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Glycoside hydrolases active on microbial exopolysaccharide α-glucans: structures and function. Essays Biochem 2023; 67:505-520. [PMID: 36876882 DOI: 10.1042/ebc20220219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 03/07/2023]
Abstract
Glucose is the most abundant monosaccharide in nature and is an important energy source for living organisms. Glucose exists primarily as oligomers or polymers and organisms break it down and consume it. Starch is an important plant-derived α-glucan in the human diet. The enzymes that degrade this α-glucan have been well studied as they are ubiquitous throughout nature. Some bacteria and fungi produce α-glucans with different glucosidic linkages compared with that of starch, and their structures are quite complex and not fully understood. Compared with enzymes that degrade the α-(1→4) and α-(1→6) linkages in starch, biochemical and structural studies of the enzymes that catabolize α-glucans from these microorganisms are limited. This review focuses on glycoside hydrolases that act on microbial exopolysaccharide α-glucans containing α-(1→6), α-(1→3), and α-(1→2) linkages. Recently acquired information regarding microbial genomes has contributed to the discovery of enzymes with new substrate specificities compared with that of previously studied enzymes. The discovery of new microbial α-glucan-hydrolyzing enzymes suggests previously unknown carbohydrate utilization pathways and reveals strategies for microorganisms to obtain energy from external sources. In addition, structural analysis of α-glucan degrading enzymes has revealed their substrate recognition mechanisms and expanded their potential use as tools for understanding complex carbohydrate structures. In this review, the author summarizes the recent progress in the structural biology of microbial α-glucan degrading enzymes, touching on previous studies of microbial α-glucan degrading enzymes.
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2
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Hu X, Xia B, Ru W, Zhang Y, Yang J, Zhang H. Research progress on structure and catalytic mechanism of dextranase. EFOOD 2023. [DOI: 10.1002/efd2.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Xue‐Qin Hu
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Bing‐Bing Xia
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Wei‐Juan Ru
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Yu‐Xin Zhang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Jing‐Wen Yang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
| | - Hong‐Bin Zhang
- School of Food and Biological Engineering Hefei University of Technology Hefei China
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3
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Ru WJ, Xia BB, Zhang YX, Yang JW, Zhang HB, Hu XQ. Development of thermostable dextranase from Streptococcus mutans (SmdexTM) through in silico design employing B-factor and Cartesian-ΔΔG. J Biotechnol 2022; 360:142-151. [PMID: 36343755 DOI: 10.1016/j.jbiotec.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
The thermal stability of enzymes dramatically limits their application in the industrial field. Based on the crystal structure, we conducted a semi-rational design according to the B-factor and free energy values to improve the stability of dextranase from Streptococcus mutans (SmdexTM). The B-factor values of Asn102, Asn503, Asp501 and Asp500 were the highest predicted by B-FITTER. Then Rosetta was used to simulate the saturation mutations of Asn102, Asn503, Asp501 and Asp500. The mutated amino acid was designed according to the change of acG. The results showed that the thermal stability of N102P, N102C, D500G, and D500T was improved, and the half-lives of N102P/D500G and N102P/D500T at 45 °C were increased to 3.14 times and 2.44 times, respectively. Analyzing the interaction of amino acids by using Discovery Studio 4.5, it was observed that the thermal stability of dextranase was improved due to the increase in hydrophobicity and the number of hydrogen bonds of the mutant enzyme. The catalytic efficiency of N102P/D500T was increased. Compared with the hydrolyzed products of SmdexTM, the mutant enzymes do not change the specificity of hydrolysates.
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Affiliation(s)
- Wei-Juan Ru
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, China
| | - Bing-Bing Xia
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, China
| | - Yu-Xin Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, China
| | - Jing-Wen Yang
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, China
| | - Hong-Bin Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, China.
| | - Xue-Qin Hu
- School of Food and Biological Engineering, Hefei University of Technology, Anhui, China.
