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Xie X, Ban X, Gu Z, Li C, Hong Y, Cheng L, Li Z. Structure-Based Engineering of a Maltooligosaccharide-Forming Amylase To Enhance Product Specificity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:838-844. [PMID: 31896254 DOI: 10.1021/acs.jafc.9b07234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Maltooligosaccharide-forming amylases (MFAses) are promising tools for a variety of food industry applications because they convert starch into functional maltooligosaccharides. The MFAse from Bacillus stearothermophilus STB04 (BstMFAse) is a thermostable enzyme that preferentially produces maltopentaose and maltohexaose. An X-ray crystal structure of the BstMFAse-acarbose complex suggested that mutation of glycine 109 would increase its maltohexaose specificity. Using site-directed mutagenesis, glycine 109 was replaced with several different amino acids. Mutant-containing asparagine (G109N), aspartic acid (G109D), and phenylalanine (G109F) produced 36.1, 42.4, and 39.0% maltohexaose from starch, respectively, which was greater than that produced by the wild-type (32.9%). These mutants also exhibited substantially altered oligosaccharide hydrolysis patterns in favor of maltohexaose production. Homology models suggested that the mutants form extra interactions with the substrate at subsite -6, which were responsible for the enhanced maltohexaose specificity of BstMFAse. The results of this study support the proposition that binding of the substrate's nonreducing end in the nonreducing end-subsite of the MFAse active center plays a crucial role in its 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
| | - Xiaofeng Ban
- 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
- Collaborative Innovation Center of Food Safety and Quality Control , 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
- Collaborative Innovation Center of Food Safety and Quality Control , 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
- Collaborative Innovation Center of Food Safety and Quality Control , 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
- Collaborative Innovation Center of Food Safety and Quality Control , Jiangnan University , Wuxi 214122 , People's Republic of China
| | - 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
- Collaborative Innovation Center of Food Safety and Quality Control , Jiangnan University , Wuxi 214122 , People's Republic of China
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Zhang Z, Jin T, Xie X, Ban X, Li C, Hong Y, Cheng L, Gu Z, Li Z. Structure of maltotetraose-forming amylase from Pseudomonas saccharophila STB07 provides insights into its product specificity. Int J Biol Macromol 2019; 154:1303-1313. [PMID: 31751711 DOI: 10.1016/j.ijbiomac.2019.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/25/2019] [Accepted: 11/02/2019] [Indexed: 11/27/2022]
Abstract
The maltooligosaccharide-forming amylases (MFAses) degrade starch into maltooligosaccharides which potentially benefit human diet and grow popular in food processing, but little has been studied about their product specificity and structures. We focused on this topic and provide evidence through an X-ray crystal structure of the maltotetraose (G4)-forming amylase from Pseudomonas saccharophila STB07 (MFAps), as well as co-crystal structures of MFAps with G4 and with pseudo-maltoheptaose (pseudo-G7) determined at up to 1.1 Å resolution. G4 and pseudo-G7 occupy active cleft subsites -4 to -1 and -4 to +3 respectively. Binding induces conformational changes in the active sites except Asp193, working as the base catalyst. Comparison of the MFAps structure with those of other α-amylases revealed obvious differences in the loop structures providing dominant interactions between protein and substrate in the non-reducing side of the active sites cleft. These structures at the non-reducing end may govern the G4 specificity of MFAps and also be relevant to its exo-type action pattern.
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Affiliation(s)
- Ziqian Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Tengchuan Jin
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA; School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027, People's Republic of China.
| | - Xiaofang Xie
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xiaofeng Ban
- 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; Collaborative Innovation Center for Food Safety and Quality Control, 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
| | - 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; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - 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; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, People's Republic of China.
