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Abchir O, Khedraoui M, Nour H, Yamari I, Errougui A, Samadi A, Chtita S. Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations. Pharmaceuticals (Basel) 2024; 17:261. [PMID: 38399476 PMCID: PMC10892212 DOI: 10.3390/ph17020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
In response to the increasing prevalence of diabetes mellitus and the limitations associated with the current treatments, there is a growing need to develop novel medications for this disease. This study is focused on creating new compounds that exhibit a strong inhibition of alpha-glucosidase, which is a pivotal enzyme in diabetes control. A set of 33 triazole derivatives underwent an extensive QSAR analysis, aiming to identify the key factors influencing their inhibitory activity against α-glucosidase. Using the multiple linear regression (MLR) model, seven promising compounds were designed as potential drugs. Molecular docking and dynamics simulations were employed to shed light on the mode of interaction between the ligands and the target, and the stability of the obtained complexes. Furthermore, the pharmacokinetic properties of the designed compounds were assessed to predict their behavior in the human body. The binding free energy was also calculated using MMGBSA method and revealed favorable thermodynamic properties. The results highlighted three novel compounds with high biological activity, strong binding affinity to the target enzyme, and suitability for oral administration. These results offer interesting prospects for the development of effective and well-tolerated medications against diabetes mellitus.
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Affiliation(s)
- Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Meriem Khedraoui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Hassan Nour
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Abdelkbir Errougui
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
| | - Abdelouahid Samadi
- Department of Chemistry, College of Science, United Arab Emirates University (UAEU), Al Ain P.O. Box 15551, United Arab Emirates
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca 7955, Morocco; (O.A.); (M.K.); (A.E.)
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2
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Guo W, Xiao Y, Fu X, Long Z, Wu Y, Lin Q, Ren K, Jiang L. Identification of novel α-glucosidase and ACE inhibitory peptides from Douchi using peptidomics approach and molecular docking. Food Chem X 2023; 19:100779. [PMID: 37780236 PMCID: PMC10534093 DOI: 10.1016/j.fochx.2023.100779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 10/03/2023] Open
Abstract
In this study, the effect of Douchi extract (DWE) on α-glucosidase and angiotensin-converting enzymes (ACE) were investigated, and several novel peptides with inhibitory activity against α-glucosidase and ACE were identified using peptidomics approach based on UPLC-MS/MS. The average inhibition rates of DWE on α-glucosidase and ACE were 73.75-78.10% and 4.56-27.07%, respectively. In the DWE, a total of 710 peptides were detected. Two novel peptides with potential inhibitory activity against α-glucosidase were identified using the correlation analysis, database alignment and molecular docking methods. They were DVFRAIPSEVL and DRPSINGLAGAN, with the IC50 values of 0.121 and 0.128 mg/mL, respectively. Also, four novel peptides with potential inhibitory activity against ACE were identified: PSSPFTDLWD, EEQDERQFPF, PVPVPVQQAFPF and PSSPFTDL, with IC50 values of 1.388, 0.041, 0.761 and 0.097 mg/mL, respectively. These results indicated that combining peptidomics and molecular docking is an effective alternative strategy for rapidly screening numbers of novel bioactive peptides from foods.
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Affiliation(s)
- Weidan Guo
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yu Xiao
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiangjin Fu
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
- Nutrition and Health Products Engineering Technology Research Center of Hunan Province, Changsha 410004, China
- Hunan Provincial Engineering Technology Research Center of Seasonings Green Manufacturing, Changsha 410004, China
- Hunan Provincial Key Laboratory of Special Medical Food, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhao Long
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan Provincial Engineering Technology Research Center of Seasonings Green Manufacturing, Changsha 410004, China
- Hunan Provincial Key Laboratory of Special Medical Food, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yue Wu
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan Provincial Key Laboratory of Special Medical Food, Central South University of Forestry and Technology, Changsha 410004, China
| | - Qinlu Lin
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
- Nutrition and Health Products Engineering Technology Research Center of Hunan Province, Changsha 410004, China
- Hunan Provincial Engineering Technology Research Center of Seasonings Green Manufacturing, Changsha 410004, China
- Hunan Provincial Key Laboratory of Special Medical Food, Central South University of Forestry and Technology, Changsha 410004, China
| | - Kangzi Ren
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Liwen Jiang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China
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3
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Wayllace NM, Martín M, Busi MV, Gomez-Casati DF. Microbial glucoamylases: structural and functional properties and biotechnological uses. World J Microbiol Biotechnol 2023; 39:293. [PMID: 37653355 DOI: 10.1007/s11274-023-03731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Glucoamylases (GAs) are one of the principal groups of enzymes involved in starch hydrolysis and belong to the glycosylhydrolase family. They are classified as exo-amylases due to their ability to hydrolyze α-1,4 glycosidic bonds from the non-reducing end of starch, maltooligosaccharides, and related substrates, releasing β-D-glucose. Structurally, GAs possess a characteristic catalytic domain (CD) with an (α/α)6 fold and exhibit five conserved regions within this domain. The CD may or may not be linked to a non-catalytic domain with variable functions depending on its origin. GAs are versatile enzymes with diverse applications in food, biofuel, bioplastic and other chemical industries. Although fungal GAs are commonly employed for these purposes, they have limitations such as their low thermostability and an acidic pH requirement. Alternatively, GAs derived from prokaryotic organisms are a good option to save costs as they exhibit greater thermostability compared to fungal GAs. Moreover, a group of cold-adapted GAs from psychrophilic organisms demonstrates intriguing properties that make them suitable for application in various industries. This review provides a comprehensive overview of the structural and sequential properties as well as biotechnological applications of GAs in different industrial processes.
