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Zhao Y, Zhang B, Gu H, Xu T, Chen Q, Li J, Zhou P, Guan X, He L, Liang Y, Zhang K, Liu S, Shi K. A mutant GH3 family β-glucosidase from Oenococcus oeni exhibits superior adaptation to wine stresses and potential for improving wine aroma and phenolic profiles. Food Microbiol 2024; 119:104458. [PMID: 38225057 DOI: 10.1016/j.fm.2023.104458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024]
Abstract
In this study, we conducted a comprehensive investigation into a GH3 family β-glucosidase (BGL) from the wild-type strain of Oenococcus oeni and its mutated counterpart from the acid-tolerant mutant strain. Our analysis revealed the mutant BGL's remarkable capacity to adapt to wine-related stress conditions, including heightened tolerance to low pH, elevated ethanol concentrations, and metal ions. Additionally, the mutant BGL exhibited superior hydrolytic activity towards various substrates. Through de novo modeling, we identified specific amino acid mutations responsible for its resilience to low pH and high ethanol environments. In simulated wine conditions, the mutant BGL outperformed both wild-type and commercial BGLs, efficiently releasing terpene and phenolic aglycones from glycosides in wine grapes. These findings not only expand our understanding of O. oeni BGLs but also highlight their potential in enhancing wine production. The mutant BGL's enhanced adaptation to wine stress conditions opens promising avenue for improving wine quality and flavor.
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Affiliation(s)
- Yuzhu Zhao
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Biying Zhang
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Huawei Gu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Tongxin Xu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiling Chen
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Jin Li
- COFCO GreatWall Wine, Penglai, Shandong, China
| | | | - Xueqiang Guan
- Shandong Academy of Grape / Shandong Technology Innovation Center of Wine Grape and Wine, Jinan, Shandong, China
| | - Ling He
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanying Liang
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Kekun Zhang
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuwen Liu
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China.
| | - Kan Shi
- College of Enology, College of Life Sciences, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Life Science Research Core Services, Northwest A&F University, Yangling, Shaanxi, China.
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Wahhab BH, Oyewusi HA, Wahab RA, Mohammad Hood MH, Abdul Hamid AA, Al-Nimer MS, Edbeib MF, Kaya Y, Huyop F. Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey. J Biomol Struct Dyn 2024; 42:1429-1442. [PMID: 37038649 DOI: 10.1080/07391102.2023.2199870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 04/01/2023] [Indexed: 04/12/2023]
Abstract
This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Batool Hazim Wahhab
- Department of Microbiology, Faculty of Medicine, Al-Mustansiriyah University, Iraq
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Marwan Salih Al-Nimer
- Department of Pharmacology, College of Medicine, University of Diyala, Baqubah, Iraq
| | - Mohamed Faraj Edbeib
- Department of Medical Laboratories, Faculty of Medical Technology, Bani Walid University, Libya
| | - Yilmaz Kaya
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
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Mohammad Hood MH, Tengku Abdul Hamid TH, Abdul Wahab RA, Huyop FZ, Kaya Y, Abdul Hamid AAA. Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic Macrophomina phaseolina. J Biomol Struct Dyn 2022; 41:2831-2847. [PMID: 35174777 DOI: 10.1080/07391102.2022.2039772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Efficacy of a β-1,4-glucosidase from Trichoderma harzianum T12 (ThBglT12) in disrupting the cell wall of the phytopathogenic fungus M. phaseolina (Macrophomina phaseolina) was studied, as the underlying molecular mechanisms of cell wall recognition remains elusive. In this study, the binding location identified by a consensus of residues predicted by COACH tool, blind docking, and multiple sequence alignment revealed that molecular recognition by ThBglT12 occurred through interactions between the α-1,3-glucan, β-1,3-glucan, β-1,3/1,4-glucan, and chitin components of M. phaseolina, with corresponding binding energies of -7.4, -7.6, -7.5 and -7.8 kcal/mol. The residue consensus verified the participation of Glu172, Tyr304, Trp345, Glu373, Glu430, and Trp431 in the active site pocket of ThBglT12 to bind the ligands, of which Trp345 was the common interacting residue. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), total energy, and minimum distance calculation from molecular dynamics (MD) simulation further confirmed the stability and the closeness of the binding ligands into the ThBglT12 active site pocket. The h-bond occupancy by Glu373 and Trp431 instated the role of the nucleophile for substrate recognition and specificity, crucial for cleaving the β-1,4 linkage. Further investigation showed that the proximity of Glu373 to the anomeric carbon of β-1,3/1,4-glucan (3.5 Å) and chitin (5.5 Å) indicates the nucleophiles' readiness to form enzyme-substrate intermediates. Plus, the neighboring water molecule appeared to be correctly positioned and oriented towards the anomeric carbon to hydrolyze the β-1,3/1,4-glucan and chitin, in less than 4.0 Å. In a nutshell, the study verified that the ThBglT12 is a good alternative fungicide to inhibit the growth of M. phaseolina.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Pahang, Malaysia