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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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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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Kaira GS, Kapoor M. How substrate subsites in GH26 endo-mannanase contribute towards mannan binding. Biochem Biophys Res Commun 2019; 510:358-363. [DOI: 10.1016/j.bbrc.2019.01.085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/18/2019] [Indexed: 01/05/2023]
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6
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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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Seung D, Thalmann M, Sparla F, Abou Hachem M, Lee SK, Issakidis-Bourguet E, Svensson B, Zeeman SC, Santelia D. Arabidopsis thaliana AMY3 is a unique redox-regulated chloroplastic α-amylase. J Biol Chem 2013; 288:33620-33633. [PMID: 24089528 DOI: 10.1074/jbc.m113.514794] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
α-Amylases are glucan hydrolases that cleave α-1,4-glucosidic bonds in starch. In vascular plants, α-amylases can be classified into three subfamilies. Arabidopsis has one member of each subfamily. Among them, only AtAMY3 is localized in the chloroplast. We expressed and purified AtAMY3 from Escherichia coli and carried out a biochemical characterization of the protein to find factors that regulate its activity. Recombinant AtAMY3 was active toward both insoluble starch granules and soluble substrates, with a strong preference for β-limit dextrin over amylopectin. Activity was shown to be dependent on a conserved aspartic acid residue (Asp(666)), identified as the catalytic nucleophile in other plant α-amylases such as the barley AMY1. AtAMY3 released small linear and branched glucans from Arabidopsis starch granules, and the proportion of branched glucans increased after the predigestion of starch with a β-amylase. Optimal rates of starch digestion in vitro was achieved when both AtAMY3 and β-amylase activities were present, suggesting that the two enzymes work synergistically at the granule surface. We also found that AtAMY3 has unique properties among other characterized plant α-amylases, with a pH optimum of 7.5-8, appropriate for activity in the chloroplast stroma. AtAMY3 is also redox-regulated, and the inactive oxidized form of AtAMY3 could be reactivated by reduced thioredoxins. Site-directed mutagenesis combined with mass spectrometry analysis showed that a disulfide bridge between Cys(499) and Cys(587) is central to this regulation. This work provides new insights into how α-amylase activity may be regulated in the chloroplast.
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Affiliation(s)
- David Seung
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Matthias Thalmann
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Francesca Sparla
- Department of Experimental Evolutionary Biology, University of Bologna, I-40126 Bologna, Italy
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Sang Kyu Lee
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | | | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Samuel C Zeeman
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Diana Santelia
- Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland.
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8
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Biotransformation of indole by whole cells of recombinant biphenyl dioxygenase and biphenyl-2,3-dihydrodiol-2,3-dehydrogenase. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2012.12.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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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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10
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Mótyán JA, Fazekas E, Mori H, Svensson B, Bagossi P, Kandra L, Gyémánt G. Transglycosylation by barley α-amylase 1. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.06.010] [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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11
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Mohammadi M, Viger JF, Kumar P, Barriault D, Bolin JT, Sylvestre M. Retuning Rieske-type oxygenases to expand substrate range. J Biol Chem 2011; 286:27612-21. [PMID: 21653696 DOI: 10.1074/jbc.m111.255174] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. BphAE(p4), a variant biphenyl dioxygenase generated from Burkholderia xenovorans LB400 BphAE(LB400) by the double substitution T335A/F336M, and BphAE(RR41), obtained by changing Asn(338), Ile(341), and Leu(409) of BphAE(p4) to Gln(338), Val(341), and Phe(409), metabolize dibenzofuran two and three times faster than BphAE(LB400), respectively. Steady-state kinetic measurements of single- and multiple-substitution mutants of BphAE(LB400) showed that the single T335A and the double N338Q/L409F substitutions contribute significantly to enhanced catalytic activity toward dibenzofuran. Analysis of crystal structures showed that the T335A substitution relieves constraints on a segment lining the catalytic cavity, allowing a significant displacement in response to dibenzofuran binding. The combined N338Q/L409F substitutions alter substrate-induced conformational changes of protein groups involved in subunit assembly and in the chemical steps of the reaction. This suggests a responsive induced fit mechanism that retunes the alignment of protein atoms involved in the chemical steps of the reaction. These enzymes can thus expand their substrate range through mutations that alter the constraints or plasticity of the catalytic cavity to accommodate new substrates or that alter the induced fit mechanism required to achieve proper alignment of reaction-critical atoms or groups.