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Akram F, Aqeel A, Shoaib M, Haq IU, Shah FI. Multifarious revolutionary aspects of microbial keratinases: an efficient green technology for future generation with prospective applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:86913-86932. [PMID: 36271998 DOI: 10.1007/s11356-022-23638-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Since the dawn of century, tons of keratin bio-waste is generated by the poultry industry annually, and they end up causing environmental havoc. Keratins are highly flexible fibrous proteins which exist in α- and β- forms and provide mechanical strength and stability to structural appendages. The finding of broad-spectrum protease, keratinase, from thermophilic bacteria and fungi, has provided an eco-friendly solution to hydrolyze the peptide bonds in highly recalcitrant keratinous substances such as nails, feathers, claws, and horns into valuable amino acids. Microorganisms produce these proteolytic enzymes by techniques of solid-state and submerged fermentation. However, solid-state fermentation is considered as a yielding approach for the production of thermostable keratinases. This review prioritized the molecular and biochemical properties of microbial keratinases, and the role of keratinases in bringing prodigious impact for the sustainable progress of the economy. It also emphasizes on the current development in keratinase production with the focus to improve the biochemical properties related to enzyme's catalytic activity and stability, and production of mutant and cloned microbial strains to improve the yield of keratinases. Recently, multitude molecular approaches have been employed to enhance enzyme's productivity, activity, and thermostability which makes them suitable for pharmaceutical industry and for the production of animal feed, organic fertilizers, biogas, clearing of animal hides, and detergent formulation. Hence, it can be surmised that microbial keratinolytic enzymes are the conceivable candidates for numerous commercial and industrial applications.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Minahil Shoaib
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
- Pakistan Academy of Science, Islamabad, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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5
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Cloning of Cold-Adapted Dextranase and Preparation of High Degree Polymerization Isomaltooligosaccharide. Catalysts 2022. [DOI: 10.3390/catal12070784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Intestinal diseases are mainly caused by a decrease in the relative abundance of probiotics and an increase in the number of pathogenic bacteria due to dysbiosis of the intestinal flora. High degree polymerization isomaltooligosaccharide (IMO) can promote probiotic metabolism and proliferation. In this study, the dextranase (PsDex1711) gene of marine bacterial Pseudarthrobacter sp. RN22 was cloned and expressed in Escherichia coli BL21 (DE3). The optimal pH and temperature of the dextranase were 6.0 and 30 °C, respectively, showing the highest stability at 20 °C. The dextran T70 could be hydrolyzed to produce IMO3, IMO4, IMO5, and IMO6 with a high degree of polymerization. The hydrolysate of 1 mg/mL could significantly promote the growth of Lactobacillus and Bifidobacterium after 12 h culture and the formation of biofilms by 58.2%. The hydrolysates could promote the proliferation of probiotics. Furthermore, the IC50 of scavenging rate of DPPH, hydroxyl radical, and superoxide anion was less than 20 mg/mL. This study provides a crucial theoretical basis for the application of dextranase such as pharmaceutical and food industries.
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Pang B, He J, Zhang W, Huang H, Wang Y, Wang M, Du G, Kang Z. Active Expression of Human Hyaluronidase PH20 and Characterization of Its Hydrolysis Pattern. Front Bioeng Biotechnol 2022; 10:885888. [PMID: 35646856 PMCID: PMC9136067 DOI: 10.3389/fbioe.2022.885888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/12/2022] [Indexed: 12/21/2022] Open
Abstract
Hyaluronidases are a group of glycosidases catalyzing the degradation of hyaluronic acid (HA). Because of the advantages of effectively hydrolyzing the HA-rich matrix and low immunogenicity, human hyaluronidase PH20 (hPH20) is widely used in the medical field. Here, we realized the active expression of recombinant hPH20 by Pichia pastoris under a methanol-induced promoter PAOX1. By optimizing the composition of the C-terminal domain and fusing protein tags, we constructed a fusion mutant AP2-△491C with the extracellular hyaluronidase activity of 258.1 U·L-1 in a 3-L bioreactor, the highest expression level of recombinant hPH20 produced by microbes. Furthermore, we found recombinant hPH20 hydrolyzed the β-1,4 glycosidic bonds sequentially from the reducing end of o-HAs, with HA6 NA as the smallest substrate. The result will provide important theoretical guidance for the directed evolution of the enzyme to prepare multifunctional o-HAs with specific molecular weights.
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Affiliation(s)
- Bo Pang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Jing He
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Weijiao Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Hao Huang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Yang Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Miao Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Guocheng Du
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Zhen Kang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Science Center for Future Foods, Jiangnan University, Wuxi, China
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Kashyap A, Gupta R. N-truncation in lipase Lip11 from Yarrowia lipolytica alleviates substrate inhibition with improved stability and efficiency ensuing distinct structural modifications. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Liu N, Li X, Wang M, Zhang F, Wang C, Zhang K, Wang H, Xu S, Hu W, Gu L. DexA70, the Truncated Form of a Self-Produced Dextranase, Effectively Disrupts Streptococcus mutans Biofilm. Front Microbiol 2021; 12:737458. [PMID: 34650538 PMCID: PMC8505985 DOI: 10.3389/fmicb.2021.737458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022] Open
Abstract
Billions of people suffer from dental caries every year in spite of the effort to reduce the prevalence over the past few decades. Streptococcus mutans is the leading member of a specific group of cariogenic bacteria that cause dental caries. S. mutans forms biofilm, which is highly resistant to harsh environment, host immunity, and antimicrobial treatments. In this study, we found that S. mutans biofilm is highly resistant to both antimicrobial agents and lysozyme. DexA70, the truncated form of DexA (amino acids 100–732), a dextranase in S. mutans, prevents S. mutans biofilm formation and disassembles existing biofilms within minutes at nanomolar concentrations when supplied exogenously. DexA70 treatment markedly enhances biofilm sensitivity to antimicrobial agents and lysozyme, indicating its great potential in combating biofilm-related dental caries.
