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Kuchtová A, Janeček Š. Domain evolution in enzymes of the neopullulanase subfamily. Microbiology (Reading) 2016; 162:2099-2115. [DOI: 10.1099/mic.0.000390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrea Kuchtová
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
| | - Štefan Janeček
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
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52
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Møller MS, Henriksen A, Svensson B. Structure and function of α-glucan debranching enzymes. Cell Mol Life Sci 2016; 73:2619-41. [PMID: 27137180 PMCID: PMC11108273 DOI: 10.1007/s00018-016-2241-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 10/21/2022]
Abstract
α-Glucan debranching enzymes hydrolyse α-1,6-linkages in starch/glycogen, thereby, playing a central role in energy metabolism in all living organisms. They belong to glycoside hydrolase families GH13 and GH57 and several of these enzymes are industrially important. Nine GH13 subfamilies include α-glucan debranching enzymes; isoamylase and glycogen debranching enzymes (GH13_11); pullulanase type I/limit dextrinase (GH13_12-14); pullulan hydrolase (GH13_20); bifunctional glycogen debranching enzyme (GH13_25); oligo-1 and glucan-1,6-α-glucosidases (GH13_31); pullulanase type II (GH13_39); and α-amylase domains (GH13_41) in two-domain amylase-pullulanases. GH57 harbours type II pullulanases. Specificity differences, domain organisation, carbohydrate binding modules, sequence motifs, three-dimensional structures and specificity determinants are discussed. The phylogenetic analysis indicated that GH13_39 enzymes could represent a "missing link" between the strictly α-1,6-specific debranching enzymes and the enzymes with dual specificity and α-1,4-linkage preference.
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Affiliation(s)
- Marie Sofie Møller
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00, Lund, Sweden.
| | - Anette Henriksen
- Global Research Unit, Department of Large Protein Biophysics and Formulation, Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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53
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Janeček Š, Gabriško M. Remarkable evolutionary relatedness among the enzymes and proteins from the α-amylase family. Cell Mol Life Sci 2016; 73:2707-25. [PMID: 27154042 PMCID: PMC11108405 DOI: 10.1007/s00018-016-2246-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022]
Abstract
The α-amylase is a ubiquitous starch hydrolase catalyzing the cleavage of the α-1,4-glucosidic bonds in an endo-fashion. Various α-amylases originating from different taxonomic sources may differ from each other significantly in their exact substrate preference and product profile. Moreover, it also seems to be clear that at least two different amino acid sequences utilizing two different catalytic machineries have evolved to execute the same α-amylolytic specificity. The two have been classified in the Cabohydrate-Active enZyme database, the CAZy, in the glycoside hydrolase (GH) families GH13 and GH57. While the former and the larger α-amylase family GH13 evidently forms the clan GH-H with the families GH70 and GH77, the latter and the smaller α-amylase family GH57 has only been predicted to maybe define a future clan with the family GH119. Sequences and several tens of enzyme specificities found throughout all three kingdoms in many taxa provide an interesting material for evolutionarily oriented studies that have demonstrated remarkable observations. This review emphasizes just the three of them: (1) a close relatedness between the plant and archaeal α-amylases from the family GH13; (2) a common ancestry in the family GH13 of animal heavy chains of heteromeric amino acid transporter rBAT and 4F2 with the microbial α-glucosidases; and (3) the unique sequence features in the primary structures of amylomaltases from the genus Borrelia from the family GH77. Although the three examples cannot represent an exhaustive list of exceptional topics worth to be interested in, they may demonstrate the importance these enzymes possess in the overall scientific context.
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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.
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius in Trnava, Nám. J. Herdu 2, 91701, Trnava, Slovakia.
| | - Marek Gabriško
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia
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54
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Martínez MM, Pico J, Gómez M. Synergistic maltogenic α-amylase and branching treatment to produce enzyme-resistant molecular and supramolecular structures in extruded maize matrices. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2016.02.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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55
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Cyclodextrin Glycosyl Transferase (CGTase): An Overview of Their Production and Biotechnological Applications. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1201/b19347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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56
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Nisha M, Satyanarayana T. Characteristics, protein engineering and applications of microbial thermostable pullulanases and pullulan hydrolases. Appl Microbiol Biotechnol 2016; 100:5661-79. [DOI: 10.1007/s00253-016-7572-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/17/2022]
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57
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Jeon HY, Kim NR, Lee HW, Choi HJ, Choung WJ, Koo YS, Ko DS, Shim JH. Characterization of a Novel Maltose-Forming α-Amylase from Lactobacillus plantarum subsp. plantarum ST-III. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:2307-2314. [PMID: 26919577 DOI: 10.1021/acs.jafc.5b05892] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A novel maltose (G2)-forming α-amylase from Lactobacillus plantarum subsp. plantarum ST-III was expressed in Escherichia coli and characterized. Analysis of conserved amino acid sequence alignments showed that L. plantarum maltose-producing α-amylase (LpMA) belongs to glycoside hydrolase family 13. The recombinant enzyme (LpMA) was a novel G2-producing α-amylase. The properties of purified LpMA were investigated following enzyme purification. LpMA exhibited optimal activity at 30 °C and pH 3.0. It produced only G2 from the hydrolysis of various substrates, including maltotriose (G3), maltopentaose (G5), maltosyl β-cyclodextrin (G2-β-CD), amylose, amylopectin, and starch. However, LpMA was unable to hydrolyze cyclodextrins. Reaction pattern analysis using 4-nitrophenyl-α-d-maltopentaoside (pNPG5) demonstrated that LpMA hydrolyzed pNPG5 from the nonreducing end, indicating that LpMA is an exotype α-amylase. Kinetic analysis revealed that LpMA had the highest catalytic efficiency (kcat/Km ratio) toward G2-β-CD. Compared with β-amylase, a well-known G2-producing enzyme, LpMA produced G2 more efficiently from liquefied corn starch due to its ability to hydrolyze G3.