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Affiliation(s)
- Mahmood Mohammadi
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval, Quebec H7V 1B7, Canada
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12
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Computer-aided subsite mapping of α-amylases. Carbohydr Res 2011; 346:410-5. [DOI: 10.1016/j.carres.2010.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/30/2010] [Accepted: 12/03/2010] [Indexed: 11/19/2022]
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13
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Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution. J Mol Biol 2010; 405:531-47. [PMID: 21073881 DOI: 10.1016/j.jmb.2010.11.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 11/23/2022]
Abstract
The biphenyl dioxygenase of Burkholderia xenovorans LB400 is a multicomponent Rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (PCBs). The structural bases for the substrate specificity of the enzyme's oxygenase component (BphAE(LB400)) are largely unknown. BphAE(p4), a variant previously obtained through directed evolution, transforms several chlorobiphenyls, including 2,6-dichlorobiphenyl, more efficiently than BphAE(LB400), yet differs from the parent oxygenase at only two positions: T335A/F336M. Here, we compare the structures of BphAE(LB400) and BphAE(p4) and examine the biochemical properties of two BphAE(LB400) variants with single substitutions, T335A or F336M. Our data show that residue 336 contacts the biphenyl and influences the regiospecificity of the reaction, but does not enhance the enzyme's reactivity toward 2,6-dichlorobiphenyl. By contrast, residue 335 does not contact biphenyl but contributes significantly to expansion of the enzyme's substrate range. Crystal structures indicate that Thr335 imposes constraints through hydrogen bonds and nonbonded contacts to the segment from Val320 to Gln322. These contacts are lost when Thr is replaced by Ala, relieving intramolecular constraints and allowing for significant movement of this segment during binding of 2,6-dichlorobiphenyl, which increases the space available to accommodate the doubly ortho-chlorinated congener 2,6-dichlorobiphenyl. This study provides important insight about how Rieske-type oxygenases can expand substrate range through mutations that increase the plasticity and/or mobility of protein segments lining the catalytic cavity.
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Nomme J, Renodon-Cornière A, Asanomi Y, Sakaguchi K, Stasiak AZ, Stasiak A, Norden B, Tran V, Takahashi M. Design of potent inhibitors of human RAD51 recombinase based on BRC motifs of BRCA2 protein: modeling and experimental validation of a chimera peptide. J Med Chem 2010; 53:5782-91. [PMID: 20684611 PMCID: PMC2917172 DOI: 10.1021/jm1002974] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.
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Affiliation(s)
- Julian Nomme
- UMR 6204 U-3B, Centre National de la Recherche Scientifique & Universite de Nantes, France
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15
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Hekmat O, Lo Leggio L, Rosengren A, Kamarauskaite J, Kolenova K, Stålbrand H. Rational Engineering of Mannosyl Binding in the Distal Glycone Subsites of Cellulomonas fimi Endo-β-1,4-mannanase: Mannosyl Binding Promoted at Subsite −2 and Demoted at Subsite −3,. Biochemistry 2010; 49:4884-96. [DOI: 10.1021/bi100097f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Omid Hekmat
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Leila Lo Leggio
- Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Anna Rosengren
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Jurate Kamarauskaite
- Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Katarina Kolenova
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Henrik Stålbrand
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
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16
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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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17
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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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Hachem MA, Bozonnet S, Willemoës M, Kramhøft B, Fukuda K, Bønsager BC, Jensen MT, Nøhr J, Tranier S, Juge N, Robert X, Haser R, Aghajari N, Svensson B. Interactions of barley α-amylase isozymes with Ca2 + , substrates and proteinaceous inhibitors. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500516163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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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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20