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Affiliation(s)
- Nan Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xin Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Maofeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kundi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hongwei Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Singh R, Ren Z, Shi Y, Lin S, Kwon K, Balamurugan S, Rai V, Mante F, Koo H, Daniell H. Affordable oral health care: dental biofilm disruption using chloroplast made enzymes with chewing gum delivery. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2113-2125. [PMID: 34076337 PMCID: PMC8486246 DOI: 10.1111/pbi.13643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 05/09/2023]
Abstract
Current approaches for oral health care rely on procedures that are unaffordable to impoverished populations, whereas aerosolized droplets in the dental clinic and poor oral hygiene may contribute to spread of several infectious diseases including COVID-19, requiring new solutions for dental biofilm/plaque treatment at home. Plant cells have been used to produce monoclonal antibodies or antimicrobial peptides for topical applications to decrease colonization of pathogenic microbes on dental surface. Therefore, we investigated an affordable method for dental biofilm disruption by expressing lipase, dextranase or mutanase in plant cells via the chloroplast genome. Antibiotic resistance gene used to engineer foreign genes into the chloroplast genome were subsequently removed using direct repeats flanking the aadA gene and enzymes were successfully expressed in marker-free lettuce transplastomic lines. Equivalent enzyme units of plant-derived lipase performed better than purified commercial enzymes against biofilms, specifically targeting fungal hyphae formation. Combination of lipase with dextranase and mutanase suppressed biofilm development by degrading the biofilm matrix, with concomitant reduction of bacterial and fungal accumulation. In chewing gum tablets formulated with freeze-dried plant cells, expressed protein was stable up to 3 years at ambient temperature and was efficiently released in a time-dependent manner using a mechanical chewing simulator device. Development of edible plant cells expressing enzymes eliminates the need for purification and cold-chain transportation, providing a potential translatable therapeutic approach. Biofilm disruption through plant enzymes and chewing gum-based delivery offers an effective and affordable dental biofilm control at home particularly for populations with minimal oral care access.
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Affiliation(s)
- Rahul Singh
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Zhi Ren
- Divisions of Community Oral Health & Pediatric DentistryDepartment of OrthodonticsSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Yao Shi
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shina Lin
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Kwang‐Chul Kwon
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shanmugaraj Balamurugan
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Vineeta Rai
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Francis Mante
- Department of Preventive and Restorative DentistrySchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Hyun Koo
- Divisions of Community Oral Health & Pediatric DentistryDepartment of OrthodonticsSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Center for Innovation & Precision DentistrySchool of Dental Medicine and School of Engineering & Applied SciencesUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Center for Innovation & Precision DentistrySchool of Dental Medicine and School of Engineering & Applied SciencesUniversity of PennsylvaniaPhiladelphiaPAUSA
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10
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Chen H, Pu Y, Zou Q, Hou D, Chen S. Enzymatic degradation of aqueous dextrans as affected by initial molecular weight and concentration. Polym Bull (Berl) 2021. [DOI: 10.1007/s00289-020-03351-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Banerjee A, Kumar A, Ghosh KK, Mitra P. Estimating Change in Foldability Due to Multipoint Deletions in Protein Structures. J Chem Inf Model 2020; 60:6679-6690. [PMID: 33225697 DOI: 10.1021/acs.jcim.0c00802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insertions/deletions of amino acids in the protein backbone potentially result in altered structural/functional specifications. They can either contribute positively to the evolutionary process or can result in disease conditions. Despite being the second most prevalent form of protein modification, there are no databases or computational frameworks that delineate harmful multipoint deletions (MPD) from beneficial ones. We introduce a positive unlabeled learning-based prediction framework (PROFOUND) that utilizes fold-level attributes, environment-specific properties, and deletion site-specific properties to predict the change in foldability arising from such MPDs, both in the non-loop and loop regions of protein structures. In the absence of any protein structure dataset to study MPDs, we introduce a dataset with 153 MPD instances that lead to native-like folded structures and 7650 unlabeled MPD instances whose effect on the foldability of the corresponding proteins is unknown. PROFOUND on 10-fold cross-validation on our newly introduced dataset reports a recall of 82.2% (86.6%) and a fall out rate (FR) of 14.2% (20.6%), corresponding to MPDs in the protein loop (non-loop) region. The low FR suggests that the foldability in proteins subject to MPDs is not random and necessitates unique specifications of the deleted region. In addition, we find that additional evolutionary attributes contribute to higher recall and lower FR. The first of a kind foldability prediction system owing to MPD instances and the newly introduced dataset will potentially aid in novel protein engineering endeavors.
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Affiliation(s)
- Anupam Banerjee
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Amit Kumar
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Kushal Kanti Ghosh
- Department of Computer Science and Engineering, Jadavpur University, Kolkata 700032, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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12
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Dextran degradation by sonoenzymolysis: Degradation rate, molecular weight, mass fraction, and degradation kinetics. Int J Biol Macromol 2020; 169:60-66. [PMID: 33338523 DOI: 10.1016/j.ijbiomac.2020.12.091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 11/21/2022]
Abstract
To study dextran degradation by sonoenzymolysis, the degradation rate, the change of molecular weight, the mass fractions of fragments of certain molecular weight, and the degradation kinetics were analyzed and compared with the corresponding parameters under ultrasonic and enzymolysis treatments. The degradation rate improved greatly and the time required to stabilize the rate was shortened compared with ultrasonic treatment, for example, more than 120 min was needed at 4 W/mL for ultrasonic treatment before stabilization with the degradation rate of 77.41%, whereas 80 min was needed for sonoenzymolysis treatment with the degradation rate of 91.44%. A lower molecular weight limit was established (7.15 × 104 Da at 4 W/mL for sonoenzymolysis treatment compared with 19.61 × 104 Da at 4 W/mL for ultrasonic treatment), with decreased time to approach the new limiting molecular weight (80 min compared with more than 120 min). The mass fraction of 104-105 Da fragment increased (61.02% at 4 W/mL for sonoenzymolysis treatment compared with 42.98% at 4 W/mL for ultrasonic treatment) and the dextran degradation kinetics for sonoenzymolysis under lower ultrasonic intensity fitted the Malhotra model well. Sonoenzymolysis treatment at the ultrasonic intensity of 4 W/mL for 80 min resulted in more 104-105 Da fragments in a shorter time. The results indicated that sonoenzymolysis can be applied as an efficient method to obtain clinical dextran.