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Affiliation(s)
- Hye-Yeon Jeon
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
| | - Na-Ri Kim
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
| | - Hye-Won Lee
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
| | - Hye-Jeong Choi
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
| | - Woo-Jae Choung
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
| | - Ye-Seul Koo
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
| | - Dam-Seul Ko
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
| | - Jae-Hoon Shim
- Department of Food Science and Nutrition, and Center for Aging and Health Care, Hallym University , Hallymdaehak-gil 1, Chuncheon, Gwangwon-do 200-702, Korea
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58
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Vieira ACF, Serra AC, Veiga FJ, Gonsalves AMDR, Basit AW, Murdan S. Diclofenac-β-cyclodextrin for colonic drug targeting: In vivo performance in rats. Int J Pharm 2016; 500:366-70. [PMID: 26784980 DOI: 10.1016/j.ijpharm.2016.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 12/17/2022]
Abstract
The aim of this in vivo study was to assess the ability of the prodrug conjugate diclofenac-β-cyclodextrin to release diclofenac in the colon following oral administration, using sulfapyridine (a metabolite of sulfasalazine) as a marker of colonic absorption. Two groups of rats were used; the test rats received a suspension containing the two prodrugs, diclofenac-β-cyclodextrin and sulfasalazine, while the control rats received a suspension containing the corresponding free drugs, sodium diclofenac and sulfapyridine. The rats were fasted overnight with free access to water before and throughout the first 12h of the study. Blood was collected from the tail vein at pre-determined time points and the plasma analyzed for the concentrations of diclofenac and sulfapyridine. Following the oral administration of the two prodrugs, a more extended absorption profile was observed and Cmax was achieved 10h post-dose, in contrast to rapid absorption of the free drugs (tmax of diclofenac being 1.3h, and that of sulfapyridine being 2.1h). In addition to a later tmax, conjugation of diclofenac to β-cyclodextrin also resulted in a reduced Cmax and a reduced AUC. The same tmax for diclofenac-β-cyclodextrin as for sulfasalazine confirms the colonic metabolism of diclofenac-β-cyclodextrin. This study shows the potential of this new cyclodextrin-based prodrug to target and release diclofenac specifically in the colon following oral administration.
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Affiliation(s)
- Amélia C F Vieira
- Department of Pharmaceutics, UCL School of Pharmacy, London, United Kingdom; Centre for Pharmaceutical Studies, Laboratory of Pharmaceutical Science, Faculty of Pharmacy, University of Coimbra, Portugal; Chymiotechnon and Department of Chemistry, Faculty of Science and Technology, University of Coimbra, Portugal
| | - Arménio C Serra
- Chymiotechnon and Department of Chemistry, Faculty of Science and Technology, University of Coimbra, Portugal
| | - Francisco J Veiga
- Centre for Pharmaceutical Studies, Laboratory of Pharmaceutical Science, Faculty of Pharmacy, University of Coimbra, Portugal
| | | | - Abdul W Basit
- Department of Pharmaceutics, UCL School of Pharmacy, London, United Kingdom
| | - Sudaxshina Murdan
- Department of Pharmaceutics, UCL School of Pharmacy, London, United Kingdom.
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Ahmad N, Mehboob S, Rashid N. Starch-processing enzymes — emphasis on thermostable 4-α-glucanotransferases. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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60
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Sequence, Structure, and Binding Analysis of Cyclodextrinase (TK1770) from T. kodakarensis (KOD1) Using an In Silico Approach. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:179196. [PMID: 26819569 PMCID: PMC4706853 DOI: 10.1155/2015/179196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/12/2015] [Accepted: 11/01/2015] [Indexed: 01/04/2023]
Abstract
Thermostable cyclodextrinase (Tk1770 CDase) from hyperthermophilic archaeon Thermococcus kodakarensis (KOD1) hydrolyzes cyclodextrins into linear dextrins. The sequence of Tk1770 CDase retrieved from UniProt was aligned with sequences of sixteen CD hydrolyzing enzymes and a phylogenetic tree was constructed using Bayesian inference. The homology model of Tk1770 CDase was constructed and optimized with Modeller v9.14 program. The model was validated with ProSA server and PROCHECK analysis. Four conserved regions and the catalytic triad consisting of Asp411, Glu437, and Asp502 of GH13 family were identified in catalytic site. Also an additional fifth conserved region downstream to the fourth region was also identified. The structure of Tk1770 CDase consists of an additional N'-domain and a helix-loop-helix motif that is conserved in all archaeal CD hydrolyzing enzymes. The N'-domain contains an extended loop region that forms a part of catalytic domain and plays an important role in stability and substrate binding. The docking of substrate into catalytic site revealed the interactions with different conserved residues involved in substrate binding and formation of enzyme-substrate complex.
