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Mirzaee Z, Jafarian V, Khalifeh K. Enhancement of the structure and biochemical function of cyclomaltodextrinase from the Anoxybacillus flavithermus ZNU-NGA with site-directed mutagenesis. Int Microbiol 2024:10.1007/s10123-024-00554-2. [PMID: 38980560 DOI: 10.1007/s10123-024-00554-2] [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: 01/31/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
This study was conducted to examine the role of the central domain of cyclomaltodextrinase in terms of stability, substrate specificity, becoming dodecameric form, and enzyme activity. To this end, H403R/L309V double-point mutation and T280Q single-point mutation were performed at the central domain and (β/α)8-barrel. The results indicated that the activity of the H403R/L309V mutant at the optimal pH and temperature increased by about 25% and 40%, respectively. Plus, the irreversible thermal inactivation of the H403R/L309V mutant at 60 °C and 160 min was approximately twice of the enzyme without mutation. Both mutants underwent significant structural change relative to the wild enzyme and subsequently a significant catalytic activity. However, the catalytic efficiency (kcat/Km) of the H403R/L309V mutant increased in the presence of beta- and gamma-cyclomaltodextrin substrates compared to the wild enzyme and T280Q mutant. As a result, by applying the L309V mutant and given the smaller size of the valine, leucine spatial inhibition in the wild protein seems to decline, and also it facilitates the substrate access to active site amino acids. Moreover, as gamma substrate is larger, eliminating the effect of spatial inhibition on this substrate has a greater effect on improving the catalytic activity of this enzyme.
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Affiliation(s)
- Ziba Mirzaee
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey.
| | - Vahab Jafarian
- Department of Biology, Faculty of Sciences, University of Guilan, Guilan, Iran.
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
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Chen L, Yi Z, Fang Y, Jin Y, Xiao Y, Zhao D, Luo H, He H, Sun Q, Zhao H. Uncovering key residues responsible for the thermostability of a thermophilic 1,3(4)-β-d-glucanase from Nong flavor Daqu by rational design. Enzyme Microb Technol 2020; 142:109672. [PMID: 33220875 DOI: 10.1016/j.enzmictec.2020.109672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 11/17/2022]
Abstract
Fungal 1,3(4)-β-D-glucanases were usually applied in brewing and feedstuff industries, however, the thermostability limits the most their application. The characterized 1,3(4)-β-D-glucanase (NFEg16A) from Chinese Nong-flavor (NF) Daqu showed the highest thermostability among GH16 fungal 1,3(4)-β-D-glucanases, with half-lives of thermal inactivation (t1/2) of 44.9 min at 90 °C, so multiple rational designs were used to identify the key residues for its thermostability. Based on protein sequence and 3D structure analyses around the catalytic regions. Nine site-mutants were constructed, among which N173Y and S187A were identified as the most thermotolerant and thermolabile ones, with t1/2 values of 61 min and 14.0 min at 90 °C, respectively. Therefore, N173 and S187 were then selected as "hotspots" for site-saturation mutagenesis. Interestingly, most of the N173 and S187 variants exhibited a similar thermostability to that of N173Y and S187A, respectively, confirming their different roles in the thermostability of NFEg16A. In addition, each S187A and its surrounding substitutions (D144 N and T164 N) was independently detrimental to the thermostability of NFEg16A, since the t1/2 (90 °C) of S187A, D144 N and T164 N were 14.0 min, 20.6 min and 27.2 min, respectively. Surprisingly, combinatorial substitution of S187A with D144 N or T164 N showed positive effects on the thermostability, with the increase of t1/2 (90 °C) to 30.9 min and 63.5 min for S187A-D144 N and S187A-T164 N, respectively. More importantly, S187A-T164 N showed higher thermostability than that of wild type. In short, we successfully identified two key sites and their surrounding residues in response to the thermostability of NFEg16A and further improved its thermostability by several rational designs. These findings could be used for the protein engineering of homologous 1,3(4)-β-D-glucanases, as well as other enzyme family members with high similarities.
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Affiliation(s)
- Lanchai Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhuolin Yi
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yao Xiao
- Analytical and Testing Center, Sichuan University of Science and Engineering, Zigong 643000, PR China
| | - Dong Zhao
- Wuliangye Group, Yibin 644007, PR China
| | - Huibo Luo
- Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Bioengineering College, Sichuan University of Science & Engineering, Zigong 64300, PR China
| | - Hui He
- Department of Liquor Making Engineering, Moutai College, Renhuai 564501, PR China
| | - Qun Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.
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Mehrvand J, Hayati Roodbari N, Hassani L, Jafarian V, Khalifeh K. An evolution-based designing and characterization of mutants of cyclomaltodextrinase: Molecular modeling and spectroscopic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 230:118055. [PMID: 31955121 DOI: 10.1016/j.saa.2020.118055] [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: 10/31/2019] [Revised: 01/05/2020] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
Cyclomaltodextrinase (CDase) is a member of the alpha-amylase family GH13, the subfamily GH13_20. In addition to CDase and neopullulanase, this subfamily also contains maltogenic amylase. They have common structural features, but different substrate specificity. In current work, a combination of bioinformatics and experimental tools were used for designing and constructions of single and double mutants of a new variant of CDase from Anoxybacillus flavithermus. Considering the evolutionary variable positions 123 and 127 at the dimer interface of subunits in the alpha-amylase family, these positions in CDase were modified and three mutants, including A123V, C127Q and A123V/C127Q were constructed. The tertiary structure of WT and mutants were made with the MODELLER program, and the phylogenetic tree of homologous protein sequences was built with selected programs in Phylip package. Enzyme kinetic studies revealed that the catalytic efficiency of mutants, especially double one, is lower than the WT enzyme. Heat-induced denaturation experiments were monitored by measuring the UV/Vis signal at 280 nm, and it was found that WT protein is structurally more stable at 25 °C. However, it is more susceptible to changes in temperature compared to the double mutant. It was concluded that the positions 123 and 127 at the dimeric interface of CDase, not only could affect the conformational stability; but also; the catalytic properties of the enzyme by setting up the active site configuration in the dimeric state.
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Affiliation(s)
- Jamshid Mehrvand
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Nasim Hayati Roodbari
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Leila Hassani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Vahab Jafarian
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
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