Kim TD

References (22)

Title : Dual functional roles of a novel bifunctional beta-lactamase\/esterase from Lactococcus garvieae - Le_2022_Int.J.Biol.Macromol__
Author(s) : Le L , Yoo W , Wang Y , Jeon S , Kim KK , Kim HW , Kim TD
Ref : Int J Biol Macromol , : , 2022
Abstract : A novel bifunctional beta-lactamase/esterase (LgLacI), which is capable of hydrolyzing beta-lactam-containing antibiotics including ampicillin, oxacillin, and cefotaxime as well as synthesizing biodiesels, was cloned from Lactococcus garvieae. Unlike most bacterial esterases/lipases that have G-x-S-x-G motif, LgLacI, which contains S-x-x-K catalytic motif, has sequence similarities to bacterial family VIII esterase as well as beta-lactamases. The catalytic properties of LgLacI were explored using a wide range of biochemical methods including spectroscopy, assays, structural modeling, mutagenesis, and chromatography. We confirmed the bifunctional property of LgLacI hydrolyzing both esters and beta-lactam antibiotics. This study provides novel perspectives into a bifunctional enzyme from L. garvieae, which can degrade beta-lactam antibiotics with high esterase activity.
ESTHER : Le_2022_Int.J.Biol.Macromol__
PubMedSearch : Le_2022_Int.J.Biol.Macromol__
PubMedID: 35183603

Title : Identification, Characterization, and Preliminary X-ray Diffraction Analysis of a Novel Esterase (ScEst) from Staphylococcus chromogenes - Hwang_2022_Crystals_12_546
Author(s) : Hwang J , Jeon S , Lee M.J , Yoo W , Chang J , Kim KK , Lee JH , Do H , Kim TD
Ref : Crystals , 12 :546 , 2022
Abstract : Ester prodrugs can develop novel antibiotics and have potential therapeutic applications against multiple drug-resistant bacteria. The antimicrobial activity of these prodrugs is activated after being cleaved by the esterases produced by the pathogen. Here, novel esterase ScEst originating from Staphylococcus chromogenes NCTC10530, which causes dairy cow mastitis, was identified, characterized, and analyzed using X-ray crystallography. The gene encoding ScEst was cloned into the pVFT1S vector and overexpressed in E. coli. The recombinant ScEst protein was obtained by affinity and size-exclusion purification. ScEst showed substrate preference for the short chain length of acyl derivatives. It was crystallized in an optimized solution composed of 0.25 M ammonium citrate tribasic (pH 7.0) and 20% PEG 3350 at 296 K. A total of 360 X-ray diffraction images were collected at a 1.66 A resolution. ScEst crystal belongs to the space group of P212121 with the unit cell parameters of a = 50.23 A, b = 68.69 A, c = 71.15 A, and alpha = beta = gamma = 90deg. Structure refinement after molecular replacement is under progress. Further biochemical studies will elucidate the hydrolysis mechanism of ScEst. Overall, this study is the first to report the functional characterization of an esterase from Staphylococcus chromogenes, which is potentially useful in elaborating its hydrolysis mechanism
ESTHER : Hwang_2022_Crystals_12_546
PubMedSearch : Hwang_2022_Crystals_12_546
PubMedID:
Gene_locus related to this paper: stacr-SUM13810

Title : Sequence Analysis and Preliminary X-ray Crystallographic Analysis of an Acetylesterase (LgEstI) from Lactococcus garvieae - Do_2022_Crystals_12_46
Author(s) : Do H , Wang Y , Lee CW , Yoo W , Jeon S , Hwang J , Lee MJ , Kim KK , Kim HW , Lee JH , Kim TD
Ref : Crystals , 12 :46 , 2022
Abstract : A gene encoding LgEstI was cloned from a bacterial fish pathogen, Lactococcus garvieae. Sequence and bioinformatic analysis revealed that LgEstI is close to the acetyl esterase family and had maximum similarity to a hydrolase (UniProt: Q5UQ83) from Acanthamoeba polyphaga mimivirus (APMV). Here, we present the results of LgEstI overexpression and purification, and its preliminary X-ray crystallographic analysis. The wild-type LgEstI protein was overexpressed in Escherichia coli, and its enzymatic activity was tested using p-nitrophenyl of varying lengths. LgEstI protein exhibited higher esterase activity toward p-nitrophenyl acetate. To better understand the mechanism underlying LgEstI activity and subject it to protein engineering, we determined the high-resolution crystal structure of LgEstI. First, the wild-type LgEstI protein was crystallized in 0.1 M Tris-HCl buffer (pH 7.1), 0.2 M calcium acetate hydrate, and 19% (w/v) PEG 3000, and the native X-ray diffraction dataset was collected up to 2.0 A resolution. The crystal structure was successfully determined using a molecular replacement method, and structure refinement and model building are underway. The upcoming complete structural information of LgEstI may elucidate the substrate-binding mechanism and provide novel strategies for subjecting LgEstI to protein engineering.
ESTHER : Do_2022_Crystals_12_46
PubMedSearch : Do_2022_Crystals_12_46
PubMedID:
Gene_locus related to this paper: 9lact-a0a5m9r5n4