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61
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Rat skeletal muscle glycogen degradation pathways reveal differential association of glycogen-related proteins with glycogen granules. J Physiol Biochem 2015; 71:267-80. [PMID: 25875859 DOI: 10.1007/s13105-015-0407-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
Abstract
Glycogenin, glycogen-debranching enzyme (GDE) and glycogen phosphorylase (GP) are important enzymes that contribute to glycogen particle metabolism. In Long-Evans Hooded rat whole muscle homogenates prepared from extensor digitorum longus (EDL, fast-twitch) and soleus (SOL, oxidative, predominantly slow twitch), it was necessary to include α-amylase, which releases glucosyl units from glycogen, to detect glycogenin but not GDE or GP. Up to ∼12 % of intramuscular glycogen pool was broken down using either in vitro electrical stimulation or leaving muscle at room temperature >3 h (delayed, post-mortem). Electrical stimulation did not reveal glycogenin unless α-amylase was added, although in post-mortem muscle ∼50 and ∼30 % of glycogenin in EDL and SOL muscles, respectively, was detected compared to the amount detected with α-amylase treatment. Single muscle fibres were dissected from fresh or post-mortem EDL muscles, mechanically skinned to remove surface membrane and the presence of glycogenin, GDE and GP as freely diffusible proteins (i.e. cytoplasmic localization) compared by Western blotting. Diffusibility of glycogenin (∼20 %) and GP (∼60 %) was not different between muscles, although GDE increased from ∼15 % diffusible in fresh muscle to ∼60 % in post-mortem muscle. Under physiologically relevant circumstances, in rat muscle and within detection limits: (1) The total cellular pool of glycogenin is always associated with glycogen granules, (2) GDE is associated with glycogen granules with over half the total pool associated with the outer tiers of glycogen, (3) GP is only ever weakly associated with glycogen granules and (4) addition of α-amylase is necessary in order to detect glycogenin, but not GDE or GP.
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62
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Recombinant cyclodextrinase from Thermococcus kodakarensis KOD1: expression, purification, and enzymatic characterization. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:397924. [PMID: 25688178 PMCID: PMC4321091 DOI: 10.1155/2015/397924] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/15/2014] [Accepted: 01/07/2015] [Indexed: 11/18/2022]
Abstract
A gene encoding a cyclodextrinase from Thermococcus kodakarensis KOD1 (CDase-Tk) was identified and characterized. The gene encodes a protein of 656 amino acid residues with a molecular mass of 76.4 kDa harboring four conserved regions found in all members of the α-amylase family. A recombinant form of the enzyme was purified by ion-exchange chromatography, and its catalytic properties were examined. The enzyme was active in a broad range of pH conditions (pHs 4.0–10.0), with an optimal pH of 7.5 and a temperature optimum of 65°C. The purified enzyme preferred to hydrolyze β-cyclodextrin (CD) but not α- or γ-CD, soluble starch, or pullulan. The final product from β-CD was glucose. The Vmax and Km values were 3.13 ± 0.47 U mg−1 and 2.94 ± 0.16 mg mL−1 for β-CD. The unique characteristics of CDase-Tk with a low catalytic temperature and substrate specificity are discussed, and the starch utilization pathway in a broad range of temperatures is also proposed.
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63
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Abdul Manas NH, Pachelles S, Mahadi NM, Illias RM. The characterisation of an alkali-stable maltogenic amylase from Bacillus lehensis G1 and improved malto-oligosaccharide production by hydrolysis suppression. PLoS One 2014; 9:e106481. [PMID: 25221964 PMCID: PMC4164441 DOI: 10.1371/journal.pone.0106481] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/06/2014] [Indexed: 01/31/2023] Open
Abstract
A maltogenic amylase (MAG1) from alkaliphilic Bacillus lehensis G1 was cloned, expressed in Escherichia coli, purified and characterised for its hydrolysis and transglycosylation properties. The enzyme exhibited high stability at pH values from 7.0 to 10.0. The hydrolysis of β-cyclodextrin (β-CD) produced malto-oligosaccharides of various lengths. In addition to hydrolysis, MAG1 also demonstrated transglycosylation activity for the synthesis of longer malto-oligosaccharides. The thermodynamic equilibrium of the multiple reactions was shifted towards synthesis when the reaction conditions were optimised and the water activity was suppressed, which resulted in a yield of 38% transglycosylation products consisting of malto-oligosaccharides of various lengths. Thin layer chromatography and high-performance liquid chromatography analyses revealed the presence of malto-oligosaccharides with a higher degree of polymerisation than maltoheptaose, which has never been reported for other maltogenic amylases. The addition of organic solvents into the reaction further suppressed the water activity. The increase in the transglycosylation-to-hydrolysis ratio from 1.29 to 2.15 and the increased specificity toward maltopentaose production demonstrated the enhanced synthetic property of the enzyme. The high transglycosylation activity of maltogenic amylase offers a great advantage for synthesising malto-oligosaccharides and rare carbohydrates.
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Affiliation(s)
- Nor Hasmaliana Abdul Manas
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Samson Pachelles
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Nor Muhammad Mahadi
- Comparative Genomics and Genetics Research Centre, Malaysia Genome Institute, Kajang, Selangor, Malaysia
| | - Rosli Md. Illias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
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64
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Noor YM, Samsulrizal NH, Jema'on NA, Low KO, Ramli ANM, Alias NI, Damis SIR, Fuzi SFZM, Isa MNM, Murad AMA, Raih MFM, Bakar FDA, Najimudin N, Mahadi NM, Illias RM. A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1. Gene 2014; 545:253-61. [PMID: 24811681 DOI: 10.1016/j.gene.2014.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 04/27/2014] [Accepted: 05/03/2014] [Indexed: 10/25/2022]
Abstract
Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99 Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium-proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes.