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Nielsen MM, Seo ES, Bozonnet S, Aghajari N, Robert X, Haser R, Svensson B. Multi-site substrate binding and interplay in barley α-amylase 1. FEBS Lett 2008; 582:2567-71. [DOI: 10.1016/j.febslet.2008.06.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 06/14/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
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21
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Bozonnet S, Jensen MT, Nielsen MM, Aghajari N, Jensen MH, Kramhøft B, Willemoës M, Tranier S, Haser R, Svensson B. The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity. FEBS J 2007; 274:5055-67. [PMID: 17803687 DOI: 10.1111/j.1742-4658.2007.06024.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some starch-degrading enzymes accommodate carbohydrates at sites situated at a certain distance from the active site. In the crystal structure of barley alpha-amylase 1, oligosaccharide is thus bound to the 'sugar tongs' site. This site on the non-catalytic domain C in the C-terminal part of the molecule contains a key residue, Tyr380, which has numerous contacts with the oligosaccharide. The mutant enzymes Y380A and Y380M failed to bind to beta-cyclodextrin-Sepharose, a starch-mimic resin used for alpha-amylase affinity purification. The K(d) for beta-cyclodextrin binding to Y380A and Y380M was 1.4 mm compared to 0.20-0.25 mm for the wild-type, S378P and S378T enzymes. The substitution in the S378P enzyme mimics Pro376 in the barley alpha-amylase 2 isozyme, which in spite of its conserved Tyr378 did not bind oligosaccharide at the 'sugar tongs' in the structure. Crystal structures of both wild-type and S378P enzymes, but not the Y380A enzyme, showed binding of the pseudotetrasaccharide acarbose at the 'sugar tongs' site. The 'sugar tongs' site also contributed importantly to the adsorption to starch granules, as Kd = 0.47 mg.mL(-1) for the wild-type enzyme increased to 5.9 mg.mL(-1) for Y380A, which moreover catalyzed the release of soluble oligosaccharides from starch granules with only 10% of the wild-type activity. beta-cyclodextrin both inhibited binding to and suppressed activity on starch granules for wild-type and S378P enzymes, but did not affect these properties of Y380A, reflecting the functional role of Tyr380. In addition, the Y380A enzyme hydrolyzed amylose with reduced multiple attack, emphasizing that the 'sugar tongs' participates in multivalent binding of polysaccharide substrates.
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Affiliation(s)
- Sophie Bozonnet
- Enzyme and Protein Chemistry, BioCentrum-DTU, Technical University of Denmark
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22
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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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23
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Suenaga H, Goto M, Furukawa K. Active-site engineering of biphenyl dioxygenase: effect of substituted amino acids on substrate specificity and regiospecificity. Appl Microbiol Biotechnol 2006; 71:168-76. [PMID: 16217654 DOI: 10.1007/s00253-005-0135-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 07/19/2005] [Accepted: 08/08/2005] [Indexed: 10/25/2022]
Abstract
Biphenyl dioxygenase (Bph Dox) catalyzes the initial dioxygenation step in the metabolism of biphenyl. The large subunit (BphA1) of Bph Dox plays a crucial role in the determination of the substrate specificity of biphenyl-related compounds including polychlorinated biphenyls (PCBs). Previously, the substitution of Asn at Thr-376 near the active-site iron in the BphA1 of Pseudomonas pseudoalcaligenes KF707 expanded the oxidation range and altered the regiospecificity of Bph Dox for PCBs. In this study, we replaced Thr-376 with Gly, Ser, Gln, Tyr, Val, Phe, Asp, and Lys and expressed these enzymes in Escherichia coli. Bph Dox mutants of Thr376Asn, Thr376Val, Thr376Phe, and Thr376Lys showed novel degradation activity for dibenzofuran, which is a poor substrate for KF707 Bph Dox. All active Bph Dox mutants showed altered regiospecificity with 2,2'-dichlorobiphenyl and 2,5,4'-trichlorobiphenyl. The Thr376Gly, Thr376Val, Thr376Phe, and Thr376Asp Bph Dox mutants introduced molecular oxygen at the 2,3 position of 2,2'-dichlorobiphenyl, forming 2-chloro-2',3'-dihydroxybiphenyl with concomitant dechlorination. The Bph Dox mutants of Thr376Gly, Thr376Ser, Thr376Asp, and Thr376Lys attacked 2,5,4'-trichlorobiphenyl via both 2',3'- and 3,4-dioxygenation activities. In particular, the Thr376Phe Bph Dox mutant exhibited enhanced and expanded degradation activities toward all of the compounds tested. Further site-directed mutation was induced to change the oxidizing character of KF707 Bph Dox to that of the Bph Dox of Burkholderia xenovorans LB400 by the substitution of two amino acids, Ile335Phe and Thr376Asn, near the active-site.