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Affiliation(s)
- Natael M Wayllace
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Mariana Martín
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - María V Busi
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
| | - Diego F Gomez-Casati
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
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4
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Liu D, Liu Q, Guo W, Liu Y, Wu M, Zhang Y, Li J, Sun W, Wang X, He Q, Tian C. Development of Genetic Tools in Glucoamylase-Hyperproducing Industrial Aspergillus niger Strains. BIOLOGY 2022; 11:biology11101396. [PMID: 36290301 PMCID: PMC9599018 DOI: 10.3390/biology11101396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Glucoamylase is one of the most needed industrial enzymes in the food and biofuel industries. Aspergillus niger is a commonly used cell factory for the production of commercial glucoamylase. For decades, genetic manipulation has promoted significant progress in industrial fungi for strain engineering and in obtaining deep insights into their genetic features. However, genetic engineering is more laborious in the glucoamylase-producing industrial strains A. niger N1 and O1 because their fungal features of having few conidia (N1) or of being aconidial (O1) make them difficult to perform transformation on. In this study, we targeted A. niger N1 and O1 and successfully developed high-efficiency transformation tools. We also constructed a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 editing marker-free system using an autonomously replicating plasmid to express Cas9 protein and to guide RNA and the selectable marker. By using the genetic tools developed here, we generated nine albino deletion mutants. After three rounds of sub-culturing under nonselective conditions, the albino deletions lost the autonomously replicating plasmid. Together, the tools and optimization process above provided a good reference to manipulate the tough working industrial strain, not only for the further engineering these two glucoamylase-hyperproducing strains, but also for other industrial strains. Abstract The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes, particularly glucoamylase. Although a variety of genetic techniques have been successfully used in wild-type A. niger, the transformation of industrially used strains with few conidia (e.g., A. niger N1) or that are even aconidial (e.g., A. niger O1) remains laborious. Herein, we developed genetic tools, including the protoplast-mediated transformation and Agrobacterium tumefaciens-mediated transformation of the A. niger strains N1 and O1 using green fluorescent protein as a reporter marker. Following the optimization of various factors for protoplast release from mycelium, the protoplast-mediated transformation efficiency reached 89.3% (25/28) for N1 and 82.1% (32/39) for O1. The A. tumefaciens-mediated transformation efficiency was 98.2% (55/56) for N1 and 43.8% (28/64) for O1. We also developed a marker-free CRISPR/Cas9 genome editing system using an AMA1-based plasmid to express the Cas9 protein and sgRNA. Out of 22 transformants, 9 albA deletion mutants were constructed in the A. niger N1 background using the protoplast-mediated transformation method and the marker-free CRISPR/Cas9 system developed here. The genome editing methods improved here will accelerate the elucidation of the mechanism of glucoamylase hyperproduction in these industrial fungi and will contribute to the use of efficient targeted mutation in other industrial strains of A. niger.
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Affiliation(s)
- Dandan Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Wenzhu Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yin Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Min Wu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xingji Wang
- Longda Biotechnology Inc., Linyi 276400, China
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Correspondence: (Q.H.); (C.T.); Tel.: +86-10-62731206 (Q.H.); +86-22-84861947 (C.T.)
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Q.H.); (C.T.); Tel.: +86-10-62731206 (Q.H.); +86-22-84861947 (C.T.)
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Wang JW, Han PJ, Han DY, Zhou S, Li K, He PY, Zhen P, Yu HX, Liang ZR, Wang XW, Bai FY. Genetic diversity and population structure of the amylolytic yeast Saccharomycopsis fibuligera associated with Baijiu fermentation in China. J Microbiol 2021; 59:753-762. [PMID: 34219208 DOI: 10.1007/s12275-021-1115-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 11/30/2022]
Abstract
The amylolytic yeast Saccharomycopsis fibuligera is a predominant species in starters and the early fermentation stage of Chinese liquor (Baijiu). However, the genetic diversity of the species remains largely unknown. Here we sequenced the genomes of 97 S. fibuligera strains from different Chinese Baijiu companies. The genetic diversity and population structure of the strains were analyzed based on 1,133 orthologous genes and the whole genome single nucleotide polymorphisms (SNPs). Four main lineages were recognized. One lineage contains 60 Chinese strains which are exclusively homozygous with relatively small genome sizes (18.55-18.72 Mb) and low sequence diversity. The strains clustered in the other three lineages are heterozygous with larger genomes (21.85-23.72 Mb) and higher sequence diversity. The genomes of the homozygous strains showed nearly 100% coverage with the genome of the reference strain KPH12 and the sub-genome A of the hybrid strain KJJ81 at the above 98% sequence identity level. The genomes of the heterozygous strains showed nearly 80% coverage with both the sub-genome A and the whole genome of KJJ81, suggesting that the Chinese heterozygous strains are also hybrids with nearly 20% genomes from an unidentified source. Eighty-three genes were found to show significant copy number variation between different lineages. However, remarkable lineage specific variations in glucoamylase and α-amylase activities and growth profiles in different carbon sources and under different environmental conditions were not observed, though strains exhibiting relatively high glucoamylase activity were mainly found from the homozygous lineage.
