1
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Kumar A, Kumar Singh V, Kayastha AM. Studies on α-amylase inhibition by acarbose and quercetin using fluorescence, circular dichroism, docking, and dynamics simulations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 314:124160. [PMID: 38513313 DOI: 10.1016/j.saa.2024.124160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
This study looked at the effects of acarbose (ACA) and quercetin (QUE) on α-amylase activity, employing QUE and ACA to measure enzyme activity. The study observed that both drugs suppressed α-amylase activity, with greater inhibition reported at higher concentrations. The use of tryptophan residues as an intrinsic fluorescence probe permitted the observation of conformational changes in α-amylase, with CD measurements utilized to explore the secondary structure in the presence of QUE and ACA. Docking studies revealed an effective interaction between α-amylase, quercetin and acarbose, with a higher binding energy. Finally, a trajectory analysis was done to establish the stability and volatility of these complexes. These findings have potential significance for the development of new α-amylase-related therapeutics.
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Affiliation(s)
- Avinash Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Vinay Kumar Singh
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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2
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Tan X, Zhang S, Malde AK, Tan X, Gilbert RG. Effects of chickpea protein fractions on α-amylase activity in digestion. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Božić N, Rozeboom HJ, Lončar N, Slavić MŠ, Janssen DB, Vujčić Z. Characterization of the starch surface binding site on Bacillus paralicheniformis α-amylase. Int J Biol Macromol 2020; 165:1529-1539. [PMID: 33058974 DOI: 10.1016/j.ijbiomac.2020.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/03/2020] [Accepted: 10/03/2020] [Indexed: 11/16/2022]
Abstract
α-Amylase from Bacillus paralicheniformis (BliAmy), belonging to GH13_5 subfamily of glycoside hydrolases, was proven to be a highly efficient raw starch digesting enzyme. The ability of some α-amylases to hydrolyze raw starch is related to the existence of surface binding sites (SBSs) for polysaccharides that can be distant from the active site. Crystallographic studies performed on BliAmy in the apo form and of enzyme bound with different oligosaccharides and oligosaccharide precursors revealed binding of these ligands to one SBS with two amino acids F257 and Y358 mainly involved in complex formation. The role of this SBS in starch binding and degradation was probed by designing enzyme variants mutated in this region (F257A and Y358A). Kinetic studies with different substrates show that starch binding through the SBS is disrupted in the mutants and that F257 and Y358 contributed cumulatively to binding and hydrolysis. Mutation of both sites (F257A/Y358A) resulted in a 5-fold lower efficacy with raw starch as substrate and at least 5.5-fold weaker binding compared to the wild type BliAmy, suggesting that the ability of BliAmy to hydrolyze raw starch with high efficiency is related to the level of its adsorption onto starch granules.
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Affiliation(s)
- Nataša Božić
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Henriëtte J Rozeboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Nikola Lončar
- GECCO Biotech, Nijenborgh 4, Groningen 9747AG, the Netherlands
| | - Marinela Šokarda Slavić
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Dick B Janssen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Zoran Vujčić
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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4
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Xie X, Qiu G, Zhang Z, Ban X, Gu Z, Li C, Hong Y, Cheng L, Li Z. Importance of Trp139 in the product specificity of a maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04. Appl Microbiol Biotechnol 2019; 103:9433-9442. [DOI: 10.1007/s00253-019-10194-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/23/2019] [Accepted: 10/03/2019] [Indexed: 01/30/2023]
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5
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New insights into the origin and evolution of α-amylase genes in green plants. Sci Rep 2019; 9:4929. [PMID: 30894656 PMCID: PMC6426938 DOI: 10.1038/s41598-019-41420-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/05/2018] [Indexed: 01/16/2023] Open
Abstract
Gene duplication is a source of genetic materials and evolutionary changes, and has been associated with gene family expansion. Functional divergence of duplicated genes is strongly directed by natural selections such as organism diversification and novel feature acquisition. We show that, plant α-amylase gene family (AMY) is comprised of six subfamilies (AMY1-AMY6) that fell into two ancient phylogenetic lineages (AMY3 and AMY4). Both AMY1 and AMY2 are grass-specific and share a single-copy ancestor, which is derived from grass AMY3 genes that have undergone massive tandem and whole-genome duplications during evolution. Ancestral features of AMY4 and AMY5/AMY6 genes have been retained among four green algal sequences (Chrein_08.g362450, Vocart_0021s0194, Dusali_0430s00012 and Monegl_16464), suggesting a gene duplication event following Chlorophyceae diversification. The observed horizontal gene transfers between plant and bacterial AMYs, and chromosomal locations of AMY3 and AMY4 genes in the most ancestral green body (C. reinhardtii), provide evidences for the monophyletic origin of plant AMYs. Despite subfamily-specific sequence divergence driven by natural selections, the active site and SBS1 are well-conserved across different AMY isoforms. The differentiated electrostatic potentials and hydrogen bands-forming residue polymorphisms, further imply variable digestive abilities for a broad substrates in particular tissues or subcellular localizations.
