1
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Ma J, Jiang Z, Yan Q, Lv A, Li Y, Yang S. Structural and functional analysis of SpGlu64A: a novel glycoside hydrolase family 64 laminaripentaose-producing β-1,3-glucanase from Streptomyces pratensis. FEBS J 2024; 291:2009-2022. [PMID: 38380733 DOI: 10.1111/febs.17094] [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: 09/07/2023] [Revised: 01/05/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
Laminaripentaose (L5)-producing β-1,3-glucanases can preferentially cleave the triple-helix curdlan into β-1,3-glucooligosaccharides, especially L5. In this study, a newly identified member of the glycoside hydrolase family 64, β-1,3-glucanase from Streptomyces pratensis (SpGlu64A), was functionally and structurally characterized. SpGlu64A shared highest identity (30%) with a β-1,3-glucanase from Streptomyces matensis. The purified SpGlu64A showed maximal activity at pH 7.5 and 50 °C, and exhibited strict substrate specificity toward curdlan (83.1 U·mg-1). It efficiently hydrolyzed curdlan to produce L5 as the end product. The overall structure of SpGlu64A consisted of a barrel domain and a mixed (α/β) domain, which formed an unusually wide groove with a crescent-like structure. In the two complex structures (SpGlu64A-L3 and SpGlu64A-L4), two oligosaccharide chains were captured and the triple-helical structure was relatively compatible with the wide groove, which suggested the possibility of binding to the triple-helical β-1,3-glucan. A catalytic framework (β6-β9-β10) and the steric hindrance formed by the side chains of residues Y161, N163, and H393 in the catalytic groove were predicted to complete the exotype-like cleavage manner. On the basis of the structure, a fusion protein with the CBM56 domain (SpGlu64A-CBM) and a mutant (Y161F; by site-directed mutation) were obtained, with 1.2- and 1.7-fold increases in specific activity, respectively. Moreover, the combined expression of SpGlu64A-CBM and -Y161F improved the enzyme activity by 2.63-fold. The study will not only be helpful in understanding the reaction mechanism of β-1,3-glucanases but will also provide a basis for further enzyme engineering.
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Affiliation(s)
- Junwen Ma
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Qiaojuan Yan
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing, China
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, China
| | - Ang Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yanxiao Li
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing, China
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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2
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Takashima T, Komori N, Uechi K, Taira T. Characterization of an antifungal β-1,3-glucanase from Ficus microcarpa latex and comparison of plant and bacterial β-1,3-glucanases for fungal cell wall β-glucan degradation. PLANTA 2023; 258:116. [PMID: 37946063 DOI: 10.1007/s00425-023-04271-4] [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: 06/28/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023]
Abstract
MAIN CONCLUSION Each β-1,3-glucanase with antifungal activity or yeast lytic activity hydrolyzes different structures of β-1,3-glucans in the fungal cell wall, respectively. Plants express several glycoside hydrolases that target chitin and β-glucan in fungal cell walls and inhibit pathogenic fungal infection. An antifungal β-1,3-glucanase was purified from gazyumaru (Ficus microcarpa) latex, designated as GlxGluA, and the corresponding gene was cloned and expressed in Escherichia coli. The sequence shows that GlxGluA belongs to glycoside hydrolase family 17 (GH17). To investigate how GlxGluA acts to degrade fungal cell wall β-glucan, it was compared with β-1,3-glucanase with different substrate specificities. We obtained recombinant β-1,3-glucanase (designated as CcGluA), which belongs to GH64, from the bacterium Cellulosimicrobium cellulans. GlxGluA inhibited the growth of the filamentous fungus Trichoderma viride but was unable to lyse the yeast Saccharomyces cerevisiae. In contrast, CcGluA lysed yeast cells but had a negligible inhibitory effect on the growth of filamentous fungi. GlxGluA degraded the cell wall of T. viride better than CcGluA, whereas CcGluA degraded the cell wall of S. cerevisiae more efficiently than GlxGluA. These results suggest that the target substrates in fungal cell walls differ between GlxGluA (GH17 class I β-1,3-glucanase) and CcGluA (GH64 β-1,3-glucanase).
