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Rhimi M, Da Lage JL, Haser R, Feller G, Aghajari N. Structural and Functional Characterization of Drosophila melanogaster α-Amylase. Molecules 2023; 28:5327. [PMID: 37513201 PMCID: PMC10384113 DOI: 10.3390/molecules28145327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Insects rely on carbohydrates such as starch and glycogen as an energy supply for growth of larvae and for longevity. In this sense α-amylases have essential roles under extreme conditions, e.g., during nutritional or temperature stress, thereby contributing to survival of the insect. This makes them interesting targets for combating insect pests. Drosophila melanogaster α-amylase, DMA, which belongs to the glycoside hydrolase family 13, sub family 15, has been studied from an evolutionary, biochemical, and structural point of view. Our studies revealed that the DMA enzyme is active over a broad temperature and pH range, which is in agreement with the fluctuating environmental changes with which the insect is confronted. Crystal structures disclosed a new nearly fully solvated metal ion, only coordinated to the protein via Gln263. This residue is only conserved in the subgroup of D. melanogaster and may thus contribute to the enzyme adaptive response to large temperature variations. Studies of the effect of plant inhibitors and the pseudo-tetrasaccharide inhibitor acarbose on DMA activity, allowed us to underline the important role of the so-called flexible loop on activity/inhibition, but also to suggest that the inhibition modes of the wheat inhibitors WI-1 and WI-3 on DMA, are likely different.
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Affiliation(s)
- Moez Rhimi
- Molecular Microbiology and Structural Biochemistry, UMR5086, CNRS, University of Lyon 1, 7 Passage du Vercors, F-69367 Lyon, CEDEX 07, France
| | - Jean-Luc Da Lage
- Evolution, Génomes, Comportement, Ecologie, UMR 9191 University Paris-Saclay-CNRS-IRD, F-91190 Gif-sur-Yvette, France
| | - Richard Haser
- Molecular Microbiology and Structural Biochemistry, UMR5086, CNRS, University of Lyon 1, 7 Passage du Vercors, F-69367 Lyon, CEDEX 07, France
| | - Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR5086, CNRS, University of Lyon 1, 7 Passage du Vercors, F-69367 Lyon, CEDEX 07, France
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2
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Pijning T, Gangoiti J, te Poele EM, Börner T, Dijkhuizen L. Insights into Broad-Specificity Starch Modification from the Crystal Structure of Limosilactobacillus Reuteri NCC 2613 4,6-α-Glucanotransferase GtfB. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13235-13245. [PMID: 34708648 PMCID: PMC8587608 DOI: 10.1021/acs.jafc.1c05657] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 05/31/2023]
Abstract
GtfB-type α-glucanotransferase enzymes from glycoside hydrolase family 70 (GH70) convert starch substrates into α-glucans that are of interest as food ingredients with a low glycemic index. Characterization of several GtfBs showed that they differ in product- and substrate specificity, especially with regard to branching, but structural information is limited to a single GtfB, preferring mostly linear starches and featuring a tunneled binding groove. Here, we present the second crystal structure of a 4,6-α-glucanotransferase (Limosilactobacillus reuteri NCC 2613) and an improved homology model of a 4,3-α-glucanotransferase GtfB (L. fermentum NCC 2970) and show that they are able to convert both linear and branched starch substrates. Compared to the previously described GtfB structure, these two enzymes feature a much more open binding groove, reminiscent of and evolutionary closer to starch-converting GH13 α-amylases. Sequence analysis of 287 putative GtfBs suggests that only 20% of them are similarly "open" and thus suitable as broad-specificity starch-converting enzymes.