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Affiliation(s)
- Yusuf Muhammad Noor
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nurul Hidayah Samsulrizal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Noor Azah Jema'on
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Kheng Oon Low
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Aizi Nor Mazila Ramli
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Noor Izawati Alias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Siti Intan Rosdianah Damis
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Siti Fatimah Zaharah Mohd Fuzi
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Mohd Firdaus Mohd Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rosli Md Illias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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65
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Ghollasi M, Ghanbari-Safari M, Khajeh K. Improvement of thermal stability of a mutagenised α-amylase by manipulation of the calcium-binding site. Enzyme Microb Technol 2013; 53:406-13. [DOI: 10.1016/j.enzmictec.2013.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 10/26/2022]
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66
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Protein adaptations in archaeal extremophiles. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:373275. [PMID: 24151449 PMCID: PMC3787623 DOI: 10.1155/2013/373275] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/26/2013] [Accepted: 08/14/2013] [Indexed: 12/25/2022]
Abstract
Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.
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67
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Ben Mabrouk S, Ayadi-Zouari D, Ben Hlima H, Bejar S. Changes in the catalytic properties and substrate specificity of Bacillus sp. US149 maltogenic amylase by mutagenesis of residue 46. ACTA ACUST UNITED AC 2013; 40:947-53. [DOI: 10.1007/s10295-013-1300-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/29/2013] [Indexed: 11/30/2022]
Abstract
Abstract
Maltogenic amylase from Bacillus sp. US149 (MAUS149) is a cyclodextrin (CD)-degrading enzyme with a high preference for CDs over maltooligosaccharides. In this study, we investigated the roles of residue Asp46 in the specificity and catalytic properties of MAUS149 by using site-directed mutagenesis. Three mutated enzymes (D46V, D46G and D46N) were constructed and studied. The three mutants were found to be similar to the wild-type MAUS149 regarding thermoactivity, thermostability and pH profile. Nevertheless, the kinetic parameters for all the substrates of the mutant enzymes D46V and D46G were altered enormously as compared with those of the wild type. Indeed, the K m values of MAUS149/D46G for all substrates were strongly increased. Nevertheless, the affinity and catalytic efficiency of MAUS149/D46V toward β-CD were increased fivefold as compared with those of MAUS149. Molecular modelling suggests that residue D46 forms a salt bridge with residue K282. This bond would maintain the arrangement of side chains of residues Y45 and W47 in a particular orientation that promotes access to the catalytic site and maintains the substrate therein. Hence, any replacement with uncharged amino acids influenced the flexibility of the gate wall at the substrate binding cleft resulting in changes in substrate selectivity.
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Affiliation(s)
- Sameh Ben Mabrouk
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
| | - Dorra Ayadi-Zouari
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
| | - Hajer Ben Hlima
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
| | - Samir Bejar
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
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Nasrollahi S, Golalizadeh L, Sajedi RH, Taghdir M, Asghari SM, Rassa M. Substrate preference of a Geobacillus maltogenic amylase: A kinetic and thermodynamic analysis. Int J Biol Macromol 2013; 60:1-9. [DOI: 10.1016/j.ijbiomac.2013.04.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
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69
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Trp358 is a key residue for the multiple catalytic activities of multifunctional amylase OPMA-N from Bacillus sp. ZW2531-1. Appl Microbiol Biotechnol 2013; 98:2101-11. [DOI: 10.1007/s00253-013-5085-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 06/22/2013] [Accepted: 06/25/2013] [Indexed: 11/29/2022]
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70
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A Novel Multifunctional α-Amylase from the Thermophilic Fungus Malbranchea cinnamomea: Biochemical Characterization and Three-Dimensional Structure. Appl Biochem Biotechnol 2013; 170:420-35. [DOI: 10.1007/s12010-013-0198-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 03/12/2013] [Indexed: 10/27/2022]
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71
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Jun SY, Kim JS, Choi KH, Cha J, Ha NC. Structure of a novel α-amylase AmyB fromThermotoga neapolitanathat produces maltose from the nonreducing end of polysaccharides. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:442-50. [DOI: 10.1107/s0907444912049219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/30/2012] [Indexed: 11/11/2022]
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72
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Vieira ACF, Serra AC, Carvalho RA, Gonsalves A, Figueiras A, Veiga FJ, Basit AW, Rocha Gonsalves AMD. Microwave synthesis and in vitro stability of diclofenac-β-cyclodextrin conjugate for colon delivery. Carbohydr Polym 2013; 93:512-7. [PMID: 23499091 DOI: 10.1016/j.carbpol.2012.12.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/23/2012] [Accepted: 12/13/2012] [Indexed: 11/19/2022]
Abstract
The aim of this work was to synthesize an ester prodrug of diclofenac and β-cyclodextrin suitable for colonic delivery. The synthesis of an ester linkage between diclofenac and β-cyclodextrin was conducted by the nucleophilic substitution of mono-6-tosyl-β-cyclodextrin under microwaves irradiation. After purification, the conjugate was characterized by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry; infrared (IR) spectroscopy; proton nuclear magnetic resonance ((1)H NMR) spectroscopy; and two-dimensional rotating frame nuclear overhauser effect (ROESY) spectroscopy. The purity was qualified by high pressure liquid chromatography (HPLC). To assess its potential for colonic delivery, the conjugate was evaluated for stability in simulated gastric and small intestinal fluids, and in fecal material from humans processed within a slurry under anaerobic conditions. The conjugate was successfully synthesized with a yield of 20% following purification. The mass spectra showed the parent peak m/z 1434 corresponding to [conjugate+Na] adduct. IR and NMR results confirmed that the carboxyl group of diclofenac is covalently bound to one of the hydroxyl groups of cyclodextrin by an ester linkage. Moreover, ROESY data indicated that the formation of the conjugate is not accompanied by the inclusion of diclofenac within the cyclodextrin. The conjugate was otherwise stable in simulated gastric and small intestinal conditions, but was also readily hydrolyzed liberating diclofenac in less than 2h within the human fecal slurry. This confirmed the potential for this new prodrug as a carrier for colonic delivery.