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Affiliation(s)
- Tomoya Takashima
- Department of Bioscience and Biotechnology, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Nao Komori
- Department of Bioscience and Biotechnology, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Keiko Uechi
- Department of Bioscience and Biotechnology, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Toki Taira
- Department of Bioscience and Biotechnology, University of the Ryukyus, Okinawa, 903-0213, Japan.
- Graduate School of Agricultural Science, Kagoshima University, Kagoshima, 890-8580, Japan.
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3
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Lu Z, Rämgård C, Ergenlioğlu İ, Sandin L, Hammar H, Andersson H, King K, Inman AR, Hao M, Bulone V, McKee LS. Multiple enzymatic approaches to hydrolysis of fungal β-glucans by the soil bacterium Chitinophaga pinensis. FEBS J 2023. [PMID: 36610032 DOI: 10.1111/febs.16720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
The genome of the soil Bacteroidota Chitinophaga pinensis encodes a large number of glycoside hydrolases (GHs) with noteworthy features and potentially novel functions. Several are predicted to be active on polysaccharide components of fungal and oomycete cell walls, such as chitin, β-1,3-glucan and β-1,6-glucan. While several fungal β-1,6-glucanase enzymes are known, relatively few bacterial examples have been characterised to date. We have previously demonstrated that C. pinensis shows strong growth using β-1,6-glucan as the sole carbon source, with the efficient release of oligosaccharides from the polymer. We here characterise the capacity of the C. pinensis secretome to hydrolyse the β-1,6-glucan pustulan and describe three distinct enzymes encoded by its genome, all of which show different levels of β-1,6-glucanase activity and which are classified into different GH families. Our data show that C. pinensis has multiple tools to deconstruct pustulan, allowing the species' broad utility of this substrate, with potential implications for bacterial biocontrol of pathogens via cell wall disruption. Oligosaccharides derived from fungal β-1,6-glucans are valuable in biomedical research and drug synthesis, and these enzymes could be useful tools for releasing such molecules from microbial biomass, an underexploited source of complex carbohydrates.
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Affiliation(s)
- Zijia Lu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Carl Rämgård
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - İrem Ergenlioğlu
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lova Sandin
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Hugo Hammar
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Helena Andersson
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Katharine King
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Annie R Inman
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Mengshu Hao
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,College of Medicine & Public Health, Flinders University, Adelaide, SA, Australia
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Centre, Stockholm, Sweden
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4
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Calloni RD, Muchut RJ, Garay AS, Arias DG, Iglesias AA, Guerrero SA. Functional and structural characterization of an endo-β-1,3-glucanase from Euglena gracilis. Biochimie 2022; 208:117-128. [PMID: 36586565 DOI: 10.1016/j.biochi.2022.12.016] [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: 09/14/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Endo-β-1,3-glucanases from several organisms have attracted much attention in recent years because of their capability for in vitro degrading β-1,3-glucan as a critical step for both biofuels production and short-chain oligosaccharides synthesis. In this study, we biochemically characterized a putative endo-β-1,3-glucanase (EgrGH64) belonging to the family GH64 from the single-cell protist Euglena gracilis. The gene coding for the enzyme was heterologously expressed in a prokaryotic expression system supplemented with 3% (v/v) ethanol to optimize the recombinant protein right folding. Thus, the produced enzyme was highly purified by immobilized-metal affinity and gel filtration chromatography. The enzymatic study demonstrated that EgrGH64 could hydrolyze laminarin (KM 23.5 mg ml-1,kcat 1.20 s-1) and also, but with less enzymatic efficiency, paramylon (KM 20.2 mg ml-1,kcat 0.23 ml mg-1 s-1). The major product of the hydrolysis of both substrates was laminaripentaose. The enzyme could also use ramified β-glucan from the baker's yeast cell wall as a substrate (KM 2.10 mg ml-1, kcat 0.88 ml mg-1 s-1). This latter result, combined with interfacial kinetic analysis evidenced a protein's greater efficiency for the yeast polysaccharide, and a higher number of hydrolysis sites in the β-1,3/β-1,6-glucan. Concurrently, the enzyme efficiently inhibited the fungal growth when used at 1.0 mg/mL (15.4 μM). This study contributes to assigning a correct function and determining the enzymatic specificity of EgrGH64, which emerges as a relevant biotechnological tool for processing β-glucans.