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13
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Sharma A, Gupta G, Ahmad T, Mansoor S, Kaur B. Enzyme Engineering: Current Trends and Future Perspectives. FOOD REVIEWS INTERNATIONAL 2019. [DOI: 10.1080/87559129.2019.1695835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anshula Sharma
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Tawseef Ahmad
- Department of Biotechnology, Punjabi University, Patiala, India
| | | | - Baljinder Kaur
- Department of Biotechnology, Punjabi University, Patiala, India
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14
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Pang B, Zhou L, Cui W, Liu Z, Zhou S, Xu J, Zhou Z. A Hyperthermostable Type II Pullulanase from a Deep-Sea Microorganism Pyrococcus yayanosii CH1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9611-9617. [PMID: 31385500 DOI: 10.1021/acs.jafc.9b03376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pullulanase is a commonly used debranching enzyme in the starch processing industry. Because the starch liquefaction process requires high temperature, a thermostable pullulanase is desired. Here, a novel hyperthermostable type II pullulanase gene (pulPY) was cloned from Pyrococcus yayanosii CH1, isolated from a deep-sea hydrothermal site. PulPY was optimally active at pH 6.6 and 95 °C, retaining more than 50% activity after incubation at 95 °C for 10 h. The thermostability was significantly higher than those of most pullulanases reported previously. To further improve its activity and thermostability, the N-terminal and C-terminal domains of PulPY were truncated. The optimum temperature of the combined truncation mutant Δ28N + Δ791C increased to 100 °C with a specific activity of 32.18 U/mg, which was six times higher than that of wild-type PulPY. PulPY and the truncation mutant enzyme could realize the combined use of pullulanase with α-amylase during the starch liquefaction process to improve hydrolysis efficiency.
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Affiliation(s)
- Bo Pang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education , Jiangnan University , 1800 Lihu Avenue , Wuxi 214122 , China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education , Jiangnan University , 1800 Lihu Avenue , Wuxi 214122 , China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology of Ministry of Education , Jiangnan University , 1800 Lihu Avenue , Wuxi 214122 , China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology of Ministry of Education , Jiangnan University , 1800 Lihu Avenue , Wuxi 214122 , China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, School of Biotechnology , East China University of Science and Technology , Shanghai 200237 , P.R. China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology and State Key Laboratory of Ocean Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education , Jiangnan University , 1800 Lihu Avenue , Wuxi 214122 , China
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15
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Alginate–pectin co-encapsulation of dextransucrase and dextranase for oligosaccharide production from sucrose feedstocks. Bioprocess Biosyst Eng 2019; 42:1681-1693. [DOI: 10.1007/s00449-019-02164-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
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16
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Jiao Y, Wu Y, Chen H, Wang S, Chen L, Lv M, Fang Y, Liu S. The impact of N-terminal nonessential domains on the enzymological properties of the pullulanase from a marine Bacillus megaterium. Biotechnol Lett 2019; 41:849-857. [DOI: 10.1007/s10529-019-02686-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/02/2019] [Indexed: 12/14/2022]
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17
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Wang X, Nie Y, Xu Y. Industrially produced pullulanases with thermostability: Discovery, engineering, and heterologous expression. BIORESOURCE TECHNOLOGY 2019; 278:360-371. [PMID: 30709762 DOI: 10.1016/j.biortech.2019.01.098] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Pullulanases (EC 3.2.1.41) are well-known starch-debranching enzymes widely used to hydrolyze α-1,6-glucosidic linkages in starch, pullulan, amylopectin, and other oligosaccharides, with application potentials in food, brewing, and pharmaceutical industries. Although extensive studies are done to discover and express pullulanases, only few are available with desirable characteristics for industrial applications. This raises the challenge to mine new enzyme sources, engineer proteins based on sequence/structure, and regulate expressions. We review here the identification of extremophilic and mesophilic microbes as sources of industrial pullulanases with desirable characteristics, including acid-resistance, thermostability, and psychrotrophism. We present current advances in site-directed mutagenesis and sequence/structure-guided protein engineering of pullulanases. In addition, we discuss heterologous expression of pullulanases in prokaryotic and eukaryotic microbial systems, and address the effectiveness of the expression elements and their regulation of enzyme production. Finally, we indicate future research needs to develop desired industrial pullulanases.
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Affiliation(s)
- Xinye Wang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; The 2011 Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, China.
