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Zheng Y, Li L, Liu Q, Qin W, Yang J, Cao Y, Jiang X, Zhao G, Xian M. Boosting the free fatty acid synthesis of Escherichia coli by expression of a cytosolic Acinetobacter baylyi thioesterase. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:76. [PMID: 23057831 PMCID: PMC3524773 DOI: 10.1186/1754-6834-5-76] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Accepted: 10/05/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND Thioesterases remove the fatty acyl moiety from the fatty acyl-acyl carrier proteins (ACPs), releasing them as free fatty acids (FFAs), which can be further used to produce a variety of fatty acid-based biofuels, such as biodiesel, fatty alcohols and alkanes. Thioesterases play a key role in the regulation of the fatty acid synthesis in Escherichia coli. Therefore, exploring more promising thioesterases will contribute to the development of industrial microbial lipids production. RESULTS We cloned and expressed a cytosolic Acinetobacter baylyi thioesterase ('AcTesA) in E. coli by deleting its leader sequence. Protein sequence alignment, structure modeling and site-directed mutagenesis demonstrated that Ser10, Gly48, Asn77, Asp158 and His161 residues composed the active centre of 'AcTesA. The engineered strain that overexpressed 'AcTesA achieved a FFAs titer of up to 501.2 mg/L in shake flask, in contrast to only 20.5 mg/L obtained in wild-type E. coli, demonstrating that the expression of 'AcTesA indeed boosted the synthesis of FFAs. The 'AcTesA exhibited a substrate preference towards the C8-C16 acyl groups, with C14:0, C16:1, C12:0 and C8:0 FFAs being the top four components. Optimization of expression level of 'AcTesA made the FFAs production increase to 551.3 mg/L. The FFAs production further increased to 716.1 mg/L by optimization of the culture medium. Fed-batch fermentation was also carried out to evaluate the FFAs production in a scaleable process. Finally, 3.6 g/L FFAs were accumulated within 48 h, and a maximal FFAs yield of 6.1% was achieved in 12-16 h post induction. CONCLUSIONS For the first time, an A. baylyi thioesterase was cloned and solubly expressed in the cytosol of E. coli. This leaderless thioesterase ('AcTesA) was found to be capable of enhancing the FFAs production of E. coli. Without detailed optimization of the strain and fermentation, the finally achieved 3.6 g/L FFAs is encouraging. In addition, 'AcTesA exhibited different substrate specificity from other thioesterases previously reported, and can be used to supply the fatty acid-based biofuels with high quality of FFAs. Altogether, this study provides a promising thioesterase for FFAs production, and is of great importance in enriching the library of useful thioesterases.
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Affiliation(s)
- Yanning Zheng
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingling Li
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China
| | - Qiang Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China
| | - Jianming Yang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujin Cao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xinglin Jiang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guang Zhao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Mo Xian
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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Chepyshko H, Lai CP, Huang LM, Liu JH, Shaw JF. Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. BMC Genomics 2012; 13:309. [PMID: 22793791 PMCID: PMC3412167 DOI: 10.1186/1471-2164-13-309] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 07/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes. RESULTS In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the possible biological functions of the rice OsGELP genes. CONCLUSIONS Our current genomic analysis, for the first time, presents fundamental information on the organization of the rice OsGELP gene family. With combination of the genomic, phylogenetic, microarray expression, protein motif distribution, and protein structure analyses, we were able to create supported basis for the functional prediction of many members in the rice GDSL esterase/lipase family. The present study provides a platform for the selection of candidate genes for further detailed functional study.
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Affiliation(s)
- Hanna Chepyshko
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, Taiwan, 402, ROC
| | - Chia-Ping Lai
- Department of Food and Beverage Management, Far East University, Tainan, Taiwan, 74448, ROC
| | - Li-Ming Huang
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, 701, ROC
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan, 40227, ROC
| | - Jei-Fu Shaw
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, Taiwan, 402, ROC
- Department of Biological Science and Technology, I-Shou University, Kaohsiung, Taiwan, 84001, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, 40227, ROC
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taiwan, 115, ROC
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3
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Tang CY, Lu CL, Chang MDT, Tsai YT, Sun YJ, Chao KM, Chang JM, Chiou YH, Wu CM, Chang HT, Chou WI. Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment. J Bioinform Comput Biol 2012; 1:267-87. [PMID: 15290773 DOI: 10.1142/s0219720003000095] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2002] [Revised: 12/07/2002] [Accepted: 01/15/2003] [Indexed: 11/18/2022]
Abstract
In this paper, we design a heuristic algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant α, then the time-complexity of our CMSA algorithm for aligning K sequences is O(αKn4), where n is the maximum of the lengths of sequences. In addition, we have built up such a CMSA software system and made several experiments on the RNase sequences, which mainly function in catalyzing the degradation of RNA molecules. The resulting alignments illustrate the practicability of our method.