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Affiliation(s)
- Ju-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Sen Zhou
- Niulanshan Distillery, Shunxin Agriculture Co. Ltd., Beijing, 101301, P. R. China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Peng-Yu He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Pan Zhen
- ShanxiFenjiu Co. Ltd., Fenyang, Shanxi, 032205, P. R. China
| | - Hui-Xin Yu
- ShanxiFenjiu Co. Ltd., Fenyang, Shanxi, 032205, P. R. China
| | - Zhen-Rong Liang
- Tianlongquan Distillery Co. Ltd., Hechi, Guangxi, 546400, P. R. China
| | - Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
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6
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Božić N, Rozeboom HJ, Lončar N, Slavić MŠ, Janssen DB, Vujčić Z. Characterization of the starch surface binding site on Bacillus paralicheniformis α-amylase. Int J Biol Macromol 2020; 165:1529-1539. [PMID: 33058974 DOI: 10.1016/j.ijbiomac.2020.10.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/03/2020] [Accepted: 10/03/2020] [Indexed: 11/16/2022]
Abstract
α-Amylase from Bacillus paralicheniformis (BliAmy), belonging to GH13_5 subfamily of glycoside hydrolases, was proven to be a highly efficient raw starch digesting enzyme. The ability of some α-amylases to hydrolyze raw starch is related to the existence of surface binding sites (SBSs) for polysaccharides that can be distant from the active site. Crystallographic studies performed on BliAmy in the apo form and of enzyme bound with different oligosaccharides and oligosaccharide precursors revealed binding of these ligands to one SBS with two amino acids F257 and Y358 mainly involved in complex formation. The role of this SBS in starch binding and degradation was probed by designing enzyme variants mutated in this region (F257A and Y358A). Kinetic studies with different substrates show that starch binding through the SBS is disrupted in the mutants and that F257 and Y358 contributed cumulatively to binding and hydrolysis. Mutation of both sites (F257A/Y358A) resulted in a 5-fold lower efficacy with raw starch as substrate and at least 5.5-fold weaker binding compared to the wild type BliAmy, suggesting that the ability of BliAmy to hydrolyze raw starch with high efficiency is related to the level of its adsorption onto starch granules.
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Affiliation(s)
- Nataša Božić
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Henriëtte J Rozeboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Nikola Lončar
- GECCO Biotech, Nijenborgh 4, Groningen 9747AG, the Netherlands
| | - Marinela Šokarda Slavić
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Dick B Janssen
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, the Netherlands
| | - Zoran Vujčić
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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7
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Liu X, Zang X, Yin X, Yang W, Huang J, Huang J, Yu C, Ke C, Hong Y. Semi-synthesis of C28-modified triterpene acid derivatives from maslinic acid or corosolic acid as potential α-glucosidase inhibitors. Bioorg Chem 2020; 97:103694. [DOI: 10.1016/j.bioorg.2020.103694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 02/07/2023]
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8
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Janeček Š, Mareček F, MacGregor EA, Svensson B. Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv 2019; 37:107451. [PMID: 31536775 DOI: 10.1016/j.biotechadv.2019.107451] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 09/15/2019] [Indexed: 01/05/2023]
Abstract
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - E Ann MacGregor
- 2 Nicklaus Green, Livingston EH54 8RX, West Lothian, United Kingdom
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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9
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Baroroh U, Yusuf M, Rachman SD, Ishmayana S, Hasan K, Subroto T. Molecular dynamics study to improve the substrate adsorption of Saccharomycopsis fibuligera R64 alpha-amylase by designing a new surface binding site. Adv Appl Bioinform Chem 2019; 12:1-13. [PMID: 31239719 PMCID: PMC6559716 DOI: 10.2147/aabc.s198110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/19/2019] [Indexed: 11/23/2022] Open
Abstract
Background: Carbohydrate binding module (CBM) and surface binding site (SBS) are two important parts of amylase which respond to the raw starch digestion. They are related to the enzyme ability to adsorb and to catalyze the starch hydrolysis. However, starch processing is still expensive due to the high temperature in the gelatinization step. Therefore, direct starch digestion is more favorable. One of the solutions is to use α-amylase with high starch adsorptivity, which is expected to be capable of digesting starch below the gelatinization temperature. In Indonesia, Saccharomycopsis fibuligera R64 α-amylase (Sfamy R64) is one of the enzymes with the highest activity on starch. However, its raw starch adsorptivity was low. The aim of this study was to propose an in-silico model of Sfamy R64 mutant by introducing a new SBS using molecular dynamics (MD) simulation. Methods: The structural behavior of Sfamy R64 and positive control were studied using MD simulation. Furthermore, the mutants of Sfamy R64 were designed to have a stable SBS which mimics the positive control. The substrate affinity in all systems was evaluated using the molecular mechanics generalized Born surface area (MM/GBSA) method. Results: The stability of a new SBS constructed by seven substitutions and a loop insertion was improved throughout MD simulation. The substrate was consistently bound to the SBS over 55 ns of simulation, as compared to 14 ns in wild-type. The structural behavior of SBS in mutant and positive control was similar. The interaction energies of the positive control, wild-type, and mutant were −17.6, −5.2, and −8.2 kcal/mol, respectively. Conclusion: The enhanced substrate binding in the mutant, due to the existence of a new SBS, suggests the potential of improving starch adsorptivity of Sfamy R64. This result should be useful in developing an enzyme with better substrate adsorption based on the rational computer-aided molecular design approach.