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Omidi-Ardali H, Aminian M, Golestani A, Shahaboddin ME, Maleki M. N∆89 and C∆274 Truncated Enzymes of Chondroitinase ABC I Regain More Imperturbable Microenvironments Around Structural Components in Comparison to their Wild Type. Protein J 2019; 38:151-159. [DOI: 10.1007/s10930-019-09821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Saha P, Khan MF, Patra S. Truncated α-amylase: an improved candidate for textile processing. Prep Biochem Biotechnol 2018; 48:635-645. [DOI: 10.1080/10826068.2018.1479863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Poulomi Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Mohd Faheem Khan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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Klahan P, Okuyama M, Jinnai K, Ma M, Kikuchi A, Kumagai Y, Tagami T, Kimura A. Engineered dextranase from Streptococcus mutans enhances the production of longer isomaltooligosaccharides. Biosci Biotechnol Biochem 2018; 82:1480-1487. [PMID: 29806555 DOI: 10.1080/09168451.2018.1473026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Herein, we investigated enzymatic properties and reaction specificities of Streptococcus mutans dextranase, which hydrolyzes α-(1→6)-glucosidic linkages in dextran to produce isomaltooligosaccharides. Reaction specificities of wild-type dextranase and its mutant derivatives were examined using dextran and a series of enzymatically prepared p-nitrophenyl α-isomaltooligosaccharides. In experiments with 4-mg·mL-1 dextran, isomaltooligosaccharides with degrees of polymerization (DP) of 3 and 4 were present at the beginning of the reaction, and glucose and isomaltose were produced by the end of the reaction. Increased concentrations of the substrate dextran (40 mg·mL-1) yielded isomaltooligosaccharides with higher DP, and the mutations T558H, W279A/T563N, and W279F/T563N at the -3 and -4 subsites affected hydrolytic activities of the enzyme, likely reflecting decreases in substrate affinity at the -4 subsite. In particular, T558H increased the proportion of isomaltooligosaccharide with DP of 5 in hydrolysates following reactions with 4-mg·mL-1 dextran.Abbreviations CI: cycloisomaltooligosaccharide; CITase: CI glucanotransferase; CITase-Bc: CITase from Bacillus circulans T-3040; DP: degree of polymerization of glucose unit; GH: glycoside hydrolase family; GTF: glucansucrase; HPAEC-PAD: high performance anion-exchange chromatography-pulsed amperometric detection; IG: isomaltooligosaccharide; IGn: IG with DP of n (n, 2‒5); PNP: p-nitrophenol; PNP-Glc: p-nitrophenyl α-glucoside; PNP-IG: p-nitrophenyl isomaltooligosaccharide; PNP-IGn: PNP-IG with DP of n (n, 2‒6); SmDex: dextranase from Streptococcus mutans; SmDexTM: S. mutans ATCC25175 SmDex bearing Gln100‒Ile732.
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Affiliation(s)
- Patcharapa Klahan
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Masayuki Okuyama
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Kohei Jinnai
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Min Ma
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Asako Kikuchi
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Yuya Kumagai
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Takayoshi Tagami
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Atsuo Kimura
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
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Han Y, Gao P, Yu W, Lu X. N-Terminal seven-amino-acid extension simultaneously improves the pH stability, optimal temperature, thermostability and catalytic efficiency of chitosanase CsnA. Biotechnol Lett 2017; 40:75-82. [PMID: 28905142 DOI: 10.1007/s10529-017-2436-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/31/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To determine the effects of the extra N-terminal seven-amino-acid sequence on the function of chitosanase CsnA. RESULTS Sequence and structure analysis indicated that the mature CsnA contains a seven-amino-acid extension in a disordered form at the N-terminus. To determine the function of this sequence, both mature CsnA and its N-terminus-truncated mutant, CsnAΔN, were expressed in Escherichia coli and characterized. Compared with CsnAΔN, CsnA exhibited a 15 °C higher temperature optimum, enhanced pH stability, thermostability and catalytic efficiency. The underlying mechanisms responsible for these changes were analyzed by circular dichroism (CD) spectroscopy. CD analysis revealed that the deletion of the N-terminal sequence resulted in a decrease in the Tm of 4.3 °C and this sequence altered the secondary structure of the enzyme. CONCLUSIONS The N-terminal sequence is essential for the stability and activity of chitosanase CsnA.
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Affiliation(s)
- Yujuan Han
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province; Key Laboratory of Marine Drugs, Chinese Ministry of Education; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology; Department of Glycobiology; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Peixin Gao
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province; Key Laboratory of Marine Drugs, Chinese Ministry of Education; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology; Department of Glycobiology; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Wengong Yu
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province; Key Laboratory of Marine Drugs, Chinese Ministry of Education; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology; Department of Glycobiology; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xinzhi Lu
- Key Laboratory of Glycoscience & Glycotechnology of Shandong Province; Key Laboratory of Marine Drugs, Chinese Ministry of Education; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology; Department of Glycobiology; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
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Xu Y, Liu Y, Rasool A, E W, Li C. Sequence editing strategy for improving performance of β-glucuronidase from Aspergillus terreus. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain. Sci Rep 2016; 6:27953. [PMID: 27298079 PMCID: PMC4906391 DOI: 10.1038/srep27953] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 05/27/2016] [Indexed: 11/25/2022] Open
Abstract
The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s−1 mM−1. The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD.