| | - Tengku Haziyamin Tengku Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Pahang, Malaysia
| | - Roswanira Abdul Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, UTM Johor Bahru, Malaysia
| | - Fahrul Zaman Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Yilmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Turkey
| | - Azzmer Azzar Abdul Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Pahang, Malaysia.,Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan, Pahang, Malaysia
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Solhtalab M, Klein AR, Aristilde L. Hierarchical Reactivity of Enzyme-Mediated Phosphorus Recycling from Organic Mixtures by Aspergillus niger Phytase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2295-2305. [PMID: 33305954 DOI: 10.1021/acs.jafc.0c05924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biological recycling of inorganic phosphorus (Pi) from organic phosphorus (Po) compounds by phosphatase-type enzymes, including phytases, is an important contributor to the pool of bioavailable P to plants and microorganisms. However, studies of mixed-substrate reactions with these enzymes are lacking. Here, we explore the reactivity of a phytase extract from the fungus Aspergillus niger toward a heterogeneous mixture containing, in addition to phytate, different structures of environmentally relevant Po compounds such as ribonucleotides and sugar phosphates. Using a high-resolution liquid chromatography-mass spectrometry method to monitor simultaneously the parent Po compounds and their by-products, we captured sequential substrate-specific evolution of Pi from the mixture, with faster hydrolysis of multiphosphorylated compounds (phytate, diphosphorylated sugars, and di- and tri-phosphorylated ribonucleotides) than hydrolysis of monophosphorylated compounds (monophosphorylated sugars and monophosphorylated ribonucleotides). The interaction mechanisms and energies revealed by molecular docking simulations of each Po compound within the enzyme's active site explained the substrate hierarchy observed experimentally. Specifically, the favorable orientation for binding of the negatively charged phosphate moieties with respect to the positive potential surface of the active site was important. Collectively, our findings provide mechanistic insights about the broad but hierarchical role of phytase-type enzymes in Pi recycling from the heterogeneous assembly of Po compounds in agricultural soils or wastes.
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Affiliation(s)
- Mina Solhtalab
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Annaleise R Klein
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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Konar S, Sinha SK, Datta S, Ghorai PK. Probing the Effect of Glucose on the Activity and Stability of β-Glucosidase: An All-Atom Molecular Dynamics Simulation Investigation. ACS OMEGA 2019; 4:11189-11196. [PMID: 31460219 PMCID: PMC6648728 DOI: 10.1021/acsomega.9b00509] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/10/2019] [Indexed: 05/11/2023]
Abstract
β-Glucosidase (EC 3.2.1.21) plays an essential role in the removal of glycosyl residues from disaccharide cellobiose to produce glucose during the hydrolysis of lignocellulosic biomass. Although there exist a few β-glucosidase that are tolerant to large concentrations of glucose, these enzymes are typically prone to glucose inhibition. Understanding the basis of this inhibition is important for the production of cheaper biofuels from lignocellulose. In this study, all-atom molecular dynamics simulation at different temperatures and glucose concentrations was used to understand the molecular basis of glucose inhibition of GH1 β-glucosidase (B8CYA8) from Halothermothrix orenii. Our results show that glucose induces a broadening of the active site tunnel through residues lining the tunnel and facilitates the accumulation of glucose. In particular, we observed that glucose accumulates at the tunnel entrance and near the catalytic sites to block substrate accessibility and inhibit enzyme activity. The reduction of enzyme activity was also confirmed experimentally through specific activity measurements in the presence of 0-2.5 M glucose. We also show that the increase in glucose concentrations leads to a decrease in the number of water molecules inside the tunnel to affect substrate hydrolysis. Overall, the results help in understanding the role of residues along the active site tunnel for the engineering of glucose-tolerant β-glucosidase.
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Affiliation(s)
- Sukanya Konar
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Sushant K. Sinha
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Supratim Datta
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
- E-mail: (S.D.)
| | - Pradip Kr. Ghorai
- Department
of Chemical Sciences, Protein Engineering Laboratory, Department
of Biological Sciences, Centre for Advanced Functional Materials, and Centre for Climate
Change and Environmental Sciences, Indian
Institute of Science Education and Research Kolkata, Mohanpur 741246, India
- E-mail: (P.K.G.)