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Affiliation(s)
- Amélia C F Vieira
- Centre for Pharmaceutical Studies, Laboratory of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Portugal
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73
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Park JT, Song HN, Jung TY, Lee MH, Park SG, Woo EJ, Park KH. A novel domain arrangement in a monomeric cyclodextrin-hydrolyzing enzyme from the hyperthermophile Pyrococcus furiosus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:380-6. [DOI: 10.1016/j.bbapap.2012.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 10/28/2022]
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74
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Zelzer M, Todd SJ, Hirst AR, McDonald TO, Ulijn RV. Enzyme responsive materials: design strategies and future developments. Biomater Sci 2012; 1:11-39. [PMID: 32481995 DOI: 10.1039/c2bm00041e] [Citation(s) in RCA: 227] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enzyme responsive materials (ERMs) are a class of stimuli responsive materials with broad application potential in biological settings. This review highlights current and potential future design strategies for ERMs and provides an overview of the present state of the art in the area.
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Affiliation(s)
- Mischa Zelzer
- WestCHEM, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, U.K..
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75
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Jung TY, Li D, Park JT, Yoon SM, Tran PL, Oh BH, Janeček Š, Park SG, Woo EJ, Park KH. Association of novel domain in active site of archaic hyperthermophilic maltogenic amylase from Staphylothermus marinus. J Biol Chem 2012; 287:7979-89. [PMID: 22223643 DOI: 10.1074/jbc.m111.304774] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphylothermus marinus maltogenic amylase (SMMA) is a novel extreme thermophile maltogenic amylase with an optimal temperature of 100 °C, which hydrolyzes α-(1-4)-glycosyl linkages in cyclodextrins and in linear malto-oligosaccharides. This enzyme has a long N-terminal extension that is conserved among archaic hyperthermophilic amylases but is not found in other hydrolyzing enzymes from the glycoside hydrolase 13 family. The SMMA crystal structure revealed that the N-terminal extension forms an N' domain that is similar to carbohydrate-binding module 48, with the strand-loop-strand region forming a part of the substrate binding pocket with several aromatic residues, including Phe-95, Phe-96, and Tyr-99. A structural comparison with conventional cyclodextrin-hydrolyzing enzymes revealed a striking resemblance between the SMMA N' domain position and the dimeric N domain position in bacterial enzymes. This result suggests that extremophilic archaea that live at high temperatures may have adopted a novel domain arrangement that combines all of the substrate binding components within a monomeric subunit. The SMMA structure provides a molecular basis for the functional properties that are unique to hyperthermophile maltogenic amylases from archaea and that distinguish SMMA from moderate thermophilic or mesophilic bacterial enzymes.
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Affiliation(s)
- Tae-Yang Jung
- Department of Biological Sciences, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-701, Korea
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76
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Janeček Š, Svensson B, MacGregor EA. Structural and evolutionary aspects of two families of non-catalytic domains present in starch and glycogen binding proteins from microbes, plants and animals. Enzyme Microb Technol 2011; 49:429-40. [DOI: 10.1016/j.enzmictec.2011.07.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 07/04/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
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77
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Choi KH, Hwang S, Lee HS, Cha J. Identification of an extracellular thermostable glycosyl hydrolase family 13 α-amylase from Thermotoga neapolitana. J Microbiol 2011; 49:628-34. [PMID: 21887647 DOI: 10.1007/s12275-011-0432-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 03/09/2011] [Indexed: 10/17/2022]
Abstract
We cloned the gene for an extracellular α-amylase, AmyE, from the hyperthermophilic bacterium Thermotoga neapolitana and expressed it in Escherichia coli. The molecular mass of the enzyme was 92 kDa as a monomer. Maximum activity was observed at pH 6.5 and temperature 75°C and the enzyme was highly thermostable. AmyE hydrolyzed the typical substrates for α-amylase, including soluble starch, amylopectin, and maltooli-gosaccharides. The hydrolytic pattern of AmyE was similar to that of a typical α-amylase; however, unlike most of the calcium (Ca(2+))-dependent α-amylases, the activity of AmyE was unaffected by Ca(2+). The specific activities of AmyE towards various substrates indicated that the enzyme preferred maltooligosaccharides which have more than four glucose residues. AmyE could not hydrolyze maltose and maltotriose. When maltoheptaose was incubated with AmyE at the various time courses, the products consisting of maltose through maltopentaose was evenly formed indicating that the enzyme acts in an endo-fashion. The specific activity of AmyE (7.4 U/mg at 75° C, pH 6.5, with starch as the substrate) was extremely lower than that of other extracellular α-amylases, which indicates that AmyE may cooperate with other highly active extracellular α-amylases for the breakdown of the starch or α-glucans into maltose and maltotriose before transport into the cell in the members of Thermotoga sp.