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Affiliation(s)
- Chuan Yi Tang
- Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
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Pickens LB, Sawaya MR, Rasool H, Pashkov I, Yeates TO, Tang Y. Structural and biochemical characterization of the salicylyl-acyltranferase SsfX3 from a tetracycline biosynthetic pathway. J Biol Chem 2011; 286:41539-41551. [PMID: 21965680 PMCID: PMC3308865 DOI: 10.1074/jbc.m111.299859] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 09/28/2011] [Indexed: 11/06/2022] Open
Abstract
SsfX3 is a GDSL family acyltransferase that transfers salicylate to the C-4 hydroxyl of a tetracycline intermediate in the penultimate step during biosynthesis of the anticancer natural product SF2575. The C-4 salicylate takes the place of the more common C-4 dimethylamine functionality, making SsfX3 the first acyltransferase identified to act on a tetracycline substrate. The crystal structure of SsfX3 was determined at 2.5 Å, revealing two distinct domains as follows: an N-terminal β-sandwich domain that resembles a carbohydrate-binding module, and a C-terminal catalytic domain that contains the atypical α/β-hydrolase fold found in the GDSL hydrolase family of enzymes. The active site lies at one end of a large open binding pocket, which is spatially defined by structural elements from both the N- and C-terminal domains. Mutational analysis in the putative substrate binding pocket identified residues from both domains that are important for binding the acyl donor and acceptor. Furthermore, removal of the N-terminal carbohydrate-binding module-like domain rendered the stand-alone α/β-hydrolase domain inactive. The additional noncatalytic module is therefore proposed to be required to define the binding pocket and provide sufficient interactions with the spatially extended tetracyclic substrate. SsfX3 was also demonstrated to accept a variety of non-native acyl groups. This relaxed substrate specificity toward the acyl donor allowed the chemoenzymatic biosynthesis of C-4-modified analogs of the immediate precursor to the bioactive SF2575; these were used to assay the structure activity relationships at the C-4 position.
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Affiliation(s)
- Lauren B Pickens
- Departments of Chemical and Biomolecular Engineering, Los Angeles, California 90095
| | - Michael R Sawaya
- Departments of Chemistry and Biochemistry, Los Angeles, California 90095; Department of Howard Hughes Medical Institute, and UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Huma Rasool
- Departments of Chemical and Biomolecular Engineering, Los Angeles, California 90095
| | - Inna Pashkov
- Departments of Chemistry and Biochemistry, Los Angeles, California 90095
| | - Todd O Yeates
- Departments of Chemistry and Biochemistry, Los Angeles, California 90095; Department of Molecular Biology Institute, Los Angeles, California 90095
| | - Yi Tang
- Departments of Chemical and Biomolecular Engineering, Los Angeles, California 90095; Departments of Chemistry and Biochemistry, Los Angeles, California 90095; Department of Molecular Biology Institute, Los Angeles, California 90095.