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6
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Sellami S, Jemli S, Abdelmalek N, Cherif M, Abdelkefi-Mesrati L, Tounsi S, Jamoussi K. A novel Vip3Aa16-Cry1Ac chimera toxin: Enhancement of toxicity against Ephestia kuehniella, structural study and molecular docking. Int J Biol Macromol 2018; 117:752-761. [PMID: 29800666 DOI: 10.1016/j.ijbiomac.2018.05.161] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/14/2018] [Accepted: 05/22/2018] [Indexed: 10/16/2022]
Abstract
Bacillus thuringiensis Vip3A protein has been widely used for crop protection and for delay resistance to existing insecticidal Cry toxins. During current study, a fusion between vip3Aa16 and the toxic core sequence of cry1Ac was constructed in pHT Blue plasmid. Vip3Aa16-Cry1Ac protein was expressed in the supernatant of B. thuringiensis with a size of about 150 kDa. Bioassays tested on Ephestia kuehniella showed that the use of the chimera toxin as biopesticide improved the toxicity to reach 90% ± 2 with an enhancement of 20% compared to the single Vip3Aa16 protein. The findings indicated that the fusion protein design opens new ways to enhance Vip3A toxicity against lepidopteran species and could avoiding insect tolerance of B. thuringiensis delta-endotoxins. Through computational study, we have predicted for the first time the whole 3D structure of a Vip3A toxin. We showed that Vip3Aa16 structure is composed by three domains like Cry toxins: an N-terminal domain containing hemolysin like fold as well as two others Carbohydrate Binding Module (CBM)-like domains. Molecular docking analysis of the chimera toxin and the single Vip3Aa16 protein against specific insect receptors revealed that residues of CBM like domains are clearly involved in the binding of the toxin to receptors.
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Affiliation(s)
- Sameh Sellami
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, 3018 Sfax, Tunisia.
| | - Sonia Jemli
- Laboratory of Microbial Biotechnology and Enzymes Engineering, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Nouha Abdelmalek
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Marwa Cherif
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Lobna Abdelkefi-Mesrati
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Slim Tounsi
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, 3018 Sfax, Tunisia
| | - Kais Jamoussi
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, P.O. Box 1177, 3018 Sfax, Tunisia
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7
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Lehoczki G, Kandra L, Gyémánt G. The use of starch azure for measurement of alpha-amylase activity. Carbohydr Polym 2018; 183:263-266. [DOI: 10.1016/j.carbpol.2017.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 11/21/2017] [Accepted: 12/14/2017] [Indexed: 11/28/2022]
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8
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The Importance of Surface-Binding Site towards Starch-Adsorptivity Level in α-Amylase: A Review on Structural Point of View. Enzyme Res 2017; 2017:4086845. [PMID: 29359041 PMCID: PMC5735674 DOI: 10.1155/2017/4086845] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 10/31/2017] [Indexed: 12/04/2022] Open
Abstract
Starch is a polymeric carbohydrate composed of glucose. As a source of energy, starch can be degraded by various amylolytic enzymes, including α-amylase. In a large-scale industry, starch processing cost is still expensive due to the requirement of high temperature during the gelatinization step. Therefore, α-amylase with raw starch digesting ability could decrease the energy cost by avoiding the high gelatinization temperature. It is known that the carbohydrate-binding module (CBM) and the surface-binding site (SBS) of α-amylase could facilitate the substrate binding to the enzyme's active site to enhance the starch digestion. These sites are a noncatalytic module, which could interact with a lengthy substrate such as insoluble starch. The major interaction between these sites and the substrate is the CH/pi-stacking interaction with the glucose ring. Several mutation studies on the Halothermothrix orenii, SusG Bacteroides thetaiotamicron, Barley, Aspergillus niger, and Saccharomycopsis fibuligera α-amylases have revealed that the stacking interaction through the aromatic residues at the SBS is essential to the starch adsorption. In this review, the SBS in various α-amylases is also presented. Therefore, based on the structural point of view, SBS is suggested as an essential site in α-amylase to increase its catalytic activity, especially towards the insoluble starch.
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9
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Sindhu R, Binod P, Madhavan A, Beevi US, Mathew AK, Abraham A, Pandey A, Kumar V. Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency. BIORESOURCE TECHNOLOGY 2017; 245:1740-1748. [PMID: 28478894 DOI: 10.1016/j.biortech.2017.04.098] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
α-Amylases is one of the most important industrial enzyme which contributes to 25% of the industrial enzyme market. Though it is produced by plant, animals and microbial source, those from microbial source seems to have potential applications due to their stability and economic viability. However a large number of α-amylases from different sources have been detailed in the literature, only few numbers of them could withstand the harsh industrial conditions. Thermo-stability, pH tolerance, calcium independency and oxidant stability and starch hydrolyzing efficiency are the crucial qualities for α-amylase in starch based industries. Microbes can be genetically modified and fine tuning can be done for the production of enzymes with desired characteristics for specific applications. This review focuses on the native and recombinant α-amylases from microorganisms, their heterologous production and the recent molecular strategies which help to improve the properties of this industrial enzyme.
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Affiliation(s)
- Raveendran Sindhu
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Aravind Madhavan
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Ummalyma Sabeela Beevi
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Institute of Bioresources and Sustainable Development, Takyelpat, Imphal 795 001, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India; Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
| | - Vinod Kumar
- Center of Innovative and Applied Bioprocessing, Sector 81, Mohali, Punjab, India
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10
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Abstract
Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate–aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.