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Substrate binding versus escape dynamics in a pH-affected fungal beta-glucosidase revealed by molecular dynamics simulations. Carbohydr Res 2019; 472:127-131. [PMID: 30579119 DOI: 10.1016/j.carres.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 11/26/2018] [Accepted: 12/08/2018] [Indexed: 11/22/2022]
Abstract
The cellulolytic ability of fungal species is important to both natural and engineered biocycling of plant matter. One essential step is the conversion of cellobiose into glucose catalyzed by beta-glucosidases. Mutagenesis studies have implicated altering the substrate binding pocket to influence the pH-activity profile of this enzyme. However, structural understanding of the pH-affected substrate binding environment is lacking. Here we conducted molecular dynamics simulations of fully hydrated TrBgl2, a beta-glucosidase of Trichoderma reesei, equilibrated at its optimal pH (pH 6) and two unfavorable pHs (pH 5 and pH 7.5). We identified structural arrangement of specific residues that facilitated substrate escape from the catalytic site at pH 5 but locked the bound substrate in an unfavorable orientation at pH 7.5. For comparative analysis, we also performed simulations of a mutated TrBgl2 with previously demonstrated improved catalysis as a function of pH. We captured the responsible conformational changes in the engineered substrate binding pocket.
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Smith L, Mullin S, Schapira AHV. Insights into the structural biology of Gaucher disease. Exp Neurol 2017; 298:180-190. [PMID: 28923368 DOI: 10.1016/j.expneurol.2017.09.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/08/2017] [Accepted: 09/14/2017] [Indexed: 01/08/2023]
Abstract
Gaucher disease, the most common lysosomal storage disorder, is caused by mutations in the gene encoding the acid-β-glucosidase lysosomal hydrolase enzyme that cleaves glucocerebroside into glucose and ceramide. Reduced enzyme activity and impaired structural stability arise due to >300 known disease-causing mutations. Several of these mutations have also been associated with an increased risk of Parkinson disease (PD). Since the discovery of the acid-β-glucosidase X-ray structure, there have been major advances in our understanding of the structural properties of the protein. Analysis of specific residues has provided insight into their functional and structural importance and provided insight into the pathogenesis of Gaucher disease and the contribution to PD. Disease-causing mutations are positioned throughout the acid-β-glucosidase structure, with many located far from the active site and thus retaining some enzymatic activity however, thus far no clear relationship between mutation location and disease severity has been established. Here, we review the crystal structure of acid-β-glucosidase, while highlighting important structural aspects of the protein in detail. This review discusses the structural stability of acid-β-glucosidase, which can be altered by pH and glycosylation, and explores the relationship between known Gaucher disease and PD mutations, structural stability and disease severity.
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Affiliation(s)
- Laura Smith
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London, NW3 2PF, UK
| | - Stephen Mullin
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London, NW3 2PF, UK
| | - Anthony H V Schapira
- Department of Clinical Neurosciences, Institute of Neurology, University College London, London, NW3 2PF, UK.
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Inactivation kinetics and conformation change of Hypocrea orientalis β-glucosidase with guanidine hydrochloride. J Biosci Bioeng 2017; 124:143-149. [DOI: 10.1016/j.jbiosc.2017.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/08/2017] [Indexed: 01/05/2023]
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Molecular Structural Basis for the Cold Adaptedness of the Psychrophilic β-Glucosidase BglU in Micrococcus antarcticus. Appl Environ Microbiol 2016; 82:2021-2030. [PMID: 26801571 DOI: 10.1128/aem.03158-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/14/2016] [Indexed: 02/02/2023] Open
Abstract
Psychrophilic enzymes play crucial roles in cold adaptation of microbes and provide useful models for studies of protein evolution, folding, and dynamic properties. We examined the crystal structure (2.2-Å resolution) of the psychrophilic β-glucosidase BglU, a member of the glycosyl hydrolase 1 (GH1) enzyme family found in the cold-adapted bacterium Micrococcus antarcticus. Structural comparison and sequence alignment between BglU and its mesophilic and thermophilic counterpart enzymes (BglB and GlyTn, respectively) revealed two notable features distinct to BglU: (i) a unique long-loop L3 (35 versus 7 amino acids in others) involved in substrate binding and (ii) a unique amino acid, His299 (Tyr in others), involved in the stabilization of an ordered water molecule chain. Shortening of loop L3 to 25 amino acids reduced low-temperature catalytic activity, substrate-binding ability, the optimal temperature, and the melting temperature (Tm). Mutation of His299 to Tyr increased the optimal temperature, the Tm, and the catalytic activity. Conversely, mutation of Tyr301 to His in BglB caused a reduction in catalytic activity, thermostability, and the optimal temperature (45 to 35°C). Loop L3 shortening and H299Y substitution jointly restored enzyme activity to the level of BglU, but at moderate temperatures. Our findings indicate that loop L3 controls the level of catalytic activity at low temperatures, residue His299 is responsible for thermolability (particularly heat lability of the active center), and long-loop L3 and His299 are jointly responsible for the psychrophilic properties. The described structural basis for the cold adaptedness of BglU will be helpful for structure-based engineering of new cold-adapted enzymes and for the production of mutants useful in a variety of industrial processes at different temperatures.
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