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Affiliation(s)
- Tjaard Pijning
- Biomolecular
X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, The
Netherlands
| | - Joana Gangoiti
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, The
Netherlands
| | - Evelien M. te Poele
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, The
Netherlands
- CarbExplore
Research B.V., Zernikelaan
8, Groningen 9747 AA, The Netherlands
| | - Tim Börner
- Nestlé
Research, Société des Produits Nestlé SA, Route du Jorat 57, 1000 Lausanne, Switzerland
| | - Lubbert Dijkhuizen
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, The
Netherlands
- CarbExplore
Research B.V., Zernikelaan
8, Groningen 9747 AA, The Netherlands
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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: 12] [Impact Index Per Article: 3.0] [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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Tang S, Xu T, Peng J, Zhou K, Zhu Y, Zhou W, Cheng H, Zhou H. Overexpression of an endogenous raw starch digesting mesophilic α-amylase gene in Bacillus amyloliquefaciens Z3 by in vitro methylation protocol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:3013-3023. [PMID: 32056215 DOI: 10.1002/jsfa.10332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/07/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Mesophilic α-amylases function effectively at low temperatures with high rates of catalysis and require less energy for starch hydrolysis. Bacillus amyloliquefaciens is an essential producer of mesophilic α-amylases. However, because of the existence of the restriction-modification system, introducing exogenous DNAs into wild-type B. amyloliquefaciens is especially tricky. RESULTS α-Amylase producer B. amyloliquefaciens strain Z3 was screened and used as host for endogenous α-amylase gene expression. In vitro methylation was performed in recombinant plasmid pWB980-amyZ3. With the in vitro methylation, the transformation efficiency was increased to 0.96 × 102 colony-forming units μg-1 plasmid DNA. A positive transformant BAZ3-16 with the highest α-amylase secreting capacity was chosen for further experiments. The α-amylase activity of strain BAZ3-16 reached 288.70 ± 16.15 U mL-1 in the flask and 386.03 ± 16.25 U mL-1 in the 5-L stirred-tank fermenter, respectively. The Bacillus amyloliquefaciens Z3 expression system shows excellent genetic stability and high-level extracellular production of the target protein. Moreover, the synergistic interaction of AmyZ3 with amyloglucosidase was determined during the hydrolysis of raw starch. The hydrolysis degree reached 92.34 ± 3.41% for 100 g L-1 raw corn starch and 81.30 ± 2.92% for 100 g L-1 raw cassava starch after 24 h, respectively. CONCLUSION Methylation of the plasmid DNA removes a substantial barrier for transformation of B. amyloliquefaciens strain Z3. Furthermore, the exceptional ability to hydrolyze starch makes α-amylase AmyZ3 and strain BAZ3-16 valuable in the starch industry. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Shizhe Tang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Tingliang Xu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jing Peng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Kaiyan Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yuling Zhu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Wenbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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5
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Insights into the thermostability and product specificity of a maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04. Biotechnol Lett 2019; 42:295-303. [DOI: 10.1007/s10529-019-02780-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/27/2019] [Indexed: 01/18/2023]
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6
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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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7
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Xie X, Li Y, Ban X, Zhang Z, Gu Z, Li C, Hong Y, Cheng L, Jin T, Li Z. Crystal structure of a maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04. Int J Biol Macromol 2019; 138:394-402. [PMID: 31325505 DOI: 10.1016/j.ijbiomac.2019.07.104] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
To better understand structure-function relationships, an X-ray crystal structure of the maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04 (Bst-MFA) with bound acarbose has been determined at 2.2 Å. The structure revealed a classical three-domain fold stabilized by four calcium ions, in which CaI-CaIII form an unprecedented linear metal triad in the interior of domain B. Catalytic residues are deduced to be two aspartic acids and one glutamic acid (Asp234, Glu264, Asp331), and the acarbose is bound to surrounding amino acid residues, mainly through extensive hydrogen bonds. Furthermore, analysis of the structure indicates the existence of at least 8 subsites in Bst-MFA, six glycone sites (-6, -5, -4, -3, -2, -1) and two aglycone sites (+1, +2). Subsite +3 remains to be further explored. Sugar-binding subsites contribute to further presentation of the oligosaccharide-binding mode, which explains the product specificity of Bst-MFA to some extent. In addition, we propose a mechanism by which maltooligosaccharide-forming amylases produce particular maltooligosaccharide products, a result different from that seen with typical α-amylases. Finally, the three-dimensional structure of Bst-MFA complexed with acarbose provides the basis for further studies, designed to increase product specificity.