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5
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Ebrahimi A, Habibi-khorassani M, Haghani A. Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR, NBO and AIM analyses. Mol Phys 2011. [DOI: 10.1080/00268976.2010.521781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Karageorgos I, Tyukhtenko S, Zvonok N, Janero DR, Sallum C, Makriyannis A. Identification by nuclear magnetic resonance spectroscopy of an active-site hydrogen-bond network in human monoacylglycerol lipase (hMGL): implications for hMGL dynamics, pharmacological inhibition, and catalytic mechanism. MOLECULAR BIOSYSTEMS 2010; 6:1381-8. [PMID: 20464001 PMCID: PMC3697746 DOI: 10.1039/c004515b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Intramolecular hydrogen bonding is an important determinant of enzyme structure, catalysis, and inhibitor action. Monoacylglycerol lipase (MGL) modulates cannabinergic signaling as the main enzyme responsible for deactivating 2-arachidonoylglycerol (2-AG), a primary endocannabinoid lipid messenger. By enhancing tissue-protective 2-AG tone, targeted MGL inhibitors hold therapeutic promise for managing pain and treating inflammatory and neurodegenerative diseases. We report study of purified, solubilized human MGL (hMGL) to explore the details of hMGL catalysis by using two known covalent hMGL inhibitors, the carbamoyl tetrazole AM6701 and N-arachidonoylmaleimide (NAM), that act through distinct mechanisms. Using proton nuclear magnetic resonance spectroscopy (NMR) with purified wild-type and mutant hMGLs, we have directly observed a strong hydrogen-bond network involving Asp239 and His269 of the catalytic triad and neighboring Leu241 and Cys242 residues. hMGL inhibition by AM6701 alters this hydrogen-bonding pattern through subtle active-site structural rearrangements without influencing hydrogen-bond occupancies. Rapid carbamoylation of hMGL Ser122 by AM6701 and elimination of the leaving group is followed by a slow hydrolysis of the carbamate group, ultimately regenerating catalytically competent hMGL. In contrast, hMGL titration with NAM, which leads to cysteine alkylation, stoichiometrically decreases the population of the active-site hydrogen bonds. NAM prevents reformation of this network, and in this manner inhibits hMGL irreversibly. These data provide detailed molecular insight into the distinctive mechanisms of two covalent hMGL inhibitors and implicate a hydrogen-bond network as a structural feature of hMGL catalytic function.
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Affiliation(s)
- Ioannis Karageorgos
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, MA 02115-5000, USA 617-373-2208. Fax: +1 617-373-7493
| | - Sergiy Tyukhtenko
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, MA 02115-5000, USA 617-373-2208. Fax: +1 617-373-7493
| | - Nikolai Zvonok
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, MA 02115-5000, USA 617-373-2208. Fax: +1 617-373-7493
| | - David R. Janero
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, MA 02115-5000, USA 617-373-2208. Fax: +1 617-373-7493
| | - Christine Sallum
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, MA 02115-5000, USA 617-373-2208. Fax: +1 617-373-7493
| | - Alexandros Makriyannis
- Center for Drug Discovery, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, MA 02115-5000, USA 617-373-2208. Fax: +1 617-373-7493
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7
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Biochemical characterization of Alr1529, a novel SGNH hydrolase variant from Anabaena sp. PCC 7120. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:324-34. [PMID: 19028609 DOI: 10.1016/j.bbapap.2008.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/15/2008] [Accepted: 10/27/2008] [Indexed: 11/22/2022]
Abstract
Alr1529, a serine hydrolase from the cyanobacteria Anabaena sp. strain PCC 7120 is a member of the SGNH hydrolase superfamily. Biochemical characterization of the purified enzyme revealed that the protein is a dimer in solution and is specific for aryl esters of short chain carboxylic acids. The enzyme was regio-selective for alpha-naphthyl esters with maximum activity at pH 7.5 and has a broad optimal temperature range (25-45 degrees C). A structure based comparison of Alr1529 with other superfamily members confirmed the presence of the catalytic triad (Ser17-Asp179-His182) and oxyanion hole (Ser17-Arg54-Asn87) residues. Alr1529 exhibits a previously undescribed variation in the active site wherein a conserved Gly, a proton donor making up the oxyanion hole in the SGNH hydrolases, is substituted by Arg54. Site-directed mutagenesis studies suggest that Arg54 is crucial for substrate binding and catalytic activity. Ser17 plays a very crucial role in catalysis as evident from the 50-fold lower activity of the S17A mutant.
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8
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Mizuno H, Mal TK, Wälchli M, Kikuchi A, Fukano T, Ando R, Jeyakanthan J, Taka J, Shiro Y, Ikura M, Miyawaki A. Light-dependent regulation of structural flexibility in a photochromic fluorescent protein. Proc Natl Acad Sci U S A 2008; 105:9227-32. [PMID: 18574155 PMCID: PMC2453726 DOI: 10.1073/pnas.0709599105] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Indexed: 11/18/2022] Open
Abstract
The structural basis for the photochromism in the fluorescent protein Dronpa is poorly understood, because the crystal structures of the bright state of the protein did not provide an answer to the mechanism of the photochromism, and structural determination of the dark state has been elusive. We performed NMR analyses of Dronpa in solution at ambient temperatures to find structural flexibility of the protein in the dark state. Light-induced changes in interactions between the chromophore and beta-barrel are responsible for switching between the two states. In the bright state, the apex of the chromophore tethers to the barrel by a hydrogen bond, and an imidazole ring protruding from the barrel stabilizes the plane of the chromophore. These interactions are disrupted by strong illumination with blue light, and the chromophore, together with a part of the beta-barrel, becomes flexible, leading to a nonradiative decay process.