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11
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Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13. Sci Rep 2017; 7:44067. [PMID: 28303907 PMCID: PMC5355875 DOI: 10.1038/srep44067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/02/2017] [Indexed: 01/14/2023] Open
Abstract
Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose. Glu221 is one of the three conserved catalytic residues, and AmyP is inactivated by the E221Q mutation. Domain B of AmyPΔSBD forms a loop that protrudes from domain A, stabilizes the conformation of the active site and increases the thermostability of the enzyme. A new calcium ion is situated adjacent to the -3 subsite binding loop and may be responsible for the increased thermostability of the enzyme after the addition of calcium. Moreover, Tyr36 participates in both stacking and hydrogen bonding interactions with the sugar motif at subsite -3. This work provides the first insights into the structure of α-amylases belonging to subfamily 37 of GH13 and may contribute to the rational design of α-amylase mutants with enhanced performance in biotechnological applications.
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12
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Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization. Sci Rep 2016; 6:36100. [PMID: 27808246 PMCID: PMC5093618 DOI: 10.1038/srep36100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/10/2016] [Indexed: 11/09/2022] Open
Abstract
The bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed.
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13
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Zhang X, Caner S, Kwan E, Li C, Brayer GD, Withers SG. Evaluation of the Significance of Starch Surface Binding Sites on Human Pancreatic α-Amylase. Biochemistry 2016; 55:6000-6009. [DOI: 10.1021/acs.biochem.6b00992] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaohua Zhang
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Sami Caner
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - Emily Kwan
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | - Chunmin Li
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - Gary D. Brayer
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
| | - Stephen G. Withers
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
- Department
of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
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14
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Møller MS, Svensson B. Structural biology of starch-degrading enzymes and their regulation. Curr Opin Struct Biol 2016; 40:33-42. [DOI: 10.1016/j.sbi.2016.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/06/2016] [Accepted: 07/06/2016] [Indexed: 02/05/2023]
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15
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Cockburn D, Wilkens C, Dilokpimol A, Nakai H, Lewińska A, Abou Hachem M, Svensson B. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes. PLoS One 2016; 11:e0160112. [PMID: 27504624 PMCID: PMC4978508 DOI: 10.1371/journal.pone.0160112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/13/2016] [Indexed: 01/23/2023] Open
Abstract
Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data.
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Affiliation(s)
- Darrell Cockburn
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Casper Wilkens
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Anna Lewińska
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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16
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Mehta D, Satyanarayana T. Bacterial and Archaeal α-Amylases: Diversity and Amelioration of the Desirable Characteristics for Industrial Applications. Front Microbiol 2016; 7:1129. [PMID: 27516755 PMCID: PMC4963412 DOI: 10.3389/fmicb.2016.01129] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Abstract
Industrial enzyme market has been projected to reach US$ 6.2 billion by 2020. Major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. Among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. These are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-Amylases from different microbial sources vary in their properties, thus, suit specific applications. This review focuses on the native and recombinant α-amylases from bacteria and archaea, their production and the advancements in the molecular biology, protein engineering and structural studies, which aid in ameliorating their properties to suit the targeted industrial applications.
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Affiliation(s)
- Deepika Mehta
- Department of Microbiology, University of Delhi New Delhi, India
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17
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Emanuelle S, Brewer MK, Meekins DA, Gentry MS. Unique carbohydrate binding platforms employed by the glucan phosphatases. Cell Mol Life Sci 2016; 73:2765-2778. [PMID: 27147465 PMCID: PMC4920694 DOI: 10.1007/s00018-016-2249-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Glucan phosphatases are a family of enzymes that are functionally conserved at the enzymatic level in animals and plants. These enzymes bind and dephosphorylate glycogen in animals and starch in plants. While the enzymatic function is conserved, the glucan phosphatases employ distinct mechanisms to bind and dephosphorylate glycogen or starch. The founding member of the family is a bimodular human protein called laforin that is comprised of a carbohydrate binding module 20 (CBM20) followed by a dual specificity phosphatase domain. Plants contain two glucan phosphatases: Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). SEX4 contains a chloroplast targeting peptide, dual specificity phosphatase (DSP) domain, a CBM45, and a carboxy-terminal motif. LSF2 is comprised of simply a chloroplast targeting peptide, DSP domain, and carboxy-terminal motif. SEX4 employs an integrated DSP-CBM glucan-binding platform to engage and dephosphorylate starch. LSF2 lacks a CBM and instead utilizes two surface binding sites to bind and dephosphorylate starch. Laforin is a dimeric protein in solution and it utilizes a tetramodular architecture and cooperativity to bind and dephosphorylate glycogen. This chapter describes the biological role of glucan phosphatases in glycogen and starch metabolism and compares and contrasts their ability to bind and dephosphorylate glucans.