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Affiliation(s)
- Xiaofang Xie
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yuelong Li
- School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, People's Republic of China.
| | - Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Ziqian Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China.
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yan Hong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China.
| | - Li Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Tengchuan Jin
- School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, People's Republic of China; Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China.
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8
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Agirre J, Moroz O, Meier S, Brask J, Munch A, Hoff T, Andersen C, Wilson KS, Davies GJ. The structure of the AliC GH13 α-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the α-amylase family. Acta Crystallogr D Struct Biol 2019; 75:1-7. [PMID: 30644839 PMCID: PMC6333287 DOI: 10.1107/s2059798318014900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/21/2018] [Indexed: 10/06/2023] Open
Abstract
α-Amylases are glycoside hydrolases that break the α-1,4 bonds in starch and related glycans. The degradation of starch is rendered difficult by the presence of varying degrees of α-1,6 branch points and their possible accommodation within the active centre of α-amylase enzymes. Given the myriad industrial uses for starch and thus also for α-amylase-catalysed starch degradation and modification, there is considerable interest in how different α-amylases might accommodate these branches, thus impacting on the potential processing of highly branched post-hydrolysis remnants (known as limit dextrins) and societal applications. Here, it was sought to probe the branch-point accommodation of the Alicyclobacillus sp. CAZy family GH13 α-amylase AliC, prompted by the observation of a molecule of glucose in a position that may represent a branch point in an acarbose complex solved at 2.1 Å resolution. Limit digest analysis by two-dimensional NMR using both pullulan (a regular linear polysaccharide of α-1,4, α-1,4, α-1,6 repeating trisaccharides) and amylopectin starch showed how the Alicyclobacillus sp. enzyme could accept α-1,6 branches in at least the -2, +1 and +2 subsites, consistent with the three-dimensional structures with glucosyl moieties in the +1 and +2 subsites and the solvent-exposure of the -2 subsite 6-hydroxyl group. Together, the work provides a rare insight into branch-point acceptance in these industrial catalysts.
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Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Olga Moroz
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jesper Brask
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Astrid Munch
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Tine Hoff
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | | | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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9
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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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10
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O'Neill EC, Stevenson CEM, Tantanarat K, Latousakis D, Donaldson MI, Rejzek M, Nepogodiev SA, Limpaseni T, Field RA, Lawson DM. Structural Dissection of the Maltodextrin Disproportionation Cycle of the Arabidopsis Plastidial Disproportionating Enzyme 1 (DPE1). J Biol Chem 2015; 290:29834-53. [PMID: 26504082 PMCID: PMC4705983 DOI: 10.1074/jbc.m115.682245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 11/06/2022] Open
Abstract
The degradation of transitory starch in the chloroplast to provide fuel for the plant during the night requires a suite of enzymes that generate a series of short chain linear glucans. However, glucans of less than four glucose units are no longer substrates for these enzymes, whereas export from the plastid is only possible in the form of either maltose or glucose. In order to make use of maltotriose, which would otherwise accumulate, disproportionating enzyme 1 (DPE1; a 4-α-glucanotransferase) converts two molecules of maltotriose to a molecule of maltopentaose, which can now be acted on by the degradative enzymes, and one molecule of glucose that can be exported. We have determined the structure of the Arabidopsis plastidial DPE1 (AtDPE1), and, through ligand soaking experiments, we have trapped the enzyme in a variety of conformational states. AtDPE1 forms a homodimer with a deep, long, and open-ended active site canyon contained within each subunit. The canyon is divided into donor and acceptor sites with the catalytic residues at their junction; a number of loops around the active site adopt different conformations dependent on the occupancy of these sites. The "gate" is the most dynamic loop and appears to play a role in substrate capture, in particular in the binding of the acceptor molecule. Subtle changes in the configuration of the active site residues may prevent undesirable reactions or abortive hydrolysis of the covalently bound enzyme-substrate intermediate. Together, these observations allow us to delineate the complete AtDPE1 disproportionation cycle in structural terms.