Title : Purification and Crystallographic Analysis of a Novel Cold-Active Esterase (HaEst1) from Halocynthiibacter arcticus - Jeon_2021_Crystals_11_170
Author(s) : Jeon S , Hwang J , Yoo W , Chang JW , Do H , Kim HW , Kim KK , Lee JH , Kim TD
Ref : Crystals , 11 :170 , 2021
Abstract : This report deals with the purification, characterization, and a preliminary crystallographic study of a novel cold-active esterase (HaEst1) from Halocynthiibacter arcticus. Primary sequence analysis reveals that HaEst1 has a catalytic serine in G-x-S-x-G motif. The recombinant HaEst1 was cloned, expressed, and purified. SDS-PAGE and zymographic analysis were carried out to characterize the properties of HaEst1. A single crystal of HaEst1 was obtained in a solution containing 10% (w/v) PEG 8000/8% ethylene glycol, 0.1 M Hepes-NaOH, pH 7.5. Diffraction data were collected to 2.10 A resolution with P21 space group. The final Rmerge and Rp.i.m values were 7.6% and 3.5% for 50-2.10 A resolution. The unit cell parameters were a = 35.69 A, b = 91.21 A, c = 79.15 A, and beta = 96.9deg
ESTHER : Jeon_2021_Crystals_11_170
PubMedSearch : Jeon_2021_Crystals_11_170
PubMedID:
Gene_locus related to this paper: 9rhob-a0a126uwz8

Title : Identification, characterization, and immobilization of a novel YbfF esterase from Halomonas elongata - Yoo_2020_Int.J.Biol.Macromol_165_1139
Author(s) : Yoo W , Kim B , Jeon S , Kim KK , Kim TD
Ref : Int J Biol Macromol , 165 :1139 , 2020
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 (YbfF(Halomonas 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. YbfF(H.elongata) displayed broad substrate specificity, including that for p-nitrophenyl esters, glucose pentaacetate, tert-butyl acetate, and beta-lactam-containing compounds, with high efficiency. Based on a homology model of YbfF(H.elongata), Trp(237) 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 YbfF(H.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.
ESTHER : Yoo_2020_Int.J.Biol.Macromol_165_1139
PubMedSearch : Yoo_2020_Int.J.Biol.Macromol_165_1139
PubMedID: 33031847
Gene_locus related to this paper: haled-e1v389

Title : Characterization and mutation anaylsis of a cold-active bacterial hormone-sensitive lipase from Salinisphaera sp. P7-4 - Kim_2019_Arch.Biochem.Biophys_663_132
Author(s) : Kim BY , Yoo W , Huong Luu Le LT , Kim KK , Kim HW , Lee JH , Kim YO , Kim TD
Ref : Archives of Biochemistry & Biophysics , 663 :132 , 2019
Abstract : In mammals, hormone sensitive lipase (EC 3.1.1.79, HSL) catalyzes the hydrolysis of triacylglycerols as well as the modifications of a broad range of hydrophobic substrates containing ester linkages. HSLs are composed of an N-terminal ligand-binding domain and a C-terminal catalytic domain. Bacterial hormone-sensitive lipases (bHSLs), which are homologous to the C-terminal domain of mammalian HSLs, have a catalytic triad composed of Ser, His, and Asp. Here, a novel cold-active hormone-sensitive lipase (SaHSL) from Salinisphaera sp. P7-4 was identified, functionally characterized, and subjected to site-directed mutations. The enzymatic properties of SaHSL were investigated using several biochemical and biophysical methods. Interestingly, SaHSL exhibited the ability to act on a broad range of substrates including glyceryl tributyrate and glucose pentaacetate. Homology modeling and site-directed mutagenesis indicated that hydrophobic residues (Leu(156), Phe(164), and Val(204)) around the substrate-binding pocket were involved in substrate recognition. In addition, highly conserved amino acids (Glu(201), Arg(207), Leu(208), and Asp(227)) in the regulatory regions were found to be responsible for substrate specificity, thermostability, and enantioselectivity. In summary, this work provides new insights into the understanding of the C-terminal domain of HSL family and evidence that SaHSL can be used in a wide range of industrial applications.
ESTHER : Kim_2019_Arch.Biochem.Biophys_663_132
PubMedSearch : Kim_2019_Arch.Biochem.Biophys_663_132
PubMedID: 30653961
Gene_locus related to this paper: 9gamm-h8ypm9