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Affiliation(s)
- Umi Baroroh
- Biotechnology Master Program, Postgraduate School, Universitas Padjadjaran, Bandung 40132, West Java, Indonesia
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia.,Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, West Java, Indonesia
| | - Saadah Diana Rachman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
| | - Safri Ishmayana
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia
| | - Khomaini Hasan
- Faculty of Medicine, Universitas Jenderal Achmad Yani, Cimahi, West Java, Indonesia
| | - Toto Subroto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, West Java, Indonesia.,Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung 40133, West Java, Indonesia
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10
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Wilkens C, Tiwari MK, Webb H, Jam M, Czjzek M, Svensson B. Asp271 is critical for substrate interaction with the surface binding site in β-agarase a from Zobellia galactanivorans. Proteins 2018; 87:34-40. [PMID: 30315603 DOI: 10.1002/prot.25614] [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: 05/17/2018] [Revised: 09/11/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022]
Abstract
In the marine environment agar degradation is assured by bacteria that contain large agarolytic systems with enzymes acting in various endo- and exo-modes. Agarase A (AgaA) is an endo-glycoside hydrolase of family 16 considered to initiate degradation of agarose. Agaro-oligosaccharide binding at a unique surface binding site (SBS) in AgaA from Zobellia galactanivorans was investigated by computational methods in conjunction with a structure/sequence guided approach of site-directed mutagenesis probed by surface plasmon resonance binding analysis of agaro-oligosaccharides of DP 4-10. The crystal structure has shown that agaro-octaose interacts via H-bonds and aromatic stacking along 7 subsites (L through R) of the SBS in the inactive catalytic nucleophile mutant AgaA-E147S. D271 is centrally located in the extended SBS where it forms H-bonds to galactose and 3,6-anhydrogalactose residues of agaro-octaose at subsites O and P. We propose D271 is a key residue in ligand binding to the SBS. Thus AgaA-E147S/D271A gave slightly decreasing KD values from 625 ± 118 to 468 ± 13 μM for agaro-hexaose, -octaose, and -decaose, which represent 3- to 4-fold reduced affinity compared with AgaA-E147S. Molecular dynamics simulations and interaction analyses of AgaA-E147S/D271A indicated disruption of an extended H-bond network supporting that D271 is critical for the functional SBS. Notably, neither AgaA-E147S/W87A nor AgaA-E147S/W277A, designed to eliminate stacking with galactose residues at subsites O and Q, respectively, were produced in soluble form. W87 and W277 may thus control correct folding and structural integrity of AgaA.
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Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Manish K Tiwari
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Helen Webb
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Murielle Jam
- Laboratory for Integrative Biology of Marine Models, Station Biologique, Sorbonne University, Université Pierre et Marie Curie, Roscoff, France
| | - Mirjam Czjzek
- Laboratory for Integrative Biology of Marine Models, Station Biologique, Sorbonne University, Université Pierre et Marie Curie, Roscoff, France
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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11
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Bayraktaroğlu M, Orhan H, Evli S, Akgöl S, Aktaş Uygun D, Uygun M. Lectin attached affinity cryogels for amyloglucosidase adsorption. J Carbohydr Chem 2018. [DOI: 10.1080/07328303.2018.1487972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Melis Bayraktaroğlu
- Faculty of Science and Arts, Chemistry Division, Adnan Menderes University, Aydın, Turkey
| | - Hande Orhan
- Faculty of Science and Arts, Chemistry Division, Adnan Menderes University, Aydın, Turkey
| | - Sinem Evli
- Faculty of Science and Arts, Chemistry Division, Adnan Menderes University, Aydın, Turkey
| | - Sinan Akgöl
- Faculty of Science, Biochemistry Division, Ege University, İzmir, Turkey
| | - Deniz Aktaş Uygun
- Faculty of Science and Arts, Chemistry Division, Adnan Menderes University, Aydın, Turkey
- Nanotechnology Application and Research Center, Adnan Menderes University, Aydın, Turkey
| | - Murat Uygun
- Faculty of Science and Arts, Chemistry Division, Adnan Menderes University, Aydın, Turkey
- Nanotechnology Application and Research Center, Adnan Menderes University, Aydın, Turkey