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24
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Wang X, Nie Y, Mu X, Xu Y, Xiao R. Disorder prediction-based construct optimization improves activity and catalytic efficiency of Bacillus naganoensis pullulanase. Sci Rep 2016; 6:24574. [PMID: 27091115 PMCID: PMC4835747 DOI: 10.1038/srep24574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/31/2016] [Indexed: 11/13/2022] Open
Abstract
Pullulanase is a well-known starch-debranching enzyme. However, the production level of pullulanase is yet low in both wide-type strains and heterologous expression systems. We predicted the disorder propensities of Bacillus naganoensis pullulanase (PUL) using the bioinformatics tool, Disorder Prediction Meta-Server. On the basis of disorder prediction, eight constructs, including PULΔN5, PULΔN22, PULΔN45, PULΔN64, PULΔN78 and PULΔN106 by deleting the first 5, 22, 45, 64, 78 and 106 residues from the N-terminus, and PULΔC9 and PULΔC36 by deleting the last 9 and 36 residues from the C-terminus, were cloned into the recombinant expression vector pET-28a-PelB and auto-induced in Escherichia coli BL21 (DE3) cells. All constructs were evaluated in production level, specific activities and kinetic parameters. Both PULΔN5 and PULΔN106 gave higher production levels of protein than the wide type and displayed increased specific activities. Kinetic studies showed that substrate affinities of the mutants were improved in various degrees and the catalytic efficiency of PULΔN5, PULΔN45, PULΔN78, PULΔN106 and PULΔC9 were enhanced. However, the truncated mutations did not change the advantageous properties of the enzyme involving optimum temperature and pH for further application. Therefore, Disorder prediction-based truncation would be helpful to efficiently improve the enzyme activity and catalytic efficiency.
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Affiliation(s)
- Xinye Wang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaoqing Mu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,The 2011 Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, China
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
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Truncation of the unique N-terminal domain improved the thermos-stability and specific activity of alkaline α-amylase Amy703. Sci Rep 2016; 6:22465. [PMID: 26926401 PMCID: PMC4772547 DOI: 10.1038/srep22465] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/11/2016] [Indexed: 11/08/2022] Open
Abstract
High pH condition is of special interest for the potential applications of alkaline α-amylase in textile and detergent industries. Thus, there is a continuous demand to improve the amylase's properties to meet the requirements set by specific applications. Here we reported the systematic study of modular domain engineering to improve the specific activity and stability of the alkaline α-amylase from Bacillus pseudofirmus 703. The specific activity of the N-terminal domain truncated mutant (N-Amy) increased by ~35-fold with a significantly improved thermo-stability. Kinetic analysis demonstrated that the Kcat and Kcat/Kmof N-Amy were enhanced by 1300-fold and 425.7-fold, respectively, representing the largest catalytic activity improvement of the engineered α-amylases through the methods of domain deletion, fusion or swapping. In addition, different from the wild-type Amy703, no exogenous Ca(2+) were required for N-Amy to maintain its full catalytic activity, implying its superior potential for many industrial processes. Circular dichroism analysis and structure modeling revealed that the increased compactness and α-helical content were the main contributors for the improved thermo-stability of N-Amy, while the improved catalytic efficiency was mainly attributed by the increased conformational flexibility around the active center.
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26
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Simón M, Montiel R, Smerling A, Solórzano E, Díaz N, Álvarez-Sandoval BA, Jiménez-Marín AR, Malgosa A. Molecular analysis of ancient caries. Proc Biol Sci 2015; 281:rspb.2014.0586. [PMID: 25056622 DOI: 10.1098/rspb.2014.0586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains.
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Affiliation(s)
- Marc Simón
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Andrea Smerling
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Eduvigis Solórzano
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Nancy Díaz
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Brenda A Álvarez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Andrea R Jiménez-Marín
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Assumpció Malgosa
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
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Suzuki N, Kishine N, Fujimoto Z, Sakurai M, Momma M, Ko JA, Nam SH, Kimura A, Kim YM. Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus. J Biochem 2015; 159:331-9. [PMID: 26494689 DOI: 10.1093/jb/mvv104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/12/2015] [Indexed: 11/12/2022] Open
Abstract
The crystal structures of the wild type and catalytic mutant Asp-312→Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (β/α)8-barrel and two β-domains located at both N- and C-terminal ends. The isomaltohexaose-complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (-4 to +2) in the catalytic cleft. Marked movement of the Trp-376 side-chain along with loop 6, which was the side wall component of the cleft at subsite +1, was observed to occupy subsite +1, indicating that it might expel the cleaved aglycone subsite after the hydrolysis reaction. Structural comparison with other mesophilic enzymes indicated that several structural features of TpDex, loop deletion, salt bridge and surface-exposed charged residue, may contribute to thermostability.