Title : A novel enantioselective SGNH family esterase (NmSGNH1) from Neisseria meningitides: Characterization, mutational analysis, and ester synthesis - Yoo_2019_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids_1864_1438
Author(s) : Yoo W , Le L , Lee JH , Kim KK , Kim TD
Ref : Biochimica & Biophysica Acta Molecular & Cellular Biology Lipids , 1864 :1438 , 2019
Abstract : In Neisseria sp., SGNH family esterases are involved in bacterial pathogenesis as well as cell wall peptidoglycan maturation. Here, a novel enantioselective SGNH family esterase (NmSGNH1) from Neisseria meningitidis, which has sequence similarity to carbohydrate esterase (CE3) family, was catalytically characterized and functionally explored. NmSGNH1 exhibited a wide range of substrate specificities including naproxol acetate, tert-butyl acetate, glucose pentaacetate as well as p-nitrophenyl esters. Deletion of C-terminal residues (NmSGNH1Delta11) led to the altered substrate specificity, reduced catalytic activity, and increased thermostability. Furthermore, a hydrophobic residue of Leu(92) in the substrate-binding pocket was identified to be critical in catalytic activity, thermostability, kinetics, and enantioselectivity. Interestingly, immobilization of NmSGNH1 by hybrid nanoflowers (hNFs) and crosslinked enzyme aggregates (CLEAs) showed increased level of activity, recycling property, and enhanced stability. Finally, synthesis of butyl acetate, oleic acid esters, and fatty acid methyl esters (FAMEs) were verified. In summary, this work provides a molecular understanding of substrate specificities, catalytic regulation, immobilization, and industrial applications of a novel SGNH family esterase from Neisseria meningitidis.
ESTHER : Yoo_2019_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids_1864_1438
PubMedSearch : Yoo_2019_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids_1864_1438
PubMedID: 31325637

Title : Structural and functional characterization of a novel cold-active S-formylglutathione hydrolase (SfSFGH) homolog from Shewanella frigidimarina, a psychrophilic bacterium - Lee_2019_Microb.Cell.Fact_18_140
Author(s) : Lee CW , Yoo W , Park SH , Le L , Jeong CS , Ryu BH , Shin SC , Kim HW , Park H , Kim KK , Kim TD , Lee JH
Ref : Microb Cell Fact , 18 :140 , 2019
Abstract : BACKGROUND: S-Formylglutathione is hydrolyzed to glutathione and formate by an S-formylglutathione hydrolase (SFGH) (3.1.2.12). This thiol esterase belongs to the esterase family and is also known as esterase D. SFGHs contain highly conserved active residues of Ser-Asp-His as a catalytic triad at the active site. Characterization and investigation of SFGH from Antarctic organisms at the molecular level is needed for industrial use through protein engineering. RESULTS: A novel cold-active S-formylglutathione hydrolase (SfSFGH) from Shewanella frigidimarina, composed of 279 amino acids with a molecular mass of ~ 31.0 kDa, was characterized. Sequence analysis of SfSFGH revealed a conserved pentapeptide of G-X-S-X-G found in various lipolytic enzymes along with a putative catalytic triad of Ser148-Asp224-His257. Activity analysis showed that SfSFGH was active towards short-chain esters, such as p-nitrophenyl acetate, butyrate, hexanoate, and octanoate. The optimum pH for enzymatic activity was slightly alkaline (pH 8.0). To investigate the active site configuration of SfSFGH, we determined the crystal structure of SfSFGH at 2.32 A resolution. Structural analysis shows that a Trp182 residue is located at the active site entrance, allowing it to act as a gatekeeper residue to control substrate binding to SfSFGH. Moreover, SfSFGH displayed more than 50% of its initial activity in the presence of various chemicals, including 30% EtOH, 1% Triton X-100, 1% SDS, and 5 M urea. CONCLUSIONS: Mutation of Trp182 to Ala allowed SfSFGH to accommodate a longer chain of substrates. It is thought that the W182A mutation increases the substrate-binding pocket and decreases the steric effect for larger substrates in SfSFGH. Consequently, the W182A mutant has a broader substrate specificity compared to wild-type SfSFGH. Taken together, this study provides useful structure-function data of a SFGH family member and may inform protein engineering strategies for industrial applications of SfSFGH.
ESTHER : Lee_2019_Microb.Cell.Fact_18_140
PubMedSearch : Lee_2019_Microb.Cell.Fact_18_140
PubMedID: 31426813
Gene_locus related to this paper: shefn-SfSFGH