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12
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The Importance of Surface-Binding Site towards Starch-Adsorptivity Level in α-Amylase: A Review on Structural Point of View. Enzyme Res 2017; 2017:4086845. [PMID: 29359041 PMCID: PMC5735674 DOI: 10.1155/2017/4086845] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 10/31/2017] [Indexed: 12/04/2022] Open
Abstract
Starch is a polymeric carbohydrate composed of glucose. As a source of energy, starch can be degraded by various amylolytic enzymes, including α-amylase. In a large-scale industry, starch processing cost is still expensive due to the requirement of high temperature during the gelatinization step. Therefore, α-amylase with raw starch digesting ability could decrease the energy cost by avoiding the high gelatinization temperature. It is known that the carbohydrate-binding module (CBM) and the surface-binding site (SBS) of α-amylase could facilitate the substrate binding to the enzyme's active site to enhance the starch digestion. These sites are a noncatalytic module, which could interact with a lengthy substrate such as insoluble starch. The major interaction between these sites and the substrate is the CH/pi-stacking interaction with the glucose ring. Several mutation studies on the Halothermothrix orenii, SusG Bacteroides thetaiotamicron, Barley, Aspergillus niger, and Saccharomycopsis fibuligera α-amylases have revealed that the stacking interaction through the aromatic residues at the SBS is essential to the starch adsorption. In this review, the SBS in various α-amylases is also presented. Therefore, based on the structural point of view, SBS is suggested as an essential site in α-amylase to increase its catalytic activity, especially towards the insoluble starch.
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13
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Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13. Sci Rep 2017; 7:44067. [PMID: 28303907 PMCID: PMC5355875 DOI: 10.1038/srep44067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/02/2017] [Indexed: 01/14/2023] Open
Abstract
Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose. Glu221 is one of the three conserved catalytic residues, and AmyP is inactivated by the E221Q mutation. Domain B of AmyPΔSBD forms a loop that protrudes from domain A, stabilizes the conformation of the active site and increases the thermostability of the enzyme. A new calcium ion is situated adjacent to the -3 subsite binding loop and may be responsible for the increased thermostability of the enzyme after the addition of calcium. Moreover, Tyr36 participates in both stacking and hydrogen bonding interactions with the sugar motif at subsite -3. This work provides the first insights into the structure of α-amylases belonging to subfamily 37 of GH13 and may contribute to the rational design of α-amylase mutants with enhanced performance in biotechnological applications.
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14
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Emanuelle S, Brewer MK, Meekins DA, Gentry MS. Unique carbohydrate binding platforms employed by the glucan phosphatases. Cell Mol Life Sci 2016; 73:2765-2778. [PMID: 27147465 PMCID: PMC4920694 DOI: 10.1007/s00018-016-2249-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Glucan phosphatases are a family of enzymes that are functionally conserved at the enzymatic level in animals and plants. These enzymes bind and dephosphorylate glycogen in animals and starch in plants. While the enzymatic function is conserved, the glucan phosphatases employ distinct mechanisms to bind and dephosphorylate glycogen or starch. The founding member of the family is a bimodular human protein called laforin that is comprised of a carbohydrate binding module 20 (CBM20) followed by a dual specificity phosphatase domain. Plants contain two glucan phosphatases: Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). SEX4 contains a chloroplast targeting peptide, dual specificity phosphatase (DSP) domain, a CBM45, and a carboxy-terminal motif. LSF2 is comprised of simply a chloroplast targeting peptide, DSP domain, and carboxy-terminal motif. SEX4 employs an integrated DSP-CBM glucan-binding platform to engage and dephosphorylate starch. LSF2 lacks a CBM and instead utilizes two surface binding sites to bind and dephosphorylate starch. Laforin is a dimeric protein in solution and it utilizes a tetramodular architecture and cooperativity to bind and dephosphorylate glycogen. This chapter describes the biological role of glucan phosphatases in glycogen and starch metabolism and compares and contrasts their ability to bind and dephosphorylate glucans.