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Affiliation(s)
- Ellis C O'Neill
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Clare E M Stevenson
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Krit Tantanarat
- the Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Dimitrios Latousakis
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Matthew I Donaldson
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Martin Rejzek
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Sergey A Nepogodiev
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - Tipaporn Limpaseni
- the Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Robert A Field
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
| | - David M Lawson
- From the Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom and
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11
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Offen WA, Viksoe-Nielsen A, Borchert TV, Wilson KS, Davies GJ. Three-dimensional structure of a variant `Termamyl-like' Geobacillus stearothermophilus α-amylase at 1.9 Å resolution. Acta Crystallogr F Struct Biol Commun 2015; 71:66-70. [PMID: 25615972 PMCID: PMC4304751 DOI: 10.1107/s2053230x14026508] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/02/2014] [Indexed: 11/10/2022] Open
Abstract
The enzyme-catalysed degradation of starch is central to many industrial processes, including sugar manufacture and first-generation biofuels. Classical biotechnological platforms involve steam explosion of starch followed by the action of endo-acting glycoside hydrolases termed α-amylases and then exo-acting α-glucosidases (glucoamylases) to yield glucose, which is subsequently processed. A key enzymatic player in this pipeline is the `Termamyl' class of bacterial α-amylases and designed/evolved variants thereof. Here, the three-dimensional structure of one such Termamyl α-amylase variant based upon the parent Geobacillus stearothermophilus α-amylase is presented. The structure has been solved at 1.9 Å resolution, revealing the classical three-domain fold stabilized by Ca2+ and a Ca2+-Na+-Ca2+ triad. As expected, the structure is similar to the G. stearothermophilus α-amylase but with main-chain deviations of up to 3 Å in some regions, reflecting both the mutations and differing crystal-packing environments.
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Affiliation(s)
- Wendy A. Offen
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | | | | | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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12
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Purification and Characterization of a Liquefying α-Amylase from Alkalophilic ThermophilicBacillussp. AAH-31. Biosci Biotechnol Biochem 2014; 76:1378-83. [DOI: 10.1271/bbb.120164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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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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14
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Kumar V. Identification of the conserved spatial position of key active-site atoms in glycoside hydrolase 13 family members. Carbohydr Res 2010; 345:1564-9. [PMID: 20557875 DOI: 10.1016/j.carres.2010.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/22/2010] [Accepted: 04/27/2010] [Indexed: 11/30/2022]
Abstract
A computational study on the glycoside hydrolase 13 (GH13) family of the CAZy database has been carried out at the atomic level in order to identify the conserved positions that may be responsible for recognition of the substrate. Analysis with substrate analog-, inhibitor-, or product-bound 3D structures was carried out to find the atomic spatial arrangement of the amino acids that make -2, -1, +1, and +2 subsites and water oxygen atoms around the ligand. The identified conserved positions of subsites were independent from the nature of the amino acid. The -1 and +1 subsites have more conserved positions than the -2 and +2 subsites. Some of the clusters of the -1 and +1 subsites have atoms of the same chemical nature. A spatially conserved position for water, which is stabilized by a hydrogen bond with the carboxyl group of a proton donor (Glu) and Asp of the catalytic triad, was found in the -1 subsite of 75% of the enzymes subjected to analysis. This position could be the region of hydrolytic water.