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Affiliation(s)
- Rodrigo D Calloni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Robertino J Muchut
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina
| | - Alberto S Garay
- Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Diego G Arias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sergio A Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.
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5
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Wang Y, Zhao Y, Wang X, Zhong L, Fan Q, Lan Z, Ye X, Huang Y, Li Z, Cui Z. Functional Characterization of the Novel Laminaripentaose-Producing β-1,3-Glucanase MoGluB and Its Biocontrol of Magnaporthe oryzae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9571-9584. [PMID: 34378924 DOI: 10.1021/acs.jafc.1c03072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fungal cell wall synthesizing enzymes or remodeling enzymes represent key factors for the interaction of plant pathogen and antifungal agents, which are regarded as potential biocontrol agents. In this study, a novel endo-β-1,3-glucanase from Magnaporthe oryzae was expressed and characterized. The expression of MoGluB was significantly upregulated after 2 days of liquid culture and 48 h after infection, indicating that it may be involved in cell wall reconstitution. Purified MoGluB exhibited high activity on insoluble β-glucans, with a specific activity of 8.18 U/mg toward yeast glucan at pH 9.0 and 50 °C. MoGluB hydrolyzed pachymaran and yeast glucan into oligosaccharides dominated by laminaripentaose, suggesting that it is an endo-β-1,3-glucanase. Incubation of 8 μg of MoGluB with 106 spores/mL resulted in the inhibition of conidial germination and appressorium formation of M. oryzae, illustrating effective biocontrol activity. Hydrolysates of pachymaran induced the expression of defense genes restricting M. oryzae infection in rice plants, indicating an immunostimulatory effect of MoGluB hydrolysates.
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Affiliation(s)
- Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, P. R. China
| | - Xiaowen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Lingli Zhong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Qiwen Fan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zejun Lan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, Nanjing 210095, P. R. China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, P. R. China
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6
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Andreeva A, Kulesha E, Gough J, Murzin AG. The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. Nucleic Acids Res 2020; 48:D376-D382. [PMID: 31724711 PMCID: PMC7139981 DOI: 10.1093/nar/gkz1064] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. We report a major effort to increase the coverage of structural data, aiming to provide classification of almost all domain superfamilies with representatives in the PDB. We have also improved the database schema, provided a new API and modernised the web interface. This is by far the most significant update in coverage since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype. The database is accessible from http://scop.mrc-lmb.cam.ac.uk.
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Affiliation(s)
- Antonina Andreeva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Julian Gough
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alexey G Murzin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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7
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Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, Murakami MT. Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family. Nat Chem Biol 2020; 16:920-929. [PMID: 32451508 DOI: 10.1038/s41589-020-0554-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/22/2020] [Indexed: 11/09/2022]
Abstract
The fundamental and assorted roles of β-1,3-glucans in nature are underpinned on diverse chemistry and molecular structures, demanding sophisticated and intricate enzymatic systems for their processing. In this work, the selectivity and modes of action of a glycoside hydrolase family active on β-1,3-glucans were systematically investigated combining sequence similarity network, phylogeny, X-ray crystallography, enzyme kinetics, mutagenesis and molecular dynamics. This family exhibits a minimalist and versatile (α/β)-barrel scaffold, which can harbor distinguishing exo or endo modes of action, including an ancillary-binding site for the anchoring of triple-helical β-1,3-glucans. The substrate binding occurs via a hydrophobic knuckle complementary to the canonical curved conformation of β-1,3-glucans or through a substrate conformational change imposed by the active-site topology of some fungal enzymes. Together, these findings expand our understanding of the enzymatic arsenal of bacteria and fungi for the breakdown and modification of β-1,3-glucans, which can be exploited for biotechnological applications.
