling ability and high thermal stability compared with free LaAcE. A structural model of LaAcE was used to guide mutational analysis of hydrophobic substrate-binding region, which was composed of Leu156, Phe164, and Val204. Five mutants (L156A, F164A, V204A, L156A/F164A, and L156A/V204A) were generated and investigated to elucidate the roles of these hydrophobic residues in substrate specificity. This work provided valuable insights into the properties of LaAcE, and demonstrated that LaAcE could be used as a model enzyme of acetylesterase in lactic acid bacteria, making LaAcE a great candidate for industrial applications.
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Affiliation(s)
- Ying Wang
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology (UST), Incheon 21990, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology (UST), Incheon 21990, Republic of Korea
| | - T Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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Kim Y, Ryu BH, Kim J, Yoo W, An DR, Kim BY, Kwon S, Lee S, Wang Y, Kim KK, Kim TD. Characterization of a novel SGNH-type esterase from Lactobacillus plantarum. Int J Biol Macromol 2016; 96:560-568. [PMID: 28040493 DOI: 10.1016/j.ijbiomac.2016.12.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 12/27/2022]
Abstract
Lactic acid bacteria (LAB) are sources of a large variety of microbial ester hydrolases because they can produce a wide range of short-chain esters, phenolic alcohols, and fatty acids. Here, a novel SGNH-type esterase (LpSGNH1) from Lactobacillus plantarum WCFS1 was identified, functionally characterized, and immobilized for biotechnological applications. Homologs of LpSGNH1 are also found in many lactic acid bacteria (LAB) species. Biochemical features of LpSGNH1 were investigated using mass spectrometry, gel filtration chromatography, enzyme kinetics, fluorescence, and circular dichroism (CD) spectroscopy. LpSGNH1 were retained its activity under conditions that would be encountered during fermentations. Interestingly, LpSGNH1 exhibited the ability to act on a broad range of substrates including ketoprofen acetate, cefotaxime (CTX), and 7-aminocephalosporanic acid (7-ACA) as well as glucose pentaacetate, acetylxylan, and acetylalginate, which make LpSGNH1 a great candidate for extensive industrial applications. Furthermore, cross-linked enzyme aggregates of LpSGNH1 (CLEA-LpSGNH1) displayed recycling ability and thermal stability compared to free LpSGNH1, which could be useful for industrial applications. This work highlights the importance of LpSGNH1 in the preparation of commercial compounds, and LpSGNH1 can be used as a model system of SGNH esterases in lactic acid bacteria.
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Affiliation(s)
- Yonggyu Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Jimin Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Wanki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Deu Rae An
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - Boo-Young Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Sena Kwon
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Sojeong Lee
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Ying Wang
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, South Korea
| | - T Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, South Korea.
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Huang J, Huo YY, Ji R, Kuang S, Ji C, Xu XW, Li J. Structural insights of a hormone sensitive lipase homologue Est22. Sci Rep 2016; 6:28550. [PMID: 27328716 PMCID: PMC4916508 DOI: 10.1038/srep28550] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Hormone sensitive lipase (HSL) catalyzes the hydrolysis of triacylglycerols into fatty acids and glycerol, thus playing key roles in energy homeostasis. However, the application of HSL serving as a pharmaceutical target and an industrial biocatalyst is largely hampered due to the lack of high-resolution structural information. Here we report biochemical properties and crystal structures of a novel HSL homologue esterase Est22 from a deep-sea metagenomic library. Est22 prefers short acyl chain esters and has a very high activity with substrate p-nitrophenyl butyrate. The crystal structures of wild type and mutated Est22 with its product p-nitrophenol are solved with resolutions ranging from 1.4 Å to 2.43 Å. The Est22 exhibits a α/β-hydrolase fold consisting with a catalytic domain and a substrate-recognizing cap domain. Residues Ser188, Asp287, and His317 comprise the catalytic triad in the catalytic domain. The p-nitrophenol molecule occupies the substrate binding pocket and forms hydrogen bonds with adjacent residues Gly108, Gly109, and Gly189. Est22 exhibits a dimeric form in solution, whereas mutants D287A and H317A change to polymeric form, which totally abolished its enzymatic activities. Our study provides insights into the catalytic mechanism of HSL family esterase and facilitates the understanding for further industrial and biotechnological applications of esterases.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Siyun Kuang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, China,
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China,
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Abstract
Primordial germ cells are the progenitor cells that give rise to the gametes. In some animals, the germline is induced by zygotic transcription factors, whereas in others, primordial germ cell specification occurs via inheritance of maternally provided gene products known as germ plasm. Once specified, the primordial germ cells of some animals must acquire motility and migrate to the gonad in order to survive. In all animals examined, perinuclear structures called germ granules form within germ cells. This review focuses on some of the recent studies, conducted by several groups using diverse systems, from invertebrates to vertebrates, which have provided mechanistic insight into the molecular regulation of germ cell specification and migration.