Title : Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application - Oh_2019_Crystals_9_597
Author(s) : Oh C , Kim TD , Kim KK
Ref : , 9 :597 , 2019
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 alpha/beta/alpha sandwich architecture is most frequently found in CEHs, but 3-solenoid, beta-barrel, up-down bundle, alpha/beta/beta/alpha 4-layer sandwich, 6 or 7 propeller and alpha/beta 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.
ESTHER : Oh_2019_Crystals_9_597
PubMedSearch : Oh_2019_Crystals_9_597
PubMedID:

Title : Characterization, immobilization, and mutagenesis of a novel cold-active acetylesterase (EaAcE) from Exiguobacterium antarcticum B7 - Wang_2019_Int.J.Biol.Macromol_136_1042
Author(s) : Wang Y , Le L , Yoo W , Lee CW , Kim KK , Lee JH , Kim TD
Ref : Int J Biol Macromol , 136 :1042 , 2019
Abstract : Cold-active enzymes with distinctive properties from a psychrophilic Exiguobacterium antarcticum B7 could be excellent biocatalysts in industrial and biotechnological processes. Here, the characterization, immobilization, and site-directed mutagenesis of a novel cold-active acetylesterase (EaAcE) from E. antarcticum B7 is reported. EaAcE does not belong to any currently known lipase/esterase family, although there are some sequence similarities with family III and V members. Biochemical characterization of EaAcE was carried out using activity staining, mass spectrometry analysis, circular dichroism spectra, freeze-thaw experiments, kinetic analysis, acetic acid release assays, and enantioselectivity determination. Furthermore, immobilization of EaAcE using four different approaches was explored to enhance its thermal stability and recyclability. Based on a homology model of EaAcE, four mutations (F45A, S118A, S141A, and T216A) within the substrate-binding pocket were investigated to elucidate their roles in EaAcE catalysis and substrate specificity. This work has provided invaluable information on the properties of EaAcE, which can now be used to understand the acetylesterase enzyme family.
ESTHER : Wang_2019_Int.J.Biol.Macromol_136_1042
PubMedSearch : Wang_2019_Int.J.Biol.Macromol_136_1042
PubMedID: 31229546
Gene_locus related to this paper: exiab-EaAcE

Title : Identification, characterization, immobilization, and mutational analysis of a novel acetylesterase with industrial potential (LaAcE) from Lactobacillus acidophilus - Wang_2018_Biochim.Biophys.Acta_1862_197
Author(s) : Wang Y , Ryu BH , Yoo W , Lee CW , Kim KK , Lee JH , Kim TD
Ref : Biochimica & Biophysica Acta , 1862 :197 , 2018
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 Leu(156), Phe(164), and Val(204). 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.
ESTHER : Wang_2018_Biochim.Biophys.Acta_1862_197
PubMedSearch : Wang_2018_Biochim.Biophys.Acta_1862_197
PubMedID: 29051067
Gene_locus related to this paper: lacac-q5fmn2