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Affiliation(s)
- Hikaru Suenaga
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
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24
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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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25
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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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26
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Alonso H, Gillies MB, Cummins PL, Bliznyuk AA, Gready JE. Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase. J Comput Aided Mol Des 2005; 19:165-87. [PMID: 16059670 DOI: 10.1007/s10822-005-3693-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Accepted: 03/11/2005] [Indexed: 11/25/2022]
Abstract
R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor structural homology with the chromosomal DHFR. It presents a highly symmetrical toroidal structure, where four identical monomers contribute to the unique central active-site pore. Two reactants (dihydrofolate, DHF), two cofactors (NADPH) or one of each (R67*DHF*NADPH) can be found simultaneously within the active site, the last one being the reactive ternary complex. As the positioning of the ligands has proven elusive to empirical determination, we addressed the problem from a theoretical perspective. Several potential structures of the ternary complex were generated using the docking programs AutoDock and FlexX. The variability among the final poses, many of which conformed to experimental data, prompted us to perform a comparative scoring analysis and molecular dynamics simulations to assess the stability of the complexes. Analysis of ligand-ligand and ligand-protein interactions along the 4 ns trajectories of eight different structures allowed us to identify important inter-ligand contacts and key protein residues. Our results, combined with published empirical data, clearly suggest that multipe binding modes of the ligands are possible within R67 DHFR. While the pterin ring of DHF and the nicotinamide ring of NADPH assume a stacked endo-conformation at the centre of the pore, probably assisted by V66, Q67 and I68, the tails of the molecules extend towards opposite ends of the cavity, adopting multiple configurations in a solvent rich-environment where hydrogen-bond interactions with K32 and Y69 may play important roles.
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Affiliation(s)
- Hernán Alonso
- Computational Proteomics Group, John Curtin School of Medical Research, The Australian National University, P.O. Box 334, 2601, Canberra, ACT, Australia
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Damager I, Jensen MT, Olsen CE, Blennow A, Møller BL, Svensson B, Motawia MS. Chemical synthesis of a dual branched malto-decaose: a potential substrate for alpha-amylases. Chembiochem 2005; 6:1224-33. [PMID: 15981193 DOI: 10.1002/cbic.200400449] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A convergent block strategy for general use in efficient synthesis of complex alpha-(1-->4)- and alpha-(1-->6)-malto-oligosaccharides is demonstrated with the first chemical synthesis of a malto-oligosaccharide, the decasaccharide 6,6''''-bis(alpha-maltosyl)-maltohexaose, with two branch points. Using this chemically defined branched oligosaccharide as a substrate, the cleavage pattern of seven different alpha-amylases were investigated. Alpha-amylases from human saliva, porcine pancreas, barley alpha-amylase 2 and recombinant barley alpha-amylase 1 all hydrolysed the decasaccharide selectively. This resulted in a branched hexasaccharide and a branched tetrasaccharide. Alpha-amylases from Asperagillus oryzae, Bacillus licheniformis and Bacillus sp. cleaved the decasaccharide at two distinct sites, either producing two branched pentasaccharides, or a branched hexasaccharide and a branched tetrasaccharide. In addition, the enzymes were tested on the single-branched octasaccharide 6-alpha-maltosyl-maltohexaose, which was prepared from 6,6''''-bis(alpha-maltosyl)-maltohexaose by treatment with malt limit dextrinase. A similar cleavage pattern to that found for the corresponding linear malto-oligosaccharide substrate was observed.