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Affiliation(s)
- Florence Marlow
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY, 10461, USA; Department of Neuroscience, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY, 10461, USA
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11
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Jang E, Shim HW, Ryu BH, An DR, Yoo WK, Kim KK, Kim DW, Kim TD. Preparation of cobalt nanoparticles from polymorphic bacterial templates: A novel platform for biocatalysis. Int J Biol Macromol 2015; 81:747-53. [PMID: 26358553 DOI: 10.1016/j.ijbiomac.2015.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 08/31/2015] [Accepted: 09/04/2015] [Indexed: 12/20/2022]
Abstract
Nanoparticles have gathered significant research attention as materials for enzyme immobilization due to their advantageous properties such as low diffusion rates, ease of manipulation, and large surface areas. Here, polymorphic cobalt nanoparticles of varied sizes and shapes were prepared using Micrococcus lylae, Bacillus subtilis, Escherichia coli, Paracoccus sp., and Haloarcula vallismortis as bacterial templates. Furthermore, nine lipases/carboxylesterases were successfully immobilized on these cobalt nanoparticles. Especially, immobilized forms of Est-Y29, LmH, and Sm23 were characterized in more detail for potential industrial applications. Immobilization of enzymes onto cobalt oxide nanoparticles prepared from polymorphic bacterial templates may have potential for efficient hydrolysis on an industrial-scale, with several advantages such as high retention of enzymatic activity, increased stability, and strong reusability.
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Affiliation(s)
- Eunjin Jang
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea
| | - Hyun-Woo Shim
- School of Civil, Environmental, and Architectural Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Deu Rae An
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Wan Ki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Dong-Wan Kim
- School of Civil, Environmental, and Architectural Engineering, Korea University, Seoul 136-713, Republic of Korea
| | - T Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 140-742, Republic of Korea.
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12
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Kim K, Ryu BH, Kim SS, An DR, Ngo TD, Pandian R, Kim KK, Kim TD. Structural and biochemical characterization of a carbohydrate acetylesterase from Sinorhizobium meliloti 1021. FEBS Lett 2015; 589:117-122. [PMID: 25436419 DOI: 10.1016/j.febslet.2014.11.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 12/29/2022]
Abstract
In many microorganisms, carbohydrate acetylesterases remove the acetyl groups from various types of carbohydrates. Sm23 from Sinorhizobium meliloti is a putative member of carbohydrate esterase family 3 (CE3) in the CAZy classification system. Here, we determined the crystal structure of Sm23 at 1.75 Å resolution and investigated functional properties using biochemical methods. Furthermore, immobilized Sm23 exhibited improved stability compared with soluble Sm23, which can be used for the design of plant cell wall degrading-systems.
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Affiliation(s)
- Kyungmin Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Bum Han Ryu
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-741, Republic of Korea
| | - Sung Soo Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Deu Rae An
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-741, Republic of Korea
| | - Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Ramesh Pandian
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea.
| | - T Doohun Kim
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-741, Republic of Korea.