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Affiliation(s)
- Kyoung-Hwa Choi
- Department of Microbiology, College of Natural Sciences, Busan 609-735, Republic of Korea
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78
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Lee JY, Jeong KW, Kim YM. Epigallocatechin 3-gallate Binds to Human Salivary α-Amylase with Complex Hydrogen Bonding Interactions. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.7.2222] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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79
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Li F, Zhu X, Li Y, Cao H, Zhang Y. Functional characterization of a special thermophilic multifunctional amylase OPMA-N and its N-terminal domain. Acta Biochim Biophys Sin (Shanghai) 2011; 43:324-34. [PMID: 21355000 DOI: 10.1093/abbs/gmr013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A gene encoding a special thermophilic multifunctional amylase OPMA-N was cloned from Bacillus sp. ZW2531-1. OPMA-N has an additional 124-residue N-terminal domain compared with typical amylases and forms a relatively independent domain with a β-pleated sheet and random coil structure. Here we reported an unusual substrate and product specificities of OPMA-N and the impact of the additional N-terminal domain (1-124 aa) on the function and properties of OPMA-N. Both OPMA-N (12.82 U/mg) and its N-terminal domain-truncated ΔOPMA-N (12.55 U/mg) only degraded starch to produce oligosaccharides including maltose, maltotriose, isomaltotriose, and isomaltotetraose, but not to produce glucose. Therefore, the N-terminal domain did not determine its substrate and product specificities that were probably regulated by its C-terminal β-pleated sheet structure. However, the N-terminal domain of OPMA-N seemed to modulate its catalytic feature, leading to the production of more isomaltotriose and less maltose, and it seemed to contribute to OPMA-N's thermostability since OPMA-N showed higher activity than ΔOPMA-N in a temperature range from 40 to 80°C and the half-life (t(1/2)) was 5 h for OPMA-N and 2 h for ΔOPMA-N at 60°C. Both OPMA-N and ΔOPMA-N were Ca(2+)-independent, but their activities could be influenced by Cu(2+), Ni(2+), Zn(2+), EDTA, SDS (1 mM), or Triton-X100 (1%). Kinetic analysis and starch-adsorption assay indicated that the N-terminal domain of OPMA-N could increase the OPMA-N-starch binding and subsequently increase the catalytic efficiency of OPMA-N for starch. In particular, the N-terminal domain of OPMA-N did not determine its oligomerization, because both OPMA-N and ΔOPMA-N could exist in the forms of monomer, homodimer, and homooligomer at the same time.
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Affiliation(s)
- Fan Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, Changchun, China
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80
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Ben Mabrouk S, Aghajari N, Ben Ali M, Ben Messaoud E, Juy M, Haser R, Bejar S. Enhancement of the thermostability of the maltogenic amylase MAUS149 by Gly312Ala and Lys436Arg substitutions. BIORESOURCE TECHNOLOGY 2011; 102:1740-1746. [PMID: 20855205 DOI: 10.1016/j.biortech.2010.08.082] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/23/2010] [Accepted: 08/23/2010] [Indexed: 05/29/2023]
Abstract
Based on sequence alignments and homology modeling, Gly 312 and Lys 436 of the maltogenic amylase from Bacillus sp. US149 (MAUS149) were selected as targets for site-directed mutagenesis to improve the thermostability of the enzyme. Variants of MAUS149 with amino acid substitutions G312A, K436R and G312A-K436R had substrate specificities, kinetic parameters and pH optima similar to those of the wild-type enzyme; however, the enzymes with substitutions K436R and G312A-K436R, had an optimal temperature of 45 °C instead of the 40 °C for the wild-type enzyme. The half-life time at 55 °C increased from 15 to 25 min for the double mutant. Molecular modeling suggests that the increase in thermostability was due to new hydrophobic interactions and the formation of a salt bridge and hydrogen bond in the G312A and K436R variants, respectively. The double mutant could be a potential candidate for application in the bread industry.