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Affiliation(s)
- Shane Emanuelle
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - M. Kathryn Brewer
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - David A. Meekins
- Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
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18
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Wilkens C, Auger KD, Anderson NT, Meekins DA, Raththagala M, Abou Hachem M, Payne CM, Gentry MS, Svensson B. Plant α‐glucan phosphatases SEX4 and LSF2 display different affinity for amylopectin and amylose. FEBS Lett 2016; 590:118-28. [DOI: 10.1002/1873-3468.12027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
| | - Kyle D. Auger
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Nolan T. Anderson
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - David A. Meekins
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Madushi Raththagala
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
| | - Christina M. Payne
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Birte Svensson
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
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19
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Surface binding sites in amylase have distinct roles in recognition of starch structure motifs and degradation. Int J Biol Macromol 2015; 75:338-45. [DOI: 10.1016/j.ijbiomac.2015.01.054] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 12/31/2022]
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20
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The role of N1 domain on the activity, stability, substrate specificity and raw starch binding of amylopullulanase of the extreme thermophile Geobacillus thermoleovorans. Appl Microbiol Biotechnol 2015; 99:5461-74. [DOI: 10.1007/s00253-014-6345-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 11/25/2022]
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21
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Wilkens C, Cockburn D, Andersen S, Ole Petersen B, Ruzanski C, A. Field R, Hindsgaul O, Nakai H, McCleary B, M. Smith A, Abou Hachem M, Svensson B. Analysis of Surface Binding Sites (SBS) within GH62, GH13, and GH77. J Appl Glycosci (1999) 2015. [DOI: 10.5458/jag.jag.jag-2015_006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Darrell Cockburn
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Susan Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Bent Ole Petersen
- Carbohydrate Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10
| | | | | | - Ole Hindsgaul
- Carbohydrate Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10
| | - Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | | | | | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
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22
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23
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Kim MK, An YJ, Song JM, Jeong CS, Kang MH, Kwon KK, Lee YH, Cha SS. Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-β-1,4-d-mannanase from the Antarctic springtail,Cryptopygus antarcticus. Proteins 2014; 82:3217-23. [DOI: 10.1002/prot.24655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/15/2014] [Accepted: 07/21/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Min-Kyu Kim
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Young Jun An
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Jung Min Song
- Marine Ecosystem Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Chang-Sook Jeong
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Mee Hye Kang
- Marine Ecosystem Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Youn-Ho Lee
- Marine Ecosystem Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Division; Korea Institute of Ocean Science and Technology; Ansan 426-744 Republic of Korea
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School; Korea Maritime and Ocean University; Pusan 606-791 Republic of Korea
- Department of Marine Biotechnology; University of Science and Technology; DaeJeon 305-333 Republic of Korea
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24
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Analysis of surface binding sites (SBSs) in carbohydrate active enzymes with focus on glycoside hydrolase families 13 and 77 — a mini-review. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0373-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Roth C, Wei R, Oeser T, Then J, Föllner C, Zimmermann W, Sträter N. Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca. Appl Microbiol Biotechnol 2014; 98:7815-23. [DOI: 10.1007/s00253-014-5672-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/06/2014] [Accepted: 03/06/2014] [Indexed: 10/25/2022]
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26
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Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149-70. [PMID: 23807207 PMCID: PMC11114072 DOI: 10.1007/s00018-013-1388-z] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 05/27/2013] [Indexed: 10/26/2022]
Abstract
α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia,
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27
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Li C, Du M, Cheng B, Wang L, Liu X, Ma C, Yang C, Xu P. Close relationship of a novel Flavobacteriaceae α-amylase with archaeal α-amylases and good potentials for industrial applications. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:18. [PMID: 24485248 PMCID: PMC3922116 DOI: 10.1186/1754-6834-7-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 01/21/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Bioethanol production from various starchy materials has received much attention in recent years. α-Amylases are key enzymes in the bioconversion process of starchy biomass to biofuels, food or other products. The properties of thermostability, pH stability, and Ca-independency are important in the development of such fermentation process. RESULTS A novel Flavobacteriaceae Sinomicrobium α-amylase (FSA) was identified and characterized from genomic analysis of a novel Flavobacteriaceae species. It is closely related with archaeal α-amylases in the GH13_7 subfamily, but is evolutionary distant with other bacterial α-amylases. Based on the conserved sequence alignment and homology modeling, with minor variation, the Zn2+- and Ca2+-binding sites of FSA were predicated to be the same as those of the archaeal thermophilic α-amylases. The recombinant α-amylase was highly expressed and biochemically characterized. It showed optimum activity at pH 6.0, high enzyme stability at pH 6.0 to 11.0, but weak thermostability. A disulfide bond was introduced by site-directed mutagenesis in domain C and resulted in the apparent improvement of the enzyme activity at high temperature and broad pH range. Moreover, about 50% of the enzyme activity was detected under 100°C condition, whereas no activity was observed for the wild type enzyme. Its thermostability was also enhanced to some extent, with the half-life time increasing from 25 to 55 minutes at 50°C. In addition, after the introduction of the disulfide bond, the protein became a Ca-independent enzyme. CONCLUSIONS The improved stability of FSA suggested that the domain C contributes to the overall stability of the enzyme under extreme conditions. In addition, successfully directed modification and special evolutionary status of FSA imply its directional reconstruction potentials for bioethanol production, as well as for other industrial applications.