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Surface functional modification of self-assembled insulin nanospheres for improving intestinal absorption. Int J Biol Macromol 2014; 74:49-60. [PMID: 25433129 DOI: 10.1016/j.ijbiomac.2014.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/17/2014] [Accepted: 11/19/2014] [Indexed: 01/12/2023]
Abstract
In this work we fabricated therapeutic protein drugs such as insulin as free-carrier delivery system to improve their oral absorption efficiency. The formulation involved self-assembly of insulin into nanospheres (INS) by a novel thermal induced phase separation method. In consideration of harsh environment in gastrointestinal tract, surface functional modification of INS with ɛ-poly-L-lysine (EPL) was employed to form a core-shell structure (INS@EPL) and protect them from too fast dissociation before their arriving at target uptake sites. Both INS and INS@EPL were characterized as uniformly spherical particles with mean diameter size of 150-300 nm. The process of transient thermal treatment did not change their biological potency retention significantly. In vitro dissolution studies showed that shell cross-linked of INS with EPL improved the release profiles of insulin from the self-assembled nanospheres at intestinal pH. Confocal microscopy visualization and transport experiments proved the enhanced paracellular permeability of INS@EPL in Caco-2 cells. Compared to that of INS, enteral administration of INS@EPL at 20 IU/kg resulted in more significant hypoglycemic effects in diabetic rats up to 12 h. Accordingly, the results indicated that surface functional modification of self-assembled insulin nanospheres with shell cross-linked polycationic peptide could be a promising candidate for oral therapeutic protein delivery.
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14
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Ngo TD, Ryu BH, Ju H, Jang EJ, Kim KK, Kim TD. Crystallographic analysis and biochemical applications of a novel penicillin-binding protein/β-lactamase homologue from a metagenomic library. ACTA ACUST UNITED AC 2014; 70:2455-66. [PMID: 25195758 DOI: 10.1107/s1399004714015272] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/29/2014] [Indexed: 11/10/2022]
Abstract
Interest in penicillin-binding proteins and β-lactamases (the PBP-βL family) is increasing owing to their biological and clinical significance. In this study, the crystal structure of Est-Y29, a metagenomic homologue of the PBP-βL family, was determined at 1.7 Å resolution. In addition, complex structures of Est-Y29 with 4-nitrophenyl phosphate (4NP) and with diethyl phosphonate (DEP) at 2.0 Å resolution were also elucidated. Structural analyses showed that Est-Y29 is composed of two domains: a β-lactamase fold and an insertion domain. A deep hydrophobic patch between these domains defines a wide active site, and a nucleophilic serine (Ser58) residue is located in a groove defined primarily by hydrophobic residues between the two domains. In addition, three hydrophobic motifs, which make up the substrate-binding site, allow this enzyme to hydrolyze a wide variety of hydrophobic compounds, including fish and olive oils. Furthermore, cross-linked Est-Y29 aggregates (CLEA-Est-Y29) significantly increase the stability of the enzyme as well as its potential for extensive reuse in various deactivating conditions. The structural features of Est-Y29, together with biochemical and biophysical studies, could provide a molecular basis for understanding the properties and regulatory mechanisms of the PBP-βL family and their potential for use in industrial biocatalysts.