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan;
| | - Naomi Kishine
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan;
| | - Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan;
| | - Mutsumi Sakurai
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Mitsuru Momma
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Jin-A Ko
- Eco-Friendly Bio-material Research Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 580-185, Korea
| | - Seung-Hee Nam
- Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju 500-757, Korea
| | - Atsuo Kimura
- Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nisi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Young-Min Kim
- Department of Food Science and Technology and Functional Food Research Center, Chonnam National University, Gwangju 500-757, Korea; Bioenergy Research Center, Chonnam National University, Gwangju 500-757, Korea
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Otsuka R, Imai S, Murata T, Nomura Y, Okamoto M, Tsumori H, Kakuta E, Hanada N, Momoi Y. Application of chimeric glucanase comprising mutanase and dextranase for prevention of dental biofilm formation. Microbiol Immunol 2015; 59:28-36. [DOI: 10.1111/1348-0421.12214] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/07/2014] [Accepted: 11/17/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Ryoko Otsuka
- Department of Operative Dentistry; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
| | - Susumu Imai
- Department of Translational Research; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
| | - Takatoshi Murata
- Department of Translational Research; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
| | - Yoshiaki Nomura
- Department of Translational Research; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
| | - Masaaki Okamoto
- Department of Oral Microbiology; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
| | - Hideaki Tsumori
- Department of Chemistry; National Defense Medical College; 3-2, Namiki Tokorozawa Saitama 359-8513 Japan
| | - Erika Kakuta
- Department of Translational Research; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
| | - Nobuhiro Hanada
- Department of Translational Research; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
| | - Yasuko Momoi
- Department of Operative Dentistry; Tsurumi University School of Dental Medicine; 2-1-3 Tsurumi Tsurumi-ku Yokohama 230-8501
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29
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Biosynthesis of oligodextrans with different Mw by synergistic catalysis of dextransucrase and dextranase. Carbohydr Polym 2014; 112:387-95. [DOI: 10.1016/j.carbpol.2014.06.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/26/2014] [Accepted: 06/03/2014] [Indexed: 02/04/2023]
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30
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Molecular engineering of industrial enzymes: recent advances and future prospects. Appl Microbiol Biotechnol 2013; 98:23-9. [DOI: 10.1007/s00253-013-5370-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022]
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Integrating terminal truncation and oligopeptide fusion for a novel protein engineering strategy to improve specific activity and catalytic efficiency: alkaline α-amylase as a case study. Appl Environ Microbiol 2013; 79:6429-38. [PMID: 23956385 DOI: 10.1128/aem.02087-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, we integrated terminal truncation and N-terminal oligopeptide fusion as a novel protein engineering strategy to improve specific activity and catalytic efficiency of alkaline α-amylase (AmyK) from Alkalimonas amylolytica. First, the C terminus or N terminus of AmyK was partially truncated, yielding 12 truncated mutants, and then an oligopeptide (AEAEAKAKAEAEAKAK) was fused at the N terminus of the truncated AmyK, yielding another 12 truncation-fusion mutants. The specific activities of the truncation-fusion mutants AmyKΔC500-587::OP and AmyKΔC492-587::OP were 25.5- and 18.5-fold that of AmyK, respectively. The kcat/Km was increased from 1.0 × 10(5) liters · mol(-1) · s(-1) for AmyK to 30.6 × and 23.2 × 10(5) liters · mol(-1) · s(-1) for AmyKΔC500-587::OP and AmyKΔC492-587::OP, respectively. Comparative analysis of structure models indicated that the higher flexibility around the active site may be the main reason for the improved catalytic efficiency. The proposed terminal truncation and oligopeptide fusion strategy may be effective to engineer other enzymes to improve specific activity and catalytic efficiency.
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32
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Suzuki N, Kim YM, Momma M, Fujimoto Z, Kobayashi M, Kimura A, Funane K. Crystallization and preliminary X-ray crystallographic analysis of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:946-9. [PMID: 23908050 PMCID: PMC3729181 DOI: 10.1107/s174430911301991x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/18/2013] [Indexed: 11/10/2022]
Abstract
Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase (BcCITase) catalyses an intramolecular transglucosylation reaction and produces cycloisomaltooligosaccharides from dextran. BcCITase was overexpressed in Escherichia coli in two different forms and crystallized by the sitting-drop vapour-diffusion method. The crystal of BcCITase bearing an N-terminal His₆ tag diffracted to a resolution of 2.3 Å and belonged to space group P3₁21, containing a single molecule in the asymmetric unit. The crystal of BcCITase bearing a C-terminal His6 tag diffracted to a resolution of 1.9 Å and belonged to space group P2₁2₁2₁, containing two molecules in the asymmetric unit.