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Affiliation(s)
- Sameh Ben Mabrouk
- Laboratoire de Microorganismes et de Biomolécules, Centre de Biotechnologie de Sfax, BP 1177, Sfax 3018, Tunisia
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81
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Li D, Park JT, Li X, Kim S, Lee S, Shim JH, Park SH, Cha J, Lee BH, Kim JW, Park KH. Overexpression and characterization of an extremely thermostable maltogenic amylase, with an optimal temperature of 100 °C, from the hyperthermophilic archaeon Staphylothermus marinus. N Biotechnol 2010; 27:300-7. [DOI: 10.1016/j.nbt.2010.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Revised: 02/03/2010] [Accepted: 04/01/2010] [Indexed: 10/19/2022]
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82
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Leemhuis H, Dijkhuizen L. Engineering of Hydrolysis Reaction Specificity in the Transglycosylase Cyclodextrin Glycosyltransferase. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001614333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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83
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Bozonnet S, Kim TJ, Bønsager BC, Kramhøft B, Nielsen PK, Bak-Jensen KS, Svensson B. Engineering of Barley α-Amylase. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001618564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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84
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Veith B, Zverlov V, Lunina N, Berezina O, Raasch C, Velikodvorskaya G, Liebl W. Comparative Analysis of the Recombinant α-Glucosidases from theThermotoga neapolitanaandThermotoga maritimaMaltodextrin Utilization Gene Clusters. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001614324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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85
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Kolcuoğlu Y, Colak A, Faiz O, Belduz AO. Cloning, expression and characterization of highly thermo- and pH-stable maltogenic amylase from a thermophilic bacterium Geobacillus caldoxylosilyticus TK4. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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86
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Dumbrepatil AB, Choi JH, Park JT, Kim MJ, Kim TJ, Woo EJ, Park KH. Structural features of theNostoc punctiformedebranching enzyme reveal the basis of its mechanism and substrate specificity. Proteins 2010; 78:348-56. [DOI: 10.1002/prot.22548] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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87
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Nakagawa Y, Saburi W, Yamamoto T, Takada M, Ogawa K, Yamamoto M, Hatada Y, Nakamura N, Horikoshi K. Characterization of Two γ-Cyclodextrin-specific Enzymes from Bacillus clarkii 7364. J Appl Glycosci (1999) 2010. [DOI: 10.5458/jag.57.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
| | | | | | | | | | | | - Yuji Hatada
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Nobuyuki Nakamura
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Koki Horikoshi
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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88
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Park KM, Jun SY, Choi KH, Park KH, Park CS, Cha J. Characterization of an exo-acting intracellular alpha-amylase from the hyperthermophilic bacterium Thermotoga neapolitana. Appl Microbiol Biotechnol 2009; 86:555-66. [PMID: 19834705 DOI: 10.1007/s00253-009-2284-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 09/27/2009] [Accepted: 09/29/2009] [Indexed: 10/20/2022]
Abstract
We cloned and expressed the gene for an intracellular alpha-amylase, designated AmyB, from the hyperthermophilic bacterium Thermotoga neapolitana in Escherichia coli. The putative intracellular amylolytic enzyme contained four regions that are highly conserved among glycoside hydrolase family (GH) 13 alpha-amylases. AmyB exhibited maximum activity at pH 6.5 and 75 degrees C, and its thermostability was slightly enhanced by Ca2+. However, Ca2+ was not required for the activity of AmyB as EDTA had no effect on enzyme activity. AmyB hydrolyzed the typical substrates for alpha-amylase, including soluble starch, amylose, amylopectin, and glycogen, to liberate maltose and minor amount of glucose. The hydrolytic pattern of AmyB is most similar to those of maltogenic amylases (EC 3.2.1.133) among GH 13 alpha-amylases; however, it can be distinguished by its inability to hydrolyze pullulan and beta-cyclodextrin. AmyB enzymatic activity was negligible when acarbose, a maltotetraose analog in which a maltose residue at the nonreducing end was replaced by acarviosine, was present, indicating that AmyB cleaves maltose units from the nonreducing end of maltooligosaccharides. These results indicate that AmyB is a new type exo-acting intracellular alpha-amylase possessing distinct characteristics that distinguish it from typical alpha-amylase and cyclodextrin-/pullulan-hydrolyzing enzymes.
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Affiliation(s)
- Kyung-Min Park
- Department of Microbiology, College of Natural Sciences, Pusan National University, San 30, Jangjeon-dong, Geumjeong-gu, Busan, 609-735, Korea
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89
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Wang Y, Li F, Zhang Y. Preliminary investigation on the action modes of an oligosaccharide-producing multifunctional amylase. Appl Biochem Biotechnol 2009; 160:1955-66. [PMID: 19662349 DOI: 10.1007/s12010-009-8704-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Accepted: 06/28/2009] [Indexed: 11/27/2022]
Abstract
The action modes of an oligosaccharide-producing multifunctional amylase (OPMA) were investigated using glucose and some oligosaccharides as its substrates. OPMA did not cause the hydrolysis of maltose or isomaltose, but it catalyzed the alpha-1,6-transglycosylation of maltose to produce isomaltose or did the self-condensation of isomaltose to form isomaltotetraose and 4-O-alpha-isomaltosyl isomaltose. OPMA exhibited strong alpha-1,6-transglycosylation activity in addition to its alpha-1,4-hydrolytic activity on higher oligosaccharides substrates rather than bisaccharides. OPMA displayed high acceptor specificity in its transglycosylation or condensation reaction. OPMA seemed to only take glucose or isomaltose as the acceptor molecule in its transglycosylation or condensation reaction, which made glucose or isomaltose form higher products, and as a result, glucose or isomaltose were absent in the final products. In view of the simultaneously formation of several transglycosylation or condensation products, it was predicted that there might be separate donor and acceptor sites in OPMA's active center and the fact that the catalytically active form of this enzyme included its homodimer or homotrimer supported this prediction. Accordingly, a special pathway, isomaltose pathway, for OPMA catalysis was proposed to emphasize the central or important signification of isomaltose in OPMA catalysis.