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Affiliation(s)
- Chunfang Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China
| | - Miaofen Du
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China
| | - Bin Cheng
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China
| | - Xinqiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China
| | - Chunyu Yang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
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28
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Domain C of thermostable α-amylase of Geobacillus thermoleovorans mediates raw starch adsorption. Appl Microbiol Biotechnol 2014; 98:4503-19. [DOI: 10.1007/s00253-013-5459-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/28/2013] [Accepted: 12/08/2013] [Indexed: 10/25/2022]
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29
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Meekins DA, Guo HF, Husodo S, Paasch BC, Bridges TM, Santelia D, Kötting O, Vander Kooi CW, Gentry MS. Structure of the Arabidopsis glucan phosphatase like sex four2 reveals a unique mechanism for starch dephosphorylation. THE PLANT CELL 2013; 25:2302-14. [PMID: 23832589 PMCID: PMC3723627 DOI: 10.1105/tpc.113.112706] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/31/2013] [Accepted: 06/12/2013] [Indexed: 05/20/2023]
Abstract
Starch is a water-insoluble, Glc-based biopolymer that is used for energy storage and is synthesized and degraded in a diurnal manner in plant leaves. Reversible phosphorylation is the only known natural starch modification and is required for starch degradation in planta. Critical to starch energy release is the activity of glucan phosphatases; however, the structural basis of dephosphorylation by glucan phosphatases is unknown. Here, we describe the structure of the Arabidopsis thaliana starch glucan phosphatase like sex four2 (LSF2) both with and without phospho-glucan product bound at 2.3Å and 1.65Å, respectively. LSF2 binds maltohexaose-phosphate using an aromatic channel within an extended phosphatase active site and positions maltohexaose in a C3-specific orientation, which we show is critical for the specific glucan phosphatase activity of LSF2 toward native Arabidopsis starch. However, unlike other starch binding enzymes, LSF2 does not possess a carbohydrate binding module domain. Instead we identify two additional glucan binding sites located within the core LSF2 phosphatase domain. This structure is the first of a glucan-bound glucan phosphatase and provides new insights into the molecular basis of this agriculturally and industrially relevant enzyme family as well as the unique mechanism of LSF2 catalysis, substrate specificity, and interaction with starch granules.
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Affiliation(s)
- David A. Meekins
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Hou-Fu Guo
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Satrio Husodo
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Bradley C. Paasch
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Travis M. Bridges
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Diana Santelia
- Institute of Plant Biology, University of Zürich, 8092 Zurich, Switzerland
| | - Oliver Kötting
- Institute for Agricultural Sciences, ETH Zürich, 8092 Zurich, Switzerland
| | - Craig W. Vander Kooi
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
- Address correspondence to
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30
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Mok SC, Teh AH, Saito JA, Najimudin N, Alam M. Crystal structure of a compact α-amylase from Geobacillus thermoleovorans. Enzyme Microb Technol 2013; 53:46-54. [PMID: 23683704 DOI: 10.1016/j.enzmictec.2013.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/17/2022]
Abstract
A truncated form of an α-amylase, GTA, from thermophilic Geobacillus thermoleovorans CCB_US3_UF5 was biochemically and structurally characterized. The recombinant GTA, which lacked both the N- and C-terminal transmembrane regions, functioned optimally at 70°C and pH 6.0. While enzyme activity was not enhanced by the addition of CaCl2, GTA's thermostability was significantly improved in the presence of CaCl2. The structure, in complex with an acarbose-derived pseudo-hexasaccharide, consists of the typical three domains and binds one Ca(2+) ion. This Ca(2+) ion was strongly bound and not chelated by EDTA. A predicted second Ca(2+)-binding site, however, was disordered. With limited subsites, two novel substrate-binding residues, Y147 and Y182, may help increase substrate affinity. No distinct starch-binding domain is present, although two regions rich in aromatic residues have been observed. GTA, with a smaller domain B and several shorter loops compared to other α-amylases, has one of the most compact α-amylase folds that may contribute greatly to its tight Ca(2+) binding and thermostability.