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Young-Min Kim
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nisi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Mitsuru Momma
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Mikihiko Kobayashi
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Japan
- Department of Food and Health Science, Jissen Women’s University, 4-1-1 Osakaue, Hino 191-8510, Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nisi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Kazumi Funane
- Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Japan
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33
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Kim YM, Yamamoto E, Kang MS, Nakai H, Saburi W, Okuyama M, Mori H, Funane K, Momma M, Fujimoto Z, Kobayashi M, Kim D, Kimura A. Bacteroides thetaiotaomicronVPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J 2012; 279:3185-91. [DOI: 10.1111/j.1742-4658.2012.08698.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kim YM, Kiso Y, Muraki T, Kang MS, Nakai H, Saburi W, Lang W, Kang HK, Okuyama M, Mori H, Suzuki R, Funane K, Suzuki N, Momma M, Fujimoto Z, Oguma T, Kobayashi M, Kim D, Kimura A. Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J Biol Chem 2012; 287:19927-35. [PMID: 22461618 PMCID: PMC3370177 DOI: 10.1074/jbc.m111.339036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 03/27/2012] [Indexed: 11/06/2022] Open
Abstract
A novel endodextranase from Paenibacillus sp. (Paenibacillus sp. dextranase; PsDex) was found to mainly produce isomaltotetraose and small amounts of cycloisomaltooligosaccharides (CIs) with a degree of polymerization of 7-14 from dextran. The 1,696-amino acid sequence belonging to the glycosyl hydrolase family 66 (GH-66) has a long insertion (632 residues; Thr(451)-Val(1082)), a portion of which shares identity (35% at Ala(39)-Ser(1304) of PsDex) with Pro(32)-Ala(755) of CI glucanotransferase (CITase), a GH-66 enzyme that catalyzes the formation of CIs from dextran. This homologous sequence (Val(837)-Met(932) for PsDex and Tyr(404)-Tyr(492) for CITase), similar to carbohydrate-binding module 35, was not found in other endodextranases (Dexs) devoid of CITase activity. These results support the classification of GH-66 enzymes into three types: (i) Dex showing only dextranolytic activity, (ii) Dex catalyzing hydrolysis with low cyclization activity, and (iii) CITase showing CI-forming activity with low dextranolytic activity. The fact that a C-terminal truncated enzyme (having Ala(39)-Ser(1304)) has 50% wild-type PsDex activity indicates that the C-terminal 392 residues are not involved in hydrolysis. GH-66 enzymes possess four conserved acidic residues (Asp(189), Asp(340), Glu(412), and Asp(1254) of PsDex) of catalytic candidates. Their amide mutants decreased activity (1⁄1,500 to 1⁄40,000 times), and D1254N had 36% activity. A chemical rescue approach was applied to D189A, D340G, and E412Q using α-isomaltotetraosyl fluoride with NaN(3). D340G or E412Q formed a β- or α-isomaltotetraosyl azide, respectively, strongly indicating Asp(340) and Glu(412) as a nucleophile and acid/base catalyst, respectively. Interestingly, D189A synthesized small sized dextran from α-isomaltotetraosyl fluoride in the presence of NaN(3).
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Affiliation(s)
- Young-Min Kim
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yoshiaki Kiso
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tomoe Muraki
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Min-Sun Kang
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hiroyuki Nakai
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Wataru Saburi
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Weeranuch Lang
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hee-Kwon Kang
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masayuki Okuyama
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Haruhide Mori
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Ryuichiro Suzuki
- the National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Kazumi Funane
- the National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Japan
| | - Nobuhiro Suzuki
- the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Mitsuru Momma
- the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Zui Fujimoto
- the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Tetsuya Oguma
- the Noda Institute for Scientific Research, 399 Noda, Noda 278-0037, Japan
| | - Mikihiko Kobayashi
- the Department of Food and Health Science, Jissenn Women's University, Hino 191-8510, Japan, and
| | - Doman Kim
- the School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Korea
| | - Atsuo Kimura
- From the Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, Kimura A. Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 2012; 287:19916-26. [PMID: 22337884 DOI: 10.1074/jbc.m112.342444] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dextranase is an enzyme that hydrolyzes dextran α-1,6 linkages. Streptococcus mutans dextranase belongs to glycoside hydrolase family 66, producing isomaltooligosaccharides of various sizes and consisting of at least five amino acid sequence regions. The crystal structure of the conserved fragment from Gln(100) to Ile(732) of S. mutans dextranase, devoid of its N- and C-terminal variable regions, was determined at 1.6 Å resolution and found to contain three structural domains. Domain N possessed an immunoglobulin-like β-sandwich fold; domain A contained the enzyme's catalytic module, comprising a (β/α)(8)-barrel; and domain C formed a β-sandwich structure containing two Greek key motifs. Two ligand complex structures were also determined, and, in the enzyme-isomaltotriose complex structure, the bound isomaltooligosaccharide with four glucose moieties was observed in the catalytic glycone cleft and considered to be the transglycosylation product of the enzyme, indicating the presence of four subsites, -4 to -1, in the catalytic cleft. The complexed structure with 4',5'-epoxypentyl-α-d-glucopyranoside, a suicide substrate of the enzyme, revealed that the epoxide ring reacted to form a covalent bond with the Asp(385) side chain. These structures collectively indicated that Asp(385) was the catalytic nucleophile and that Glu(453) was the acid/base of the double displacement mechanism, in which the enzyme showed a retaining catalytic character. This is the first structural report for the enzyme belonging to glycoside hydrolase family 66, elucidating the enzyme's catalytic machinery.
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan
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36
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Suzuki N, Kim YM, Fujimoto Z, Momma M, Kang HK, Funane K, Okuyama M, Mori H, Kimura A. Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1542-4. [PMID: 22139161 PMCID: PMC3232134 DOI: 10.1107/s1744309111038425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 09/19/2011] [Indexed: 11/10/2022]
Abstract
Streptococcus mutans dextranase hydrolyzes the internal α-1,6-linkages of dextran and belongs to glycoside hydrolase family 66. An N- and C-terminal deletion mutant of S. mutans dextranase was crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 1.6 Å and belonged to space group P2(1), with unit-cell parameters a = 53.2, b = 89.7, c = 63.3 Å, β = 102.3°. Assuming that the asymmetric unit of the crystal contained one molecule, the Matthews coefficient was calculated to be 4.07 Å(3) Da(-1); assuming the presence of two molecules in the asymmetric unit it was calculated to be 2.03 Å(3) Da(-1).
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Affiliation(s)
- Nobuhiro Suzuki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Young-Min Kim
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Mitsuru Momma
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hee-Kwon Kang
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Kazumi Funane
- Applied Microbiology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba 305-8642, Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
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