Title : Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp - Park_2018_PLoS.One_13_e0206260
Author(s) : Park SH , Yoo W , Lee CW , Jeong CS , Shin SC , Kim HW , Park H , Kim KK , Kim TD , Lee JH
Ref : PLoS ONE , 13 :e0206260 , 2018
Abstract : Cold-active acetyl xylan esterases allow for reduced bioreactor heating costs in bioenergy production. Here, we isolated and characterized a cold-active acetyl xylan esterase (PbAcE) from the psychrophilic soil microbe Paenibacillus sp. R4. The enzyme hydrolyzes glucose penta-acetate and xylan acetate, reversibly producing acetyl xylan from xylan, and it shows higher activity at 4 degrees C than at 25 degrees C. We solved the crystal structure of PbAcE at 2.1-A resolution to investigate its active site and the reason for its low-temperature activity. Structural analysis showed that PbAcE forms a hexamer with a central substrate binding tunnel, and the inter-subunit interactions are relatively weak compared with those of its mesophilic and thermophilic homologs. PbAcE also has a shorter loop and different residue composition in the beta4-alpha3 and beta5-alpha4 regions near the substrate binding site. Flexible subunit movements and different active site loop conformations may enable the strong low-temperature activity and broad substrate specificity of PbAcE. In addition, PbAcE was found to have strong activity against antibiotic compound substrates, such as cefotaxime and 7-amino cephalosporanic acid (7-ACA). In conclusion, the PbAcE structure and our biochemical results provide the first example of a cold-active acetyl xylan esterase and a starting template for structure-based protein engineering.
ESTHER : Park_2018_PLoS.One_13_e0206260
PubMedSearch : Park_2018_PLoS.One_13_e0206260
PubMedID: 30379876
Gene_locus related to this paper: 9mico-6AGQ

Title : Crystal Structure and Functional Characterization of an Esterase (EaEST) from Exiguobacterium antarcticum - Lee_2017_PLoS.One_12_e0169540
Author(s) : Lee CW , Kwon S , Park SH , Kim BY , Yoo W , Ryu BH , Kim HW , Shin SC , Kim S , Park H , Kim TD , Lee JH
Ref : PLoS ONE , 12 :e0169540 , 2017
Abstract : A novel microbial esterase, EaEST, from a psychrophilic bacterium Exiguobacterium antarcticum B7, was identified and characterized. To our knowledge, this is the first report describing structural analysis and biochemical characterization of an esterase isolated from the genus Exiguobacterium. Crystal structure of EaEST, determined at a resolution of 1.9 A, showed that the enzyme has a canonical alpha/beta hydrolase fold with an alpha-helical cap domain and a catalytic triad consisting of Ser96, Asp220, and His248. Interestingly, the active site of the structure of EaEST is occupied by a peracetate molecule, which is the product of perhydrolysis of acetate. This result suggests that EaEST may have perhydrolase activity. The activity assay showed that EaEST has significant perhydrolase and esterase activity with respect to short-chain p-nitrophenyl esters (<=C8), naphthyl derivatives, phenyl acetate, and glyceryl tributyrate. However, the S96A single mutant had low esterase and perhydrolase activity. Moreover, the L27A mutant showed low levels of protein expression and solubility as well as preference for different substrates. On conducting an enantioselectivity analysis using R- and S-methyl-3-hydroxy-2-methylpropionate, a preference for R-enantiomers was observed. Surprisingly, immobilized EaEST was found to not only retain 200% of its initial activity after incubation for 1 h at 80 degrees C, but also retained more than 60% of its initial activity after 20 cycles of reutilization. This research will serve as basis for future engineering of this esterase for biotechnological and industrial applications.
ESTHER : Lee_2017_PLoS.One_12_e0169540
PubMedSearch : Lee_2017_PLoS.One_12_e0169540
PubMedID: 28125606
Gene_locus related to this paper: exiab-k0acl0

Title : Bacterial Hormone-Sensitive Lipases (bHSLs): Emerging Enzymes for Biotechnological Applications - Kim_2017_J.Microbiol.Biotechnol_27_1907
Author(s) : Kim TD
Ref : J Microbiol Biotechnol , 27 :1907 , 2017
Abstract : Lipases are important enzymes with biotechnological applications in dairy, detergent, food, fine chemicals, and pharmaceutical industries. Specifically, hormone-sensitive lipase (HSL) is an intracellular lipase that can be stimulated by several hormones, such as catecholamine, glucagon, and adrenocorticotropic hormone. Bacterial hormone-sensitive lipases (bHSLs), which are homologous to the C-terminal domain of HSL, have alpha/beta-hydrolase fold with a catalytic triad composed of His, Asp, and Ser. These bHSLs could be used for a wide variety of industrial applications because of their high activity, broad substrate specificity, and remarkable stability. In this review, the relationships among HSLs, the microbiological origins, the crystal structures, and the biotechnological properties of bHSLs are summarized.
ESTHER : Kim_2017_J.Microbiol.Biotechnol_27_1907
PubMedSearch : Kim_2017_J.Microbiol.Biotechnol_27_1907
PubMedID: 29032653