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Affiliation(s)
- Hideaki Mizuno
- *Cell Function and Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-City, Saitama 351-0198, Japan
| | - Tapas Kumar Mal
- Division of Signaling Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, MaRS Toronto Medical Dicovery Tower, Room 4-804, 101 College Street, Toronto, ON, Canada M5G 1L7
| | - Markus Wälchli
- Bruker BioSpin K. K., 3-21-5, Ninomiya, Tukuba-City, Ibaraki 305-0051, Japan; and
| | - Akihiro Kikuchi
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo 679-5198, Japan
| | - Takashi Fukano
- *Cell Function and Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-City, Saitama 351-0198, Japan
| | - Ryoko Ando
- *Cell Function and Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-City, Saitama 351-0198, Japan
| | - Jeyaraman Jeyakanthan
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo 679-5198, Japan
| | - Junichiro Taka
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo 679-5198, Japan
| | - Yoshitsugu Shiro
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo 679-5198, Japan
| | - Mitsuhiko Ikura
- Division of Signaling Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, MaRS Toronto Medical Dicovery Tower, Room 4-804, 101 College Street, Toronto, ON, Canada M5G 1L7
| | - Atsushi Miyawaki
- *Cell Function and Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-City, Saitama 351-0198, Japan
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9
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Marx JC, Poncin J, Simorre JP, Ramteke PW, Feller G. The noncatalytic triad of alpha-amylases: a novel structural motif involved in conformational stability. Proteins 2008; 70:320-8. [PMID: 17729287 DOI: 10.1002/prot.21594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chloride-activated alpha-amylases contain a noncatalytic triad, independent of the glycosidic active site, perfectly mimicking the catalytic triad of serine-proteases and of other active serine hydrolytic enzymes. Mutagenesis of Glu, His, and Ser residues in various alpha-amylases shows that this pattern is a structural determinant of the enzyme conformation that cannot be altered without losing the intrinsic stability of the protein. (1)H-(15)N NMR spectra of a bacterial alpha-amylase reveal proton signals that are identical with the NMR signature of catalytic triads and especially a deshielded proton involving a protonated histidine and displaying properties similar to that of a low barrier hydrogen bond. It is proposed that the H-bond between His and Glu of the noncatalytic triad is an unusually strong interaction, responsible for the observed NMR signal and for the weak stability of the triad mutants. Furthermore, a stringent template-based search of the Protein Data Bank demonstrated that this motif is not restricted to alpha-amylases, but is also found in 80 structures from 33 different proteins, amongst which SH2 domain-containing proteins are the best representatives.
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Affiliation(s)
- Jean-Claude Marx
- Laboratory of Biochemistry, University of Liège, Liège, Sart-Tilman, Belgium
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10
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Wu WJ, Tyukhtenko SI, Huang TH. Direct NMR resonance assignments of the active site histidine residue in Escherichia coli thioesterase I/protease I/lysophospholipase L1. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:1037-40. [PMID: 16972310 DOI: 10.1002/mrc.1901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Owing to the hydrogen-bond interaction and rapid exchange rate with the bulk water, the transverse relaxation time for the N(delta1)-H proton of the catalytic histidine in Escherichia coli thioesterase I/protease I/lysophospholipase L1 (TEP-I) is rather short. Because of its catalytic importance, it is desirable to detect and assign this proton resonance. In this paper, we report the first direct NMR correlation between the short-lived N(delta1)-H proton and its covalently attached N(delta1)-nitrogen of the catalytic His157 residue in E. coli thioesterase/protease I. We have used gradient-enhanced jump-return spin-echo HMQC (GE-JR SE HMQC) to obtain a direct correlation between the short-lived N(delta1)-H proton and its covalently attached N(delta1)-nitrogen. The sensitivity of detection for the short-lived N(delta1)-H proton was enhanced substantially by improved water suppression, in particular, the suppression of radiation damping via pulsed field gradients.
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Affiliation(s)
- Wen-Jin Wu
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan 11529, Republic of China.