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Affiliation(s)
- Shane Emanuelle
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - M. Kathryn Brewer
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - David A. Meekins
- Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
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15
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Wilkens C, Auger KD, Anderson NT, Meekins DA, Raththagala M, Abou Hachem M, Payne CM, Gentry MS, Svensson B. Plant α‐glucan phosphatases SEX4 and LSF2 display different affinity for amylopectin and amylose. FEBS Lett 2016; 590:118-28. [DOI: 10.1002/1873-3468.12027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
| | - Kyle D. Auger
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Nolan T. Anderson
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - David A. Meekins
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Madushi Raththagala
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
| | - Christina M. Payne
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Birte Svensson
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
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16
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Wilkens C, Cockburn D, Andersen S, Ole Petersen B, Ruzanski C, A. Field R, Hindsgaul O, Nakai H, McCleary B, M. Smith A, Abou Hachem M, Svensson B. Analysis of Surface Binding Sites (SBS) within GH62, GH13, and GH77. J Appl Glycosci (1999) 2015. [DOI: 10.5458/jag.jag.jag-2015_006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Darrell Cockburn
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Susan Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Bent Ole Petersen
- Carbohydrate Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10
| | | | | | - Ole Hindsgaul
- Carbohydrate Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10
| | - Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | | | | | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
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17
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Hua H, Luo H, Bai Y, Wang K, Niu C, Huang H, Shi P, Wang C, Yang P, Yao B. A thermostable glucoamylase from Bispora sp. MEY-1 with stability over a broad pH range and significant starch hydrolysis capacity. PLoS One 2014; 9:e113581. [PMID: 25415468 PMCID: PMC4240638 DOI: 10.1371/journal.pone.0113581] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/25/2014] [Indexed: 11/23/2022] Open
Abstract
Background Glucoamylase is an exo-type enzyme that converts starch completely into glucose from the non-reducing ends. To meet the industrial requirements for starch processing, a glucoamylase with excellent thermostability, raw-starch degradation ability and high glucose yield is much needed. In the present study we selected the excellent Carbohydrate-Activity Enzyme (CAZyme) producer, Bispora sp. MEY-1, as the microbial source for glucoamylase gene exploitation. Methodology/Principal Findings A glucoamylase gene (gla15) was cloned from Bispora sp. MEY-1 and successfully expressed in Pichia pastoris with a high yield of 34.1 U/ml. Deduced GLA15 exhibits the highest identity of 64.2% to the glucoamylase from Talaromyces (Rasamsonia) emersonii. Purified recombinant GLA15 was thermophilic and showed the maximum activity at 70°C. The enzyme was stable over a broad pH range (2.2–11.0) and at high temperature up to 70°C. It hydrolyzed the breakages of both α-1,4- and α-1,6-glycosidic linkages in amylopectin, soluble starch, amylose, and maltooligosaccharides, and had capacity to degrade raw starch. TLC and H1-NMR analysis showed that GLA15 is a typical glucoamylase of GH family 15 that releases glucose units from the non-reducing ends of α-glucans. The combination of Bacillus licheniformis amylase and GLA15 hydrolyzed 96.14% of gelatinized maize starch after 6 h incubation, which was about 9% higher than that of the combination with a commercial glucoamylase from Aspergillus niger. Conclusion/Significance GLA15 has a broad pH stability range, high-temperature thermostability, high starch hydrolysis capacity and high expression yield. In comparison with the commercial glucoamylase from A. niger, GLA15 represents a better candidate for application in the food industry including production of glucose, glucose syrups, and high-fructose corn syrups.
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Affiliation(s)
- Huifang Hua
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Kun Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Canfang Niu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Caihong Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Peilong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- CAAS-ICRAF Joint Laboratory on Agroforestry and Sustainable Animal Husbandry, Beijing, 100193, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- * E-mail:
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18
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19
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Bagheri A, Khodarahmi R, Mostafaie A. Purification and biochemical characterisation of glucoamylase from a newly isolated Aspergillus niger: relation to starch processing. Food Chem 2014; 161:270-8. [PMID: 24837950 DOI: 10.1016/j.foodchem.2014.03.095] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/22/2014] [Accepted: 03/19/2014] [Indexed: 11/25/2022]
Abstract
Herein, we investigate a glucoamylase from newly isolated Aspergillus niger. The enzyme was purified, using fractionation, followed by anion-exchange chromatography and then characterised. The molecular mass of the enzyme was estimated to be ∼62,000Da, using SDS-PAGE and 57151Da, based on mass spectrometry results. The pI of the protein, and optimum pH/temperature of enzyme activity were 4.4, 5 and 70°C, respectively and the kinetic parameters (Km, Vmax and kcat) were determined to be 0.33 (mgml(-1)), 0.095 (Uμg(-1)min(-1)) and 158.3 (s(-1)) for soluble starch, respectively. The glucoamylase nature of the enzyme was also confirmed using TLC and a specific substrate. Metal ions Fe(3+), Al(3+) and Hg(2+) had the highest inhibitory effect, while Ag(2)(+), Ca(2+), Zn(2+), Mg(2+) and Cd(2+) and EDTA showed no significant effect on the enzyme activity. In addition, thermal stability of the enzyme increased in the presence of starch and calcium ion. Based on the results, the purified glucoamylase appeared to be a newly isolated enzyme.