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Affiliation(s)
- Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Bum Han Ryu
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-749, Republic of Korea
| | - Hansol Ju
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-749, Republic of Korea
| | - Eun Jin Jang
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-749, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - T Doohun Kim
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-749, Republic of Korea
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15
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Adsorption of microbial esterases on Bacillus subtilis-templated cobalt oxide nanoparticles. Int J Biol Macromol 2014; 65:188-92. [DOI: 10.1016/j.ijbiomac.2014.01.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 11/18/2022]
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16
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Ryu BH, Nguyen DD, Ngo TD, Oh C, Pandian R, Kim KK, Kim TD. Crystallization and preliminary X-ray analysis of a highly stable novel SGNH hydrolase (Est24) from Sinorhizobium meliloti. Acta Crystallogr F Struct Biol Commun 2014; 70:193-5. [PMID: 24637754 PMCID: PMC3936437 DOI: 10.1107/s2053230x13033918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/16/2013] [Indexed: 11/10/2022] Open
Abstract
The SGNH hydrolase family includes enzymes that catalyze the hydrolysis of a broad range of substrates. Here, the crystallization and preliminary X-ray crystallographic studies of a novel SGNH hydrolase (Est24) from Sinorhizobium meliloti were performed. Recombinant Est24 protein containing an N-terminal His tag was expressed in Escherichia coli and purified to homogeneity. Est24 was then crystallized using a solution consisting of 0.2 M ammonium phosphate pH 4.6, 20% polyethylene glycol 3350. X-ray diffraction data were collected to a resolution of 1.45 Å with an R(merge) of 9.4%. The Est24 crystals belonged to space group C2, with unit-cell parameters a = 129.09, b = 88.63, c = 86.15 Å, α = 90.00, β = 114.30, γ = 90.00°. A molecular-replacement solution was obtained using the crystal structure of Mycobacterium smegmatis arylesterase as a template and structure refinement of Est24 is in progress.
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Affiliation(s)
- Bum Han Ryu
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-749, Republic of Korea
| | - Duy Duc Nguyen
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Changsuk Oh
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Ramesh Pandian
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - T. Doohun Kim
- Department of Applied Chemistry and Biological Engineering, College of Engineering, Ajou University, Suwon 443-749, Republic of Korea
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17
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Jang E, Ryu BH, Ju H, Doohun Kim T. Identification, characterization, and application of a virulence factor (EfEstA) from Enterococcus faecalis. BIORESOURCE TECHNOLOGY 2013; 143:691-694. [PMID: 23860564 DOI: 10.1016/j.biortech.2013.06.086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/20/2013] [Accepted: 06/23/2013] [Indexed: 06/02/2023]
Abstract
Although virulence factors from pathogenic bacteria have been proposed as promising industrial enzymes, characterization and application of these enzymes have been still unexplored. The objective of this study was to identify and characterize virulence factors from pathogenic bacteria for industrial applications. Here, a virulence factor (EfEstA) from Enterococcus faecalis was identified and characterized using SDS-PAGE, enzyme assays, and molecular modeling. In addition, it has been shown that cross-linked enzyme aggregates (CLEAs) of EfEstA exhibited improved stabilities and high recycling activities compared to free EfEstA. These characteristics of EfEstA shed light on the design of new lipase-based systems for industrial applications.
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Affiliation(s)
- Eunjin Jang
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, South Korea
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18
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Ngo TD, Ryu BH, Ju H, Jang E, Park K, Kim KK, Kim TD. Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1726-37. [PMID: 23999296 DOI: 10.1107/s0907444913013425] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 05/15/2013] [Indexed: 11/10/2022]
Abstract
Intracellular mobilization of fatty acids from triacylglycerols in mammalian adipose tissues proceeds through a series of lipolytic reactions. Among the enzymes involved, hormone-sensitive lipase (HSL) is noteworthy for its central role in energy homeostasis and the pathogenic role played by its dysregulation. By virtue of its broad substrate specificity, HSL may also serve as an industrial biocatalyst. In a previous report, Est25, a bacterial homologue of HSL, was identified from a metagenomic library by functional screening. Here, the crystal structure of Est25 is reported at 1.49 Å resolution; it exhibits an α/β-hydrolase fold consisting of a central β-sheet enclosed by α-helices on both sides. The structural features of the cap domain, the substrate-binding pocket and the dimeric interface of Est25, together with biochemical and biophysical studies including native PAGE, mass spectrometry, dynamic light scattering, gel filtration and enzyme assays, could provide a basis for understanding the properties and regulation of hormone-sensitive lipase (HSL). The increased stability of cross-linked Est25 aggregates (CLEA-Est25) and their potential for extensive reuse support the application of this preparation as a biocatalyst in biotransformation processes.