Title : Structural and biochemical characterization of a carbohydrate acetylesterase from Sinorhizobium meliloti 1021 - Kim_2015_FEBS.Lett_589_117
Author(s) : Kim K , Ryu BH , Kim SS , An DR , Ngo TD , Pandian R , Kim KK , Kim TD
Ref : FEBS Letters , 589 :117 , 2015
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 A 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.
ESTHER : Kim_2015_FEBS.Lett_589_117
PubMedSearch : Kim_2015_FEBS.Lett_589_117
PubMedID: 25436419

Title : Characterization of an Alkaline Family I.4 Lipase from Bacillus sp. W130-35 Isolated from a Tidal Mud Flat with Broad Substrate Specificity - Kim_2015_J.Microbiol.Biotechnol_25_2024
Author(s) : Kim HJ , Jung WK , Lee HW , Yoo W , Kim TD , Kim H
Ref : J Microbiol Biotechnol , 25 :2024 , 2015
Abstract : A gene encoding lipolytic enzyme, lip7-3, was isolated from Bacillus sp. W130-35 isolated from a tidal mud flat. The gene encoded a protein of 215 amino acids with a signal peptide composed of 34 amino acid residues. Lip7-3 belonged to the family I.4 lipase and showed its maximal activity at pH 9.0 and 60 degrees C. Its activity increased in the presence of 30% methanol and, remarkably, increased as well to 154.6% in the presence of Ca(2+). Lip7-3 preferred pnitrophenyl octanoate (C8) as a substrate and exhibited broad specificity for short- to longchain fatty acid esters. Additionally, Lip7-3 showed a low degree of enantioselectivity for an S-enantiomer (e.g., (S)-methyl-3-hydroxy-2-methylpropionate). It efficiently hydrolyzed glyceryl tributyrate, but did not hydrolyze glyceryl trioleate, fish oil, or olive oil. Its substrate specificity and activation by the solvent might offer a merit to the biotechnological enzyme applications like transesterification in the production of biodiesel.
ESTHER : Kim_2015_J.Microbiol.Biotechnol_25_2024
PubMedSearch : Kim_2015_J.Microbiol.Biotechnol_25_2024
PubMedID: 26370800
Gene_locus related to this paper: bacpu-w8rkh7

Title : Crystallization and preliminary X-ray analysis of a novel type of lipolytic hydrolase from Bacillus licheniformis - Ju_2014_Acta.Crystallogr.F.Struct.Biol.Commun_70_473
Author(s) : Ju H , Pandian R , Kim K , Kim KK , Kim TD
Ref : Acta Crystallographica F Struct Biol Commun , 70 :473 , 2014
Abstract : With increasing demand in biotechnological applications, the identification and characterization of novel lipolytic enzymes are of great importance. The crystallization and preliminary X-ray crystallographic study of a novel type of hydrolase from Bacillus licheniformis (BL28) are described here. Recombinant BL28 protein containing a C-terminal His tag was overproduced in Escherichia coli and purified to homogeneity. BL28 was crystallized using 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 30%(w/v) PEG 4000 as a crystallizing solution. X-ray diffraction data were collected to a resolution of 1.67 A with an Rmerge of 5.8%. The BL28 crystals belonged to the tetragonal space group P41212, with unit-cell parameters a = b = 57.89, c = 167.25 A. A molecular-replacement solution was obtained and structure refinement of BL28 is in progress.
ESTHER : Ju_2014_Acta.Crystallogr.F.Struct.Biol.Commun_70_473
PubMedSearch : Ju_2014_Acta.Crystallogr.F.Struct.Biol.Commun_70_473
PubMedID: 24699742
Gene_locus related to this paper: bacld-q65eq1

Title : Characterization and preparation of highly stable aggregates of a novel type of hydrolase (BL28) from Bacillus licheniformis - Ju_2013_Bioresour.Technol_128_81
Author(s) : Ju H , Jang E , Ryu BH , Kim TD
Ref : Bioresour Technol , 128 :81 , 2013
Abstract : A novel type of hydrolase (BL28) from Bacillus licheniformis was identified, expressed in Escherichia coli, characterized, and immobilized for industrial applications. Biochemical characteristics of BL28 were investigated by performing SDS-PAGE, mass spectrometry, enzyme assays, CD spectroscopy, intrinsic fluorescence, and in silico analysis. Furthermore, cross-linked enzyme aggregates (CLEAs) of BL28 were prepared. These CLEA-BL28 aggregates exhibited improved catalytic efficiencies and stabilities compared to free BL28 against harsh conditions of thermal or chemical stress as well as high reusability. The characteristics of the CLEA-BL28 aggregates highlight their great potentials in pharmaceutical and chemical industries.
ESTHER : Ju_2013_Bioresour.Technol_128_81
PubMedSearch : Ju_2013_Bioresour.Technol_128_81
PubMedID: 23196225
Gene_locus related to this paper: bacld-q65eq1