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Affiliation(s)
- Ahmad Bagheri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Khodarahmi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Mostafaie
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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20
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Miyazaki T, Ichikawa M, Yokoi G, Kitaoka M, Mori H, Kitano Y, Nishikawa A, Tonozuka T. Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity. FEBS J 2013; 280:4560-71. [DOI: 10.1111/febs.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Takatsugu Miyazaki
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Megumi Ichikawa
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Gaku Yokoi
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Motomitsu Kitaoka
- National Food Research Institute; National Agriculture and Food Research Organization; Tsukuba Ibaraki Japan
| | - Haruhide Mori
- Research Faculty of Agriculture; Hokkaido University; Kita-ku Sapporo Japan
| | - Yoshikazu Kitano
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
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21
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Li Z, Wei P, Cheng H, He P, Wang Q, Jiang N. Functional role of β domain in the Thermoanaerobacter tengcongensis glucoamylase. Appl Microbiol Biotechnol 2013; 98:2091-9. [PMID: 23852641 DOI: 10.1007/s00253-013-5051-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 06/04/2013] [Accepted: 06/10/2013] [Indexed: 11/28/2022]
Abstract
Thermoanaerobacter tengcongensis MB4 glucoamylase (TteGA) contains a catalytic domain (CD), which is structurally similar to eukaryotic GA, and a β domain (BD) with ambiguous function. Firstly, BD is found to be essential to TteGA activity because CD alone could not hydrolyze soluble starch. However, starch hydrolysis activity, similar to that of intact TteGA, was restored to CD in the presence of BD. Secondly, BD is found to be an important helper in the correct folding of CD because CD was mainly expressed in the inclusion bodies on its own in Escherichia coli. By contrast, intact TteGA, BD, and CD combined with BD could be expressed as soluble proteins. Additionally, BD is essential to the thermostability of TteGA because CD displayed lower thermostability compared with the intact TteGA and exhibited enhanced thermostability in the presence of BD in vitro. Truncation of TteGA or mutagenesis of the residues that participate in the interdomain interaction at its BD also led to the reduced thermostability of TteGA.
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Affiliation(s)
- Zilong Li
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
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22
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Meekins DA, Guo HF, Husodo S, Paasch BC, Bridges TM, Santelia D, Kötting O, Vander Kooi CW, Gentry MS. Structure of the Arabidopsis glucan phosphatase like sex four2 reveals a unique mechanism for starch dephosphorylation. THE PLANT CELL 2013; 25:2302-14. [PMID: 23832589 PMCID: PMC3723627 DOI: 10.1105/tpc.113.112706] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/31/2013] [Accepted: 06/12/2013] [Indexed: 05/20/2023]
Abstract
Starch is a water-insoluble, Glc-based biopolymer that is used for energy storage and is synthesized and degraded in a diurnal manner in plant leaves. Reversible phosphorylation is the only known natural starch modification and is required for starch degradation in planta. Critical to starch energy release is the activity of glucan phosphatases; however, the structural basis of dephosphorylation by glucan phosphatases is unknown. Here, we describe the structure of the Arabidopsis thaliana starch glucan phosphatase like sex four2 (LSF2) both with and without phospho-glucan product bound at 2.3Å and 1.65Å, respectively. LSF2 binds maltohexaose-phosphate using an aromatic channel within an extended phosphatase active site and positions maltohexaose in a C3-specific orientation, which we show is critical for the specific glucan phosphatase activity of LSF2 toward native Arabidopsis starch. However, unlike other starch binding enzymes, LSF2 does not possess a carbohydrate binding module domain. Instead we identify two additional glucan binding sites located within the core LSF2 phosphatase domain. This structure is the first of a glucan-bound glucan phosphatase and provides new insights into the molecular basis of this agriculturally and industrially relevant enzyme family as well as the unique mechanism of LSF2 catalysis, substrate specificity, and interaction with starch granules.
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Affiliation(s)
- David A. Meekins
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Hou-Fu Guo
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Satrio Husodo
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Bradley C. Paasch
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Travis M. Bridges
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Diana Santelia
- Institute of Plant Biology, University of Zürich, 8092 Zurich, Switzerland
| | - Oliver Kötting
- Institute for Agricultural Sciences, ETH Zürich, 8092 Zurich, Switzerland
| | - Craig W. Vander Kooi
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40535-0509
- Address correspondence to
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23
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Puspasari F, Radjasa OK, Noer AS, Nurachman Z, Syah YM, van der Maarel M, Dijkhuizen L, Janeček S, Natalia D. Raw starch-degrading α-amylase from Bacillus aquimaris MKSC 6.2: isolation and expression of the gene, bioinformatics and biochemical characterization of the recombinant enzyme. J Appl Microbiol 2012; 114:108-20. [PMID: 23020612 DOI: 10.1111/jam.12025] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 08/18/2012] [Accepted: 08/29/2012] [Indexed: 11/30/2022]
Abstract
AIMS The aims were to isolate a raw starch-degrading α-amylase gene baqA from Bacillus aquimaris MKSC 6.2, and to characterize the gene product through in silico study and its expression in Escherichia coli. METHODS AND RESULTS A 1539 complete open reading frame of a starch-degrading α-amylase gene baqA from B. aquimaris MKSC 6·2 has been determined by employing PCR and inverse PCR techniques. Bioinformatics analysis revealed that B. aquimaris MKSC 6.2 α-amylase (BaqA) has no starch-binding domain, and together with a few putative α-amylases from bacilli may establish a novel GH13 subfamily most closely related to GH13_1. Two consecutive tryptophans (Trp201 and Trp202, BaqA numbering) were identified as a sequence fingerprint of this novel GH13 subfamily. Escherichia coli cells produced the recombinant BaqA protein as inclusion bodies. The refolded recombinant BaqA protein degraded raw cassava and corn starches, but exhibited no activity with soluble starch. CONCLUSIONS A novel raw starch-degrading B. aquimaris MKSC 6.2 α-amylase BaqA is proposed to be a member of new GH13 subfamily. SIGNIFICANCE AND IMPACT OF THE STUDY This study has contributed to the overall knowledge and understanding of amylolytic enzymes that are able to bind and digest raw starch directly.