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Affiliation(s)
- Iben Damager
- The Carbohydrate Chemistry Group, Plant Biochemistry Laboratory, Department of Plant Biology and Center for Molecular Plant Physiology, The Royal Veterinary and Agricultural University, 1871 Frederiksberg C, Copenhagen, Denmark
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28
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Fukuda K, Jensen MH, Haser R, Aghajari N, Svensson B. Biased mutagenesis in the N-terminal region by degenerate oligonucleotide gene shuffling enhances secretory expression of barley alpha-amylase 2 in yeast. Protein Eng Des Sel 2005; 18:515-26. [PMID: 16155115 DOI: 10.1093/protein/gzi057] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombinant barley alpha-amylase 1 (rAMY1) and 2 (rAMY2), despite 80% sequence identity, are produced in very different amounts of 1.1 and <0.05 mg/l, respectively, by Saccharomyces cerevisiae strain S150-2B. The low yield of AMY2 practically excludes mutational analysis of structure-function relationships and protein engineering. Since different secretion levels of AMY1/AMY2 chimeras were previously ascribed to the N-terminal sequence, AMY1 residues were combinatorially introduced at the 10 non-conserved positions in His14-Gln49 of AMY2 using degenerate oligonucleotide gene shuffling (DOGS) coupled with homologous recombination in S.cerevisiae strain INVSc1. Activity screening of a partial library of 843 clones selected six having a large halo size on starch plates. Three mutants, F21M/Q44H, A42P/A47S and A42P rAMY2, also gave higher activity than wild-type in liquid culture. Only A42P showed wild-type stability and enzymatic properties. The replacement is located to a beta-->alpha loop 2 that interacts with domain B (beta-->alpha loop 3) protruding from the catalytic (beta/alpha)(8)-barrel. Most remarkably Pichia pastoris strain GS115 secreted 60 mg/l A42P compared with 3 mg/l of wild-type rAMY2. The crystal structure of A42P rAMY2 was solved and found to differ marginally from the AMY2 structure, suggesting that the high A42P yield stems from stabilization of the mature and/or intermediate form owing to the introduced proline residue. Moreover, the G to C substitution for the A42P mutation might have a positive impact on protein translation.
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Affiliation(s)
- Kenji Fukuda
- Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
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29
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Feng HY, Drone J, Hoffmann L, Tran V, Tellier C, Rabiller C, Dion M. Converting a {beta}-glycosidase into a {beta}-transglycosidase by directed evolution. J Biol Chem 2005; 280:37088-97. [PMID: 16085651 DOI: 10.1074/jbc.m502873200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Directed evolution was applied to the beta-glycosidase of Thermus thermophilus in order to increase its ability to synthesize oligosaccharide by transglycosylation. Wild-type enzyme was able to transfer the glycosyl residue with a yield of 50% by self-condensation and of about 8% by transglycosylation on disaccharides without nitrophenyl at their reducing end. By using a simple screening procedure, we could produce mutant enzymes possessing a high transferase activity. In one step of random mutagenesis and in vitro recombination, the hydrolysis of substrates and of transglycosylation products was considerably reduced. For certain mutants, synthesis by self-condensation of nitrophenyl glycosides became nearly quantitative, whereas synthesis by transglycosylation on maltose and on cellobiose could reach 60 and 75%, respectively. Because the most efficient mutations, F401S and N282T, were located just in front of the subsite (-1), molecular modeling techniques were used to explain their effects on the synthesis reaction; we can suggest that repositioning of the glycone in the (-1) subsite together with a better fit of the acceptor in the (+1) subsite might favor the attack of a glycosyl acceptor in the mutant at the expense of water. Thus these new transglycosidases constitute an interesting alternative for the synthesis of oligosaccharides by using stable and accessible donor substrates.
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Affiliation(s)
- Hui-Yong Feng
- Biotechnologie, Biocatalyse, Biorégulation (UMR CNRS 6204), Université de Nantes Faculté des Sciences et des Techniques, 2 Rue de la Houssinière, BP 92208, F-44322, Nantes Cedex 3, France
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30
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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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