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Affiliation(s)
- Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
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19
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Talekar S, Joshi A, Joshi G, Kamat P, Haripurkar R, Kambale S. Parameters in preparation and characterization of cross linked enzyme aggregates (CLEAs). RSC Adv 2013. [DOI: 10.1039/c3ra40818c] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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20
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Ryu BH, Ngo TD, Jang E, Kim S, Ju H, Kim KK, Kim TD. Identification, crystallization and preliminary X-ray diffraction analysis of esterase A from Caulobacter crescentus CB15, a family VIII lipolytic enzyme. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:560-4. [PMID: 22691788 PMCID: PMC3374513 DOI: 10.1107/s1744309112009992] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 03/06/2012] [Indexed: 11/10/2022]
Abstract
The structures and functions of family VIII lipolytic enzymes, which have moderate sequence identity to class C β-lactamases and penicillin-binding proteins, are largely unknown. Here, the X-ray crystallographic study of a family VIII esterase from Caulobacter crescentus CB15 (CcEstA) is described. Sequence analysis revealed that CcEstA has a conserved serine residue within the S-X-X-K motif which acts as a catalytic nucleophile. Recombinant protein containing an N-terminal His tag was expressed in Escherichia coli and purified to homogeneity. Functional studies showed that CcEstA acts on α- and β-naphthyl acetate as substrates. In addition, it can catalyze the hydrolysis of ketoprofen ethyl ester, a highly useful product in industrial applications. CcEstA was crystallized using a solution consisting of 1.0 M potassium/sodium tartrate, 0.1 M imidazole pH 8.0, 0.2 M NaCl, and X-ray diffraction data were collected to a resolution of 1.62 Å with an R(merge) of 9.4%. The crystals of CcEstA belonged to space group C222(1), with unit-cell parameters a = 172.23, b = 176.68, c = 47.93 Å. Structure determination is in progress.
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Affiliation(s)
- Bum Han Ryu
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| | - Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Eunjin Jang
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| | - Sungsoo Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Hansol Ju
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - T. Doohun Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
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Bae SY, Ryu BH, Jang E, Kim S, Kim TD. Characterization and immobilization of a novel SGNH hydrolase (Est24) from Sinorhizobium meliloti. Appl Microbiol Biotechnol 2012; 97:1637-47. [PMID: 22526795 DOI: 10.1007/s00253-012-4038-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/11/2012] [Accepted: 03/16/2012] [Indexed: 12/13/2022]
Abstract
A novel oligomeric SGNH hydrolase (Est24) from Sinorhizobium meliloti was identified, actively expressed in Escherichia coli, characterized, and immobilized for industrial application. Sequence analysis of Est24 revealed a putative catalytic triad (Ser¹³-Asp¹⁶³-His¹⁶⁹), with moderate homology to other SGNH hydrolases. Est24 was more active toward short-chain esters, such as p-nitrophenyl acetate, butyrate, and valerate, while the S13A mutant completely lost its activity. Moreover, the activity of Est24 toward α- and β-naphthyl acetate, and enantioselectivity on (R)- and (S)-methyl-3-hydroxy-2-methylpropionate were tested. Est24 exhibited optimum activity at mesophilic temperature ranges (45-55 °C), and slightly alkaline pH (8.0). Structural and mutagenesis studies revealed critical residues involved in the formation of a catalytic triad and substrate-binding pocket. Cross-linked enzyme aggregates (CLEAs) of Est24 with and without amyloid fibrils were prepared, and amyloid fibril-linked Est24 with amyloid fibrils retained 83 % of its initial activity after 1 h of incubation at 60 °C. The high thermal stability of immobilized Est24 highlights its potential in the pharmaceutical and chemical industries.
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Affiliation(s)
- Song Yi Bae
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, South Korea
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