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Affiliation(s)
- Sook-Chen Mok
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 Penang, Malaysia
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31
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Nielsen JW, Kramhøft B, Bozonnet S, Abou Hachem M, Stipp S, Svensson B, Willemoës M. Degradation of the starch components amylopectin and amylose by barley α-amylase 1: Role of surface binding site 2. Arch Biochem Biophys 2012; 528:1-6. [DOI: 10.1016/j.abb.2012.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 10/28/2022]
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32
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Characterization of recombinant amylopullulanase (gt-apu) and truncated amylopullulanase (gt-apuT) of the extreme thermophile Geobacillus thermoleovorans NP33 and their action in starch saccharification. Appl Microbiol Biotechnol 2012; 97:6279-92. [DOI: 10.1007/s00253-012-4538-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 10/27/2022]
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33
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Altered large-ring cyclodextrin product profile due to a mutation at Tyr-172 in the amylomaltase of Corynebacterium glutamicum. Appl Environ Microbiol 2012; 78:7223-8. [PMID: 22865069 DOI: 10.1128/aem.01366-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium glutamicum amylomaltase (CgAM) catalyzes the formation of large-ring cyclodextrins (LR-CDs) with a degree of polymerization of 19 and higher. The cloned CgAM gene was ligated into the pET-17b vector and used to transform Escherichia coli BL21(DE3). Site-directed mutagenesis of Tyr-172 in CgAM to alanine (Y172A) was performed to determine its role in the control of LR-CD production. Both the recombinant wild-type (WT) and Y172A enzymes were purified to apparent homogeneity and characterized. The Y172A enzyme exhibited lower disproportionation, cyclization, and hydrolysis activities than the WT. The k(cat)/K(m) of the disproportionation reaction of the Y172A enzyme was 2.8-fold lower than that of the WT enzyme. The LR-CD product profile from enzyme catalysis depended on the incubation time and the enzyme concentration. Interestingly, the Y172A enzyme showed a product pattern different from that of the WT CgAM at a long incubation time. The principal LR-CD products of the Y172A mutated enzyme were a cycloamylose mixture with a degree of polymerization of 28 or 29 (CD28 or CD29), while the principal LR-CD product of the WT enzyme was CD25 at 0.05 U of amylomaltase. These results suggest that Tyr-172 plays an important role in determining the LR-CD product profile of this novel CgAM.
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34
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Sørlie M, Zakariassen H, Norberg AL, Eijsink VGH. Processivity and substrate-binding in family 18 chitinases. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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35
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Leemhuis H, Pijning T, Dobruchowska JM, Dijkstra BW, Dijkhuizen L. Glycosidic bond specificity of glucansucrases: on the role of acceptor substrate binding residues. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676301] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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36
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Lin FP, Ho YH, Lin HY, Lin HJ. Effect of C-terminal truncation on enzyme properties of recombinant amylopullulanase from Thermoanaerobacter pseudoethanolicus. Extremophiles 2012; 16:395-403. [PMID: 22392283 DOI: 10.1007/s00792-012-0438-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
Abstract
The smallest and enzymatically active molecule, TetApuQ818, was localized within the C-terminal Q818 amino acid residue after serial C-terminal truncation analysis of the recombinant amylopullulanase molecule (TetApuM955) from Thermoanaerobacter pseudoethanolicus. Kinetic analyses indicated that the overall catalytic efficiency, k (cat)/K (m), of TetApuQ818 was 8-32% decreased for the pullulan and the soluble starch substrate, respectively. Changes to the substrate affinity, K (m), and the turnover rate, k (cat), were decreased significantly in both enzymatic activities of TetApuQ818. TetApuQ818 exhibited less thermostability than TetApuM955 when the temperature was raised above 85°C, but it had similar substrate-binding ability and hydrolysis products toward various substrates as TetApuM955 did. Both enzymes showed similar spectroscopies of fluorescence and circular dichroism, suggesting the active folding conformation was maintained after this C-terminal Q818 deletion. This study suggested that the binding ability of insoluble starch by TetApuM955 did not rely on the putative C-terminal carbohydrate binding module family 20 (CBM20) and two FnIII regions of TetApu, though the integrity of the AamyC module of TetApuQ818 was required for the enzyme activity.
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Affiliation(s)
- Fu-Pang Lin
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.
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37
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Rentzsch S, Podzimska D, Voegele A, Imbeck M, Müller K, Linkies A, Leubner-Metzger G. Dose- and tissue-specific interaction of monoterpenes with the gibberellin-mediated release of potato tuber bud dormancy, sprout growth and induction of α-amylases and β-amylases. PLANTA 2012; 235:137-51. [PMID: 21858448 DOI: 10.1007/s00425-011-1501-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 08/05/2011] [Indexed: 05/05/2023]
Abstract
Gibberellins (GA) are involved in bud dormancy release in several species. We show here that GA-treatment released bud dormancy, initiated bud sprouting and promoted sprout growth of excised potato tuber bud discs ('eyes'). Monoterpenes from peppermint oil (PMO) and S-(+)-carvone (CAR) interact with the GA-mediated bud dormancy release in a hormesis-type response: low monoterpene concentrations enhance dormancy release and the initiation of bud sprouting, whereas high concentrations inhibit it. PMO and CAR did, however, not affect sprout growth rate after its onset. We further show that GA-induced dormancy release is associated with tissue-specific regulation of α- and β-amylases. Molecular phylogenetic analysis shows that potato α-amylases cluster into two distinct groups: α-AMY1 and α-AMY2. GA-treatment induced transcript accumulation of members of both α-amylase groups, as well as α- and β-amylase enzyme activity in sprout and 'sub-eye' tissues. In sprouts, CAR interacts with the GA-mediated accumulation of α-amylase transcripts in an α-AMY2-specific and dose-dependent manner. Low CAR concentrations enhance the accumulation of α-AMY2-type α-amylase transcripts, but do not affect the α-AMY1-type transcripts. Low CAR concentrations also enhance the accumulation of α- and β-amylase enzyme activity in sprouts, but not in 'sub-eye' tissues. In contrast, high CAR concentrations have no appreciable effect in sprouts on the enzyme activities and the α-amylase transcript abundances of either group. The dose-dependent effects on the enzyme activities and the α-AMY2-type α-amylase transcripts in sprouts are specific for CAR but not for PMO. Different monoterpenes therefore may have specific targets for their interaction with hormone signalling pathways.