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Affiliation(s)
- Yang Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130021, People's Republic of China
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90
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Cheong KA, Cheong KA, Tang SY, Cheong TK, Cha H, Kim JW, Park KH. Thermostable and alkalophilic maltogenic amylase ofBacillus thermoalkalophilusET2 in monomer-dimer equilibrium. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500090094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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91
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Role of maltogenic amylase and pullulanase in maltodextrin and glycogen metabolism of Bacillus subtilis 168. J Bacteriol 2009; 191:4835-44. [PMID: 19465663 DOI: 10.1128/jb.00176-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The physiological functions of two amylolytic enzymes, a maltogenic amylase (MAase) encoded by yvdF and a debranching enzyme (pullulanase) encoded by amyX, in the carbohydrate metabolism of Bacillus subtilis 168 were investigated using yvdF, amyX, and yvdF amyX mutant strains. An immunolocalization study revealed that YvdF was distributed on both sides of the cytoplasmic membrane and in the periplasm during vegetative growth but in the cytoplasm of prespores. Small carbohydrates such as maltoheptaose and beta-cyclodextrin (beta-CD) taken up by wild-type B. subtilis cells via two distinct transporters, the Mdx and Cyc ABC transporters, respectively, were hydrolyzed immediately to form smaller or linear maltodextrins. On the other hand, the yvdF mutant exhibited limited degradation of the substrates, indicating that, in the wild type, maltodextrins and beta-CD were hydrolyzed by MAase while being taken up by the bacterium. With glycogen and branched beta-CDs as substrates, pullulanase showed high-level specificity for the hydrolysis of the outer side chains of glycogen with three to five glucosyl residues. To investigate the roles of MAase and pullulanase in glycogen utilization, the following glycogen-overproducing strains were constructed: a glg mutant with a wild-type background, yvdF glg and amyX glg mutants, and a glg mutant with a double mutant (DM) background. The amyX glg and glg DM strains accumulated significantly larger amounts of glycogen than the glg mutant, while the yvdF glg strain accumulated an intermediate amount. Glycogen samples from the amyX glg and glg DM strains exhibited average molecular masses two and three times larger, respectively, than that of glycogen from the glg mutant. The results suggested that glycogen breakdown may be a sequential process that involves pullulanase and MAase, whereby pullulanase hydrolyzes the alpha-1,6-glycosidic linkage at the branch point to release a linear maltooligosaccharide that is then hydrolyzed into maltose and maltotriose by MAase.
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Characterization of a novel debranching enzyme from Nostoc punctiforme possessing a high specificity for long branched chains. Biochem Biophys Res Commun 2009; 378:224-9. [DOI: 10.1016/j.bbrc.2008.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 11/07/2008] [Indexed: 11/22/2022]
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93
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Le QT, Lee CK, Kim YW, Lee SJ, Zhang R, Withers SG, Kim YR, Auh JH, Park KH. Amylolytically-resistant tapioca starch modified by combined treatment of branching enzyme and maltogenic amylase. Carbohydr Polym 2009. [DOI: 10.1016/j.carbpol.2008.06.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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94
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Buedenbender S, Schulz GE. Structural Base for Enzymatic Cyclodextrin Hydrolysis. J Mol Biol 2009; 385:606-17. [DOI: 10.1016/j.jmb.2008.10.085] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 12/01/2022]
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95
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Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M. Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. J Biol Chem 2008; 283:36328-37. [PMID: 18981178 PMCID: PMC2662298 DOI: 10.1074/jbc.m806115200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/03/2008] [Indexed: 11/06/2022] Open
Abstract
SusB, an 84-kDa alpha-glucoside hydrolase involved in the starch utilization system (sus) of Bacteroides thetaiotaomicron, belongs to glycoside hydrolase (GH) family 97. We have determined the enzymatic characteristics and the crystal structures in free and acarbose-bound form at 1.6A resolution. SusB hydrolyzes the alpha-glucosidic linkage, with inversion of anomeric configuration liberating the beta-anomer of glucose as the reaction product. The substrate specificity of SusB, hydrolyzing not only alpha-1,4-glucosidic linkages but also alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages, is clearly different from other well known glucoamylases belonging to GH15. The structure of SusB was solved by the single-wavelength anomalous diffraction method with sulfur atoms as anomalous scatterers using an in-house x-ray source. SusB includes three domains as follows: the N-terminal, catalytic, and C-terminal domains. The structure of the SusB-acarbose complex shows a constellation of carboxyl groups at the catalytic center; Glu532 is positioned to provide protonic assistance to leaving group departure, with Glu439 and Glu508 both positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water. A structural comparison with other glycoside hydrolases revealed significant similarity between the catalytic domain of SusB and those of alpha-retaining glycoside hydrolases belonging to GH27, -36, and -31 despite the differences in catalytic mechanism. SusB and the other retaining enzymes appear to have diverged from a common ancestor and individually acquired the functional carboxyl groups during the process of evolution. Furthermore, sequence comparison of the active site based on the structure of SusB indicated that GH97 included both retaining and inverting enzymes.
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Affiliation(s)
- Momoyo Kitamura
- Faculty of Advanced Life Science, Graduate School of Agriculture, Hokkaido University, Sapporo 060-0810, Japan
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96
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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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97
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Differences and similarities in enzymes from the neopullulanase subfamily isolated from thermophilic species. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0171-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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98
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Nakagawa Y, Saburi W, Takada M, Hatada Y, Horikoshi K. Gene cloning and enzymatic characteristics of a novel γ-cyclodextrin-specific cyclodextrinase from alkalophilic Bacillus clarkii 7364. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:2004-11. [DOI: 10.1016/j.bbapap.2008.08.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2008] [Revised: 08/09/2008] [Accepted: 08/25/2008] [Indexed: 10/21/2022]
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99
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Enzymatic properties of cyclomaltodextrinases: Their substrate specificity, hydrolysis pattern, and transglycosylation activity. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.1959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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100
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Genome-wide analyses of various cyclodextrin-degrading enzymes: Primary, secondary, tertiary, and quaternary structures. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.1960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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