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Affiliation(s)
- Vikash Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
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15
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Analysis of the key active subsites of glycoside hydrolase 13 family members. Carbohydr Res 2010; 345:893-8. [DOI: 10.1016/j.carres.2010.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 02/07/2010] [Accepted: 02/09/2010] [Indexed: 11/19/2022]
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16
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Novinscak A, DeCoste NJ, Surette C, Filion M. Characterization of bacterial and fungal communities in composted biosolids over a 2 year period using denaturing gradient gel electrophoresis. Can J Microbiol 2009; 55:375-87. [DOI: 10.1139/w08-152] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Composting is a microbial process that converts organic waste into a nutrient-rich end product used in horticultural and agricultural applications. The diversity and long-term succession of microorganisms found in composted biosolids has been less characterized than other composts. In this study, bacterial and fungal communities found in composted biosolids aging from 1 to 24 months were studied using denaturing gradient gel electrophoresis (DGGE) and sequencing. The results revealed high levels of diversity, where 53 bacterial species belonging to 10 phyla and 21 fungal species belonging to 4 phyla were identified. Significant differences were observed when comparing the bacterial DGGE patterns of young compost samples, whereas no differences were observed in samples over 8 months. For fungal patterns, no significant differences were observed during the first 4 months of composting, but the diversity then significantly shifted until 24 months. The results indicate that patterns of bacterial species vary during the first few months of composting, whereas fungal patterns generally vary throughout the whole process, except during early stages. The description of the main microbial groups found in composted biosolids could find various applications, including the discovery of biotechnologically relevant microorganisms and the development of novel markers allowing quantitative monitoring of key microorganisms.
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Affiliation(s)
- Amy Novinscak
- Department of Biology, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
| | - Nadine J. DeCoste
- Department of Biology, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
| | - Céline Surette
- Department of Biology, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
| | - Martin Filion
- Department of Biology, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, 165 Massey Ave, Moncton, NB E1A 3E9, Canada
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17
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Tan TC, Mijts BN, Swaminathan K, Patel BK, Divne C. Crystal Structure of the Polyextremophilic α-Amylase AmyB from Halothermothrix orenii: Details of a Productive Enzyme–Substrate Complex and an N Domain with a Role in Binding Raw Starch. J Mol Biol 2008; 378:852-70. [DOI: 10.1016/j.jmb.2008.02.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 02/15/2008] [Accepted: 02/19/2008] [Indexed: 11/15/2022]
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18
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van der Kaaij RM, Janeček Š, van der Maarel MJEC, Dijkhuizen L. Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal alpha-amylase enzymes. MICROBIOLOGY-SGM 2008; 153:4003-4015. [PMID: 18048915 DOI: 10.1099/mic.0.2007/008607-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Currently known fungal alpha-amylases are well-characterized extracellular enzymes that are classified into glycoside hydrolase subfamily GH13_1. This study describes the identification, and phylogenetic and biochemical analysis of novel intracellular fungal alpha-amylases. The phylogenetic analysis shows that they cluster in the recently identified subfamily GH13_5 and display very low similarity to fungal alpha-amylases of family GH13_1. Homologues of these intracellular enzymes are present in the genome sequences of all filamentous fungi studied, including ascomycetes and basidiomycetes. One of the enzymes belonging to this new group, Amy1p from Histoplasma capsulatum, has recently been functionally linked to the formation of cell wall alpha-glucan. To study the biochemical characteristics of this novel cluster of alpha-amylases, we overexpressed and purified a homologue from Aspergillus niger, AmyD, and studied its activity product profile with starch and related substrates. AmyD has a relatively low hydrolysing activity on starch (2.2 U mg(-1)), producing mainly maltotriose. A possible function of these enzymes in relation to cell wall alpha-glucan synthesis is discussed.