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11
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Abstract
GDSL esterases and lipases are hydrolytic enzymes with multifunctional properties such as broad substrate specificity and regiospecificity. They have potential for use in the hydrolysis and synthesis of important ester compounds of pharmaceutical, food, biochemical, and biological interests. This new subclass of lipolytic enzymes possesses a distinct GDSL sequence motif different from the GxSxG motif found in many lipases. Unlike the common lipases, GDSL enzymes do not have the so called nucleophile elbow. Studies show that GDSL hydrolases have a flexible active site that appears to change conformation with the presence and binding of the different substrates, much like the induced fit mechanism proposed by Koshland. Some of the GDSL enzymes have thioesterase, protease, arylesterase, and lysophospholipase activity, yet they appear to be the same protein with similar molecular weight ( approximately 22-60 kDa for most esterases), although some have multiple glycosylation sites with higher apparent molecular weight. GDSL enzymes have five consensus sequence (I-V) and four invariant important catalytic residues Ser, Gly, Asn, and His in blocks I, II, III, and V, respectively. The oxyanion structure led to a new designation of these enzymes as SGNH-hydrolase superfamily or subfamily. Phylogenetic analysis revealed that block IIA which belonged to the SGNH-hydrolases was found only in clade I. Therefore, this family of hydrolases represents a new example of convergent evolution of lipolytic enzymes. These enzymes have little sequence homology to true lipases. Another important differentiating feature of GDSL subfamily of lipolytic enzymes is that the serine-containing motif is closer to the N-terminus unlike other lipases where the GxSxG motif is near the center. Since the first classification of these subclass or subfamily of lipases as GDSL(S) hydrolase, progress has been made in determining the consensus sequence, crystal structure, active site and oxyanion residues, secondary structure, mechanism of catalysis, and understanding the conformational changes. Nevertheless, much still needs to be done to gain better understanding of in vivo biological function, 3-D structure, how this group of enzymes evolved to utilize many different substrates, and the mechanism of reactions. Protein engineering is needed to improve the substrate specificity, enantioselectivity, specific activity, thermostability, and heterologous expression in other hosts (especially food grade microorganisms) leading to eventual large scale production and applications. We hope that this review will rekindle interest among researchers and the industry to study and find uses for these unique enzymes.
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Affiliation(s)
- Casimir C Akoh
- Department of Food Science and Technology, University of Georgia, Athens, GA 30602-7610, USA
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12
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Tyukhtenko SI, Huang YT, Lin TH, Chen C, Chang CF, Lee SJ, Litvinchuk AV, Shaw JF, Liaw YC, Huang TH. Probing the Enzyme Catalytic Mechanism by Nuclear Magnetic Resonance - A Case Study of a Serine Protease. J CHIN CHEM SOC-TAIP 2004. [DOI: 10.1002/jccs.200400168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Tyukhtenko SI, Litvinchuk AV, Chang CF, Lo YC, Lee SJ, Shaw JF, Liaw YC, Huang TH. Sequential structural changes of Escherichia coli thioesterase/protease I in the serial formation of Michaelis and tetrahedral complexes with diethyl p-nitrophenyl phosphate. Biochemistry 2003; 42:8289-97. [PMID: 12846577 DOI: 10.1021/bi027246w] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli thioesterase/protease I (TEP-I) belongs to a new subclass of lipolytic enzymes of the serine hydrolase superfamily. Here we report the first direct NMR observation of the formation of the Michaelis complex (MC) between TEP-I and diethyl p-nitrophenyl phosphate (DENP), an active site directed inhibitor of serine protease, and its subsequent conversion to the tetrahedral complex (TC). NMR, ESI-MS, and kinetic data showed that DENP binds to TEP-I in a two-step process, a fast formation of MC followed by a slow conversion to TC. NMR chemical shift perturbation further revealed that perturbations were confined mainly to four conserved segments comprising the active site. Comparable magnitudes of chemical shift perturbations were detected in both steps. The largest chemical shift perturbation occurred around the catalytic Ser(10). In MC, the conformation of the mobile Ser(10) was stabilized, and its amide resonance became observable. From the large chemical shift perturbation upon conversion from MC to TC, we propose that the amide protons of Ser(10) and Gly(44) serve as the oxyanion hole proton donors that stabilize the tetrahedral adduct. The pattern of residues perturbed in both steps suggests a sequential, stepwise structural change upon binding of DENP. The present study also demonstrates the important catalytic roles of conserved residues in the SGNH family of proteins.
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Affiliation(s)
- Sergiy I Tyukhtenko
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan 11529, Republic of China
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