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Affiliation(s)
- Sonja Rentzsch
- Faculty of Biology, Institute for Biology II, Botany/Plant Physiology, Albert-Ludwigs-University, Schänzlestr.1, 79104, Freiburg, Germany
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38
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Cuyvers S, Dornez E, Abou Hachem M, Svensson B, Hothorn M, Chory J, Delcour JA, Courtin CM. Isothermal titration calorimetry and surface plasmon resonance allow quantifying substrate binding to different binding sites of Bacillus subtilis xylanase. Anal Biochem 2011; 420:90-2. [PMID: 21964501 PMCID: PMC4854199 DOI: 10.1016/j.ab.2011.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/22/2011] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
Abstract
Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first was a catalytically incompetent enzyme that allows substrate binding to both the AS and SBS. In the second enzyme, binding to the SBS was impaired by site-directed mutagenesis, whereas in the third enzyme, the AS was blocked using a covalent inhibitor. Both techniques were able to show that AS and SBS have a similar binding affinity.
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Affiliation(s)
- Sven Cuyvers
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre, Katholieke Universiteit Leuven, Leuven 3001, Belgium.
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39
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Biochemical characterization of two truncated forms of amylopullulanase from Thermoanaerobacterium saccharolyticum NTOU1 to identify its enzymatically active region. Appl Biochem Biotechnol 2011; 165:1047-56. [PMID: 21750992 DOI: 10.1007/s12010-011-9319-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 06/27/2011] [Indexed: 10/18/2022]
Abstract
The enzymatically active region of amylopullulanase from Thermoanaerobacterium saccharolyticum NTOU1 (TsaNTOU1Apu) was identified by truncation mutagenesis. Two truncated TsaNTOU1Apu enzymes, TsaNTOU1ApuM957 and TsaNTOU1ApuK885, were selected and characterized. Both TsaNTOU1ApuM957 and TsaNTOU1ApuK885 showed similar specific activities toward various substrates. The overall catalytic efficiency (k (cat)/apparent K (m)) for the soluble starch or pullulan substrate, however, was 20-25% lower in TsaNTOU1ApuK885 than in TsaNTOU1ApuM957. Both truncated enzymes exhibited similar thermostability and substrate-binding ability against the raw starch. The fluorescence and circular dichroism spectrometry studies indicated that TsaNTOU1ApuK885 retained an active folding conformation similar to that of TsaNTOU1ApuM957. These results indicate that a large part of the TsaNTOU1Apu, such as the C-terminal carbohydrate-binding module family 20, the second fibronectin type III, and a portion of the first FnIII motifs, could be removed without causing a serious aberrant structural change or a dramatic decrease in hydrolysis of soluble starch and pullulan.
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Cuyvers S, Dornez E, Delcour JA, Courtin CM. Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases. Crit Rev Biotechnol 2011; 32:93-107. [DOI: 10.3109/07388551.2011.561537] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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Using Surface Plasmon Resonance Technology to Screen Interactions Between Exopolysaccharides and Milk Proteins. FOOD BIOPHYS 2011. [DOI: 10.1007/s11483-011-9227-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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Zeeman SC, Kossmann J, Smith AM. Starch: its metabolism, evolution, and biotechnological modification in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2010; 61:209-34. [PMID: 20192737 DOI: 10.1146/annurev-arplant-042809-112301] [Citation(s) in RCA: 568] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bioethanol production. Here, we review recent advances in research in three key areas. First, we assess progress in identifying the enzymatic machinery required for the synthesis of amylopectin, the glucose polymer responsible for the insoluble nature of starch. Second, we discuss the pathways of starch degradation, focusing on the emerging role of transient glucan phosphorylation in plastids as a mechanism for solubilizing the surface of the starch granule. We contrast this pathway in leaves with the degradation of starch in the endosperm of germinated cereal seeds. Third, we consider the evolution of starch biosynthesis in plants from the ancestral ability to make glycogen. Finally, we discuss how this basic knowledge has been utilized to improve and diversify starch crops.