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Affiliation(s)
- R M van der Kaaij
- Centre for Carbohydrate Bioprocessing, TNO-University of Groningen, Haren, The Netherlands.,Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Š Janeček
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - M J E C van der Maarel
- Business Unit Food and Biotechnology Innovations, TNO Quality of Life, Groningen, The Netherlands.,Centre for Carbohydrate Bioprocessing, TNO-University of Groningen, Haren, The Netherlands.,Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - L Dijkhuizen
- Centre for Carbohydrate Bioprocessing, TNO-University of Groningen, Haren, The Netherlands.,Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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19
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Shirai T, Igarashi K, Ozawa T, Hagihara H, Kobayashi T, Ozaki K, Ito S. Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins. Proteins 2007; 66:600-10. [PMID: 17154418 DOI: 10.1002/prot.21255] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The crystal structure of alkaline liquefying alpha-amylase (AmyK) from the alkaliphilic Bacillus sp. KSM-1378 was determined at 2.1 A resolution. The AmyK structure belongs to the GH13 glycoside hydrolase family, which consists of three domains, and bound three calcium and one sodium ions. The alkaline adaptation mechanism of AmyK was investigated by the ancestral sequence evolutionary trace method and by extensive comparisons between alkaline and nonalkaline enzyme structures, including three other protein families: protease, cellulase, and phosphoserine aminotransferase. The consensus change for the alkaline adaptation process was a decrease in the Lys content. The loss of a Lys residue is associated with ion pair remodeling, which mainly consists of the loss of Lys-Asp/Glu ion pairs and the acquisition of Arg ion pairs, preferably Arg-Glu. The predicted replacements of the positively charged amino acids were often, although not always, used for ion pair remodeling.
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Affiliation(s)
- Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-science and Technology, Nagahama 526-0829, Japan.
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20
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Lyhne-Iversen L, Hobley TJ, Kaasgaard SG, Harris P. Structure of Bacillus halmapalus alpha-amylase crystallized with and without the substrate analogue acarbose and maltose. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:849-54. [PMID: 16946462 PMCID: PMC2242873 DOI: 10.1107/s174430910603096x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 08/07/2006] [Indexed: 11/11/2022]
Abstract
Recombinant Bacillus halmapalus alpha-amylase (BHA) was studied in two different crystal forms. The first crystal form was obtained by crystallization of BHA at room temperature in the presence of acarbose and maltose; data were collected at cryogenic temperature to a resolution of 1.9 A. It was found that the crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 47.0, b = 73.5, c = 151.1 A. A maltose molecule was observed and found to bind to BHA and previous reports of the binding of a nonasaccharide were confirmed. The second crystal form was obtained by pH-induced crystallization of BHA in a MES-HEPES-boric acid buffer (MHB buffer) at 303 K; the solubility of BHA in MHB has a retrograde temperature dependency and crystallization of BHA was only possible by raising the temperature to at least 298 K. Data were collected at cryogenic temperature to a resolution of 2.0 A. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 38.6, b = 59.0, c = 209.8 A. The structure was solved using molecular replacement. The maltose-binding site is described and the two structures are compared. No significant changes were seen in the structure upon binding of the substrates.
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Affiliation(s)
- Louise Lyhne-Iversen
- Department of Chemistry, Technical University of Denmark, Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Timothy J. Hobley
- Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Building 223, DK-2800 Kgs. Lyngby, Denmark
| | | | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Building 207, DK-2800 Kgs. Lyngby, Denmark
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21
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Kandra L, Hachem MA, Gyémánt G, Kramhøft B, Svensson B. Mapping of barley α-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft. FEBS Lett 2006; 580:5049-53. [PMID: 16949579 DOI: 10.1016/j.febslet.2006.08.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 08/10/2006] [Accepted: 08/15/2006] [Indexed: 11/25/2022]
Abstract
Subsite affinity maps of long substrate binding clefts in barley alpha-amylases, obtained using a series of maltooligosaccharides of degree of polymerization of 3-12, revealed unfavorable binding energies at the internal subsites -3 and -5 and at subsites -8 and +3/+4 defining these subsites as binding barriers. Barley alpha-amylase 1 mutants Y105A and T212Y at subsite -6 and +4 resulted in release or anchoring of bound substrate, thus modifying the affinities of other high-affinity subsites (-2 and +2) and barriers. The double mutant Y105A-T212Y displayed a hybrid subsite affinity profile, converting barriers to binding areas. These findings highlight the dynamic binding energy distribution and the versatility of long maltooligosaccharide derivatives in mapping extended binding clefts in alpha-amylases.