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Affiliation(s)
- F Puspasari
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
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24
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Cuyvers S, Dornez E, Delcour JA, Courtin CM. Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases. Crit Rev Biotechnol 2011; 32:93-107. [DOI: 10.3109/07388551.2011.561537] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Cuyvers S, Dornez E, Rezaei MN, Pollet A, Delcour JA, Courtin CM. Secondary substrate binding strongly affects activity and binding affinity of Bacillus subtilis and Aspergillus niger GH11 xylanases. FEBS J 2011; 278:1098-111. [PMID: 21261814 DOI: 10.1111/j.1742-4658.2011.08023.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The secondary substrate binding site (SBS) of Bacillus subtilis and Aspergillus niger glycoside hydrolase family 11 xylanases was studied by site-directed mutagenesis and evaluation of activity and binding properties of mutant enzymes on different substrates. Modification of the SBS resulted in an up to three-fold decrease in the relative activity of the enzymes on polymeric versus oligomeric substrates and highlighted the importance of several amino acids in the SBS forming hydrogen bonds or hydrophobic stacking interactions with substrates. Weakening of the SBS increased K(d) values by up to 70-fold in binding affinity tests using natural substrates. The impact that modifications in the SBS have both on activity and on binding affinity towards polymeric substrates clearly shows that such structural elements can increase the efficiency of these single domain enzymes on their natural substrates.
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Affiliation(s)
- Sven Cuyvers
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Leuven, Belgium
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26
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Lee J, Paetzel M. Structure of the catalytic domain of glucoamylase from Aspergillus niger. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:188-92. [PMID: 21301084 DOI: 10.1107/s1744309110049390] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 11/25/2010] [Indexed: 11/10/2022]
Abstract
Glucoamylase from Aspergillus niger is an industrially important biocatalyst that is utilized in the mass production of glucose from raw starch or soluble oligosaccharides. The G1 isoform consists of a catalytic domain and a starch-binding domain connected by a heavily glycosylated linker region. The amino-terminal catalytic domain of the G1 isoform generated by subtilisin cleavage has been crystallized at pH 8.5, which is a significantly higher pH condition than used for previously characterized glucoamylase crystals. The refined structure at 1.9 Å resolution reveals the active site of the enzyme in complex with both Tris and glycerol molecules. The ligands display both unique and analogous interactions with the substrate-binding site when compared with previous structures of homologous enzymes bound to inhibitors.
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Affiliation(s)
- Jaeyong Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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28
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Glucoamylases: structural and biotechnological aspects. Appl Microbiol Biotechnol 2010; 89:1267-73. [DOI: 10.1007/s00253-010-3034-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 11/26/2022]
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30
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Hostinová E, Janeček Š, Gašperík J. Gene Sequence, Bioinformatics and Enzymatic Characterization of α-Amylase from Saccharomycopsis fibuligera KZ. Protein J 2010; 29:355-64. [DOI: 10.1007/s10930-010-9260-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Koropatkin NM, Smith TJ. SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 2010; 18:200-15. [PMID: 20159465 DOI: 10.1016/j.str.2009.12.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 11/19/2022]
Abstract
SusG is an alpha-amylase and part of a large protein complex on the outer surface of the bacterial cell and plays a major role in carbohydrate acquisition by the animal gut microbiota. Presented here, the atomic structure of SusG has an unusual extended, bilobed structure composed of amylase at one end and an unprecedented internal carbohydrate-binding motif at the other. Structural studies further demonstrate that the carbohydrate-binding motif binds maltooligosaccharide distal to, and on the opposite side of, the amylase catalytic site. SusG has an additional starch-binding site on the amylase domain immediately adjacent to the active cleft. Mutagenesis analysis demonstrates that these two additional starch-binding sites appear to play a role in catabolism of insoluble starch. However, elimination of these sites has only a limited effect, suggesting that they may have a more important role in product exchange with other Sus components.
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Kumar P, Satyanarayana T. Microbial glucoamylases: characteristics and applications. Crit Rev Biotechnol 2009; 29:225-55. [DOI: 10.1080/07388550903136076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Nielsen MM, Bozonnet S, Seo ES, Mótyán JA, Andersen JM, Dilokpimol A, Abou Hachem M, Gyémánt G, Næsted H, Kandra L, Sigurskjold BW, Svensson B. Two Secondary Carbohydrate Binding Sites on the Surface of Barley α-Amylase 1 Have Distinct Functions and Display Synergy in Hydrolysis of Starch Granules. Biochemistry 2009; 48:7686-97. [DOI: 10.1021/bi900795a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Morten M. Nielsen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Sophie Bozonnet
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
| | - Eun-Seong Seo
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - János A. Mótyán
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Joakim M. Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Gyöngyi Gyémánt
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Henrik Næsted
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Lili Kandra
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Bent W. Sigurskjold
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
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34
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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