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Seo ES, Andersen JM, Nielsen MM, Vester-Christensen MB, Christiansen C, Jensen JM, Mótyán JA, Glaring MA, Blennow A, Kandra L, Gyémánt G, Janecek Š, Haser R, Aghajari N, Hachem MA, Svensson B. New Insight into Structure/Function Relationships in Plant .ALPHA.-Amylase Family GH13 Members. J Appl Glycosci (1999) 2010. [DOI: 10.5458/jag.57.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Christiansen C, Abou Hachem M, Janecek S, Viksø-Nielsen A, Blennow A, Svensson B. The carbohydrate-binding module family 20--diversity, structure, and function. FEBS J 2009; 276:5006-29. [PMID: 19682075 DOI: 10.1111/j.1742-4658.2009.07221.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Starch-active enzymes often possess starch-binding domains (SBDs) mediating attachment to starch granules and other high molecular weight substrates. SBDs are divided into nine carbohydrate-binding module (CBM) families, and CBM20 is the earliest-assigned and best characterized family. High diversity characterizes CBM20s, which occur in starch-active glycoside hydrolase families 13, 14, 15, and 77, and enzymes involved in starch or glycogen metabolism, exemplified by the starch-phosphorylating enzyme glucan, water dikinase 3 from Arabidopsis thaliana and the mammalian glycogen phosphatases, laforins. The clear evolutionary relatedness of CBM20s to CBM21s, CBM48s and CBM53s suggests a common clan hosting most of the known SBDs. This review surveys the diversity within the CBM20 family, and makes an evolutionary comparison with CBM21s, CBM48s and CBM53s, discussing intrafamily and interfamily relationships. Data on binding to and enzymatic activity towards soluble ligands and starch granules are summarized for wild-type, mutant and chimeric fusion proteins involving CBM20s. Noticeably, whereas CBM20s in amylolytic enzymes confer moderate binding affinities, with dissociation constants in the low micromolar range for the starch mimic beta-cyclodextrin, recent findings indicate that CBM20s in regulatory enzymes have weaker, low millimolar affinities, presumably facilitating dynamic regulation. Structures of CBM20s, including the first example of a full-length glucoamylase featuring both the catalytic domain and the SBD, are summarized, and distinct architectural and functional features of the two SBDs and roles of pivotal amino acids in binding are described. Finally, some applications of SBDs as affinity or immobilization tags and, recently, in biofuel and in planta bioengineering are presented.
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Affiliation(s)
- Camilla Christiansen
- VKR Research Centre Pro-Active Plants, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg, Denmark
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Nielsen MM, Bozonnet S, Seo ES, Mótyán JA, Andersen JM, Dilokpimol A, Abou Hachem M, Gyémánt G, Næsted H, Kandra L, Sigurskjold BW, Svensson B. Two Secondary Carbohydrate Binding Sites on the Surface of Barley α-Amylase 1 Have Distinct Functions and Display Synergy in Hydrolysis of Starch Granules. Biochemistry 2009; 48:7686-97. [DOI: 10.1021/bi900795a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Morten M. Nielsen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Sophie Bozonnet
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
| | - Eun-Seong Seo
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - János A. Mótyán
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Joakim M. Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Gyöngyi Gyémánt
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Henrik Næsted
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Lili Kandra
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Bent W. Sigurskjold
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
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Nielsen MM, Seo ES, Dilokpimol A, Andersen J, Abou Hachem M, Naested H, Willemoës M, Bozonnet S, Kandra L, Gyémánt G, Haser R, Aghajari N, Svensson B. Roles of multiple surface sites, long substrate binding clefts, and carbohydrate binding modules in the action of amylolytic enzymes on polysaccharide substrates. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701789528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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48
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Ragunath C, Manuel SG, Venkataraman V, Sait HB, Kasinathan C, Ramasubbu N. Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding. J Mol Biol 2008; 384:1232-48. [PMID: 18951906 PMCID: PMC2644404 DOI: 10.1016/j.jmb.2008.09.089] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 09/28/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
Abstract
Human salivary alpha-amylase (HSAmy) has three distinct functions relevant to oral health: (1) hydrolysis of starch, (2) binding to hydroxyapatite (HA), and (3) binding to bacteria (e.g., viridans streptococci). Although the active site of HSAmy for starch hydrolysis is well-characterized, the regions responsible for bacterial binding are yet to be defined. Since HSAmy possesses several secondary saccharide-binding sites in which aromatic residues are prominently located, we hypothesized that one or more of the secondary saccharide-binding sites harboring the aromatic residues may play an important role in bacterial binding. To test this hypothesis, the aromatic residues at five secondary binding sites were mutated to alanine to generate six mutants representing either single (W203A, Y276A, and W284A), double (Y276A/W284A and W316A/W388A), or multiple [W134A/W203A/Y276A/W284A/W316A/W388A; human salivary alpha-amylase aromatic residue multiple mutant (HSAmy-ar)] mutations. The crystal structure of HSAmy-ar as an acarbose complex was determined at a resolution of 1.5 A and compared with the existing wild-type acarbose complex. The wild-type and the mutant enzymes were characterized for their abilities to exhibit enzyme activity, starch-binding activity, HA-binding activity, and bacterial binding activity. Our results clearly showed that (1) mutation of aromatic residues does not alter the overall conformation of the molecule; (2) single or double mutants showed either moderate or minimal changes in both starch-binding activity and bacterial binding activity, whereas HSAmy-ar showed significant reduction in these activities; (3) starch-hydrolytic activity was reduced by 10-fold in HSAmy-ar; (4) oligosaccharide-hydrolytic activity was reduced in all mutants, but the action pattern was similar to that of the wild-type enzyme; and (5) HA binding was unaffected in HSAmy-ar. These results clearly show that the aromatic residues at the secondary saccharide-binding sites in HSAmy play a critical role in bacterial binding and in starch-hydrolytic functions of HSAmy.
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Affiliation(s)
- Chandran Ragunath
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Suba G.A. Manuel
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Venkat Venkataraman
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Hameetha B.R. Sait
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Chinnasamy Kasinathan
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Narayanan Ramasubbu
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
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An enzyme family reunion — similarities, differences and eccentricities in actions on α-glucans. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0164-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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