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Affiliation(s)
- Lili Kandra
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen H-4010, Hungary
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22
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Kanai R, Haga K, Akiba T, Yamane K, Harata K. Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707. Protein Sci 2006; 15:468-77. [PMID: 16452622 PMCID: PMC2249768 DOI: 10.1110/ps.051877006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 11/18/2005] [Accepted: 11/18/2005] [Indexed: 10/25/2022]
Abstract
Maltohexaose-producing amylase (G6-amylase) from alkalophilic Bacillus sp.707 predominantly produces maltohexaose (G6) in the yield of >30% of the total products from short-chain amylose (DP=17). Our previous crystallographic study showed that G6-amylase has nine subsites, from -6 to +3, and pointed out the importance of the indole moiety of Trp140 in G6 production. G6-amylase has very low levels of hydrolytic activities for oligosaccharides shorter than maltoheptaose. To elucidate the mechanism underlying G6 production, we determined the crystal structures of the G6-amylase complexes with G6 and maltopentaose (G5). In the active site of the G6-amylase/G5 complex, G5 is bound to subsites -6 to -2, while G1 and G6 are found at subsites +2 and -7 to -2, respectively, in the G6-amylase/G6 complex. In both structures, the glucosyl residue located at subsite -6 is stacked to the indole moiety of Trp140 within a distance of 4A. The measurement of the activities of the mutant enzymes when Trp140 was replaced by leucine (W140L) or by tyrosine (W140Y) showed that the G6 production from short-chain amylose by W140L is lower than that by W140Y or wild-type enzyme. The face-to-face short contact between Trp140 and substrate sugars is suggested to regulate the disposition of the glucosyl residue at subsite -6 and to govern product specificity for G6 production.
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Affiliation(s)
- Ryuta Kanai
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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23
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Abou Hachem M, Bozonnet S, Willemoës M, C. Bønsager B, Munch Nielsen M, Fukuda K, Kramhøft B, Maeda K, W. Sigurskjold B, Hägglund P, Finnie C, Mori H, Robert X, H. Jensen M, Tranier S, Aghajari N, Haser R, Svensson B. Interactions between Barley .ALPHA.-Amylases, Substrates, Inhibitors and Regulatory Proteins. J Appl Glycosci (1999) 2006. [DOI: 10.5458/jag.53.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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24
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Ozawa T, Igarashi K, Ozaki K, Kobayashi T, Suzuki A, Shirai T, Yamane T, Ito S. Molecular Modeling and Implications of a Bacillus .ALPHA.-Amylase that Acquires Enhanced Thermostability and Chelator Resistance by Deletion of an Arginine-glycine Residue. J Appl Glycosci (1999) 2006. [DOI: 10.5458/jag.53.193] [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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25
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Robert X, Haser R, Mori H, Svensson B, Aghajari N. Oligosaccharide binding to barley alpha-amylase 1. J Biol Chem 2005; 280:32968-78. [PMID: 16030022 DOI: 10.1074/jbc.m505515200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough insight into the substrate binding by describing residues defining 9 subsites, namely -7 through +2. These structures support that the pseudotetrasaccharide inhibitor acarbose is hydrolyzed by the active enzymes. Moreover, sugar binding was observed to the starch granule-binding site previously determined in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site was proposed at the glycone part of the binding cleft, and the crystal structures of the catalytic nucleophile mutant (AMY1D180A) complexed with acarbose and maltoheptaose, respectively, suggest an additional role for the nucleophile in the stabilization of the Michaelis complex. Furthermore, probable roles are outlined for the surface binding sites. Our data support a model in which the two surface sites in AMY1 can interact with amylose chains in their naturally folded form. Because of the specificities of these two sites, they may locate/orient the enzyme in order to facilitate access to the active site for polysaccharide chains. Moreover, the sugar tongs surface site could also perform the unraveling of amylose chains, with the aid of Tyr-380 acting as "molecular tweezers."
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Affiliation(s)
- Xavier Robert
- Laboratoire de BioCristallographie, IFR-128 BioSciences Lyon-Gerland, Institut de Biologie et Chimie des Protéines, UMR 5086, CNRS-UCBL1, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
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