Title : Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library - Ngo_2013_Acta.Crystallogr.D.Biol.Crystallogr_69_1726
Author(s) : Ngo TD , Ryu BH , Ju H , Jang E , Park K , Kim KK , Kim TD
Ref : Acta Crystallographica D Biol Crystallogr , 69 :1726 , 2013
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 A resolution; it exhibits an alpha/beta-hydrolase fold consisting of a central beta-sheet enclosed by alpha-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.
ESTHER : Ngo_2013_Acta.Crystallogr.D.Biol.Crystallogr_69_1726
PubMedSearch : Ngo_2013_Acta.Crystallogr.D.Biol.Crystallogr_69_1726
PubMedID: 23999296
Gene_locus related to this paper: 9bact-q4tzq3

Title : Identification, crystallization and preliminary X-ray diffraction analysis of esterase A from Caulobacter crescentus CB15, a family VIII lipolytic enzyme - Ryu_2012_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_68_560
Author(s) : Ryu BH , Ngo TD , Jang E , Kim S , Ju H , Kim KK , Kim TD
Ref : Acta Crystallographica Sect F Struct Biol Cryst Commun , 68 :560 , 2012
Abstract : The structures and functions of family VIII lipolytic enzymes, which have moderate sequence identity to class C beta-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 alpha- and beta-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 A 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 A. Structure determination is in progress.
ESTHER : Ryu_2012_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_68_560
PubMedSearch : Ryu_2012_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_68_560
PubMedID: 22691788

Title : Identification and characterization of a novel (S)-ketoprofen-specific esterase - Yoon_2007_Int.J.Biol.Macromol_41_1
Author(s) : Yoon S , Kim S , Ryu Y , Kim TD
Ref : Int J Biol Macromol , 41 :1 , 2007
Abstract : A new (S)-ketoprofen specific esterase (EST-Y29) was identified from a metagenome library from environmental samples, which showed homologies with class C-beta lactamase, penicillin binding protein, and other lipases/esterases. In order to investigate the biochemical and biophysical properties, the recombinant protein was overexpressed, purified to homogeneity, and characterized. This EST-Y29 has high catalytic activity against p-nitrophenyl esters of short fatty acids (C(2) and C(4)) and alpha-naphthyl acetate with activation energy of 30.4 kJ/mol. We have further characterized EST-Y29 using high performance liquid chromatography (HPLC), circular dichroism (CD), dynamic light scattering (DLS) and size exclusion chromatography (SEC).
ESTHER : Yoon_2007_Int.J.Biol.Macromol_41_1
PubMedSearch : Yoon_2007_Int.J.Biol.Macromol_41_1
PubMedID: 17196647

Title : Purification, crystallization and preliminary crystallographic analysis of Est25: a ketoprofen-specific hormone-sensitive lipase - Kim_2007_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_63_579
Author(s) : Kim S , Joo S , Yoon HC , Ryu Y , Kim KK , Kim TD
Ref : Acta Crystallographica Sect F Struct Biol Cryst Commun , 63 :579 , 2007
Abstract : Ketoprofen, a nonsteroidal anti-inflammatory drug, inhibits the synthesis of prostaglandin. A novel hydrolase (Est25) with high ketoprofen specificity has previously been identified using a metagenomic library from environmental samples. Recombinant Est25 protein with a histidine tag at the N-terminus was expressed in Escherichia coli and purified in a homogenous form. Est25 was crystallized from 2.4 M sodium malonate pH 7.0 and X-ray diffraction data were collected to 1.49 A using synchrotron radiation. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 197.8, b = 95.2, c = 99.4 A, beta = 97.1 degrees.
ESTHER : Kim_2007_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_63_579
PubMedSearch : Kim_2007_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_63_579
PubMedID: 17620715
Gene_locus related to this paper: 9bact-q4tzq3