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Affiliation(s)
- Camila R Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Pedro A C R Costa
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Plínio S Vieira
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | | | - Thamy L R Correa
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Evandro A Lima
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Fernanda Mandelli
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Lucelia Cabral
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Marcele P Martins
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Rosa L Cordeiro
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Atílio T Junior
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Beatriz P Souza
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Érica T Prates
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Fabio C Gozzo
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil.
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8
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Krishnan B, Srivastava SS, Sankeshi V, Garg R, Srivastava S, Sankaranarayanan R, Sharma Y. βγ-Crystallination Endows a Novel Bacterial Glycoside Hydrolase 64 with Ca 2+-Dependent Activity Modulation. J Bacteriol 2019; 201:e00392-19. [PMID: 31527113 PMCID: PMC6832075 DOI: 10.1128/jb.00392-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/05/2019] [Indexed: 01/10/2023] Open
Abstract
The prokaryotic βγ-crystallins are a large group of uncharacterized domains with Ca2+-binding motifs. We have observed that a vast number of these domains are found appended to other domains, in particular, the carbohydrate-active enzyme (CAZy) domains. To elucidate the functional significance of these prospective Ca2+ sensors in bacteria and this widespread domain association, we have studied one typical example from Clostridium beijerinckii, a bacterium known for its ability to produce acetone, butanol, and ethanol through fermentation of several carbohydrates. This novel glycoside hydrolase of family 64 (GH64), which we named glucanallin, is composed of a βγ-crystallin domain, a GH64 domain, and a carbohydrate-binding module 56 (CBM56). The substrates of GH64, β-1,3-glucans, are the targets for industrial biofuel production due to their plenitude. We have examined the Ca2+-binding properties of this protein, assayed its enzymatic activity, and analyzed the structural features of the β-1,3-glucanase domain through its high-resolution crystal structure. The reaction products resulting from the enzyme reaction of glucanallin reinforce the mixed nature of GH64 enzymes, in contrast to the prevailing notion of them being an exotype. Upon disabling Ca2+ binding and comparing different domain combinations, we demonstrate that the βγ-crystallin domain in glucanallin acts as a Ca2+ sensor and enhances the glycolytic activity of glucanallin through Ca2+ binding. We also compare the structural peculiarities of this new member of the GH64 family to two previously studied members.IMPORTANCE We have biochemically and structurally characterized a novel glucanase from the less studied GH64 family in a bacterium significant for fermentation of carbohydrates into biofuels. This enzyme displays a peculiar property of being distally modulated by Ca2+ via assistance from a neighboring βγ-crystallin domain, likely through changes in the domain interface. In addition, this enzyme is found to be optimized for functioning in an acidic environment, which is in line with the possibility of its involvement in biofuel production. Multiple occurrences of a similar domain architecture suggest that such a "βγ-crystallination"-mediated Ca2+ sensitivity may be widespread among bacterial proteins.
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Affiliation(s)
- Bal Krishnan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Indian Institute of Science Education and Research Berhampur, Odisha, India
| | | | - Venu Sankeshi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rupsi Garg
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Yogendra Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Indian Institute of Science Education and Research Berhampur, Odisha, India
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9
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Yin B, Gu H, Mo X, Xu Y, Yan B, Li Q, Ou Q, Wu B, Guo C, Jiang C. Identification and molecular characterization of a psychrophilic GH1 β-glucosidase from the subtropical soil microorganism Exiguobacterium sp. GXG2. AMB Express 2019; 9:159. [PMID: 31576505 PMCID: PMC6773797 DOI: 10.1186/s13568-019-0873-7] [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: 04/14/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
The products of bacterial β-glucosidases with favorable cold-adapted properties have industrial applications. A psychrophilic β-glucosidase gene named bglG from subtropical soil microorganism Exiguobacterium sp. GXG2 was isolated and characterized by function-based screening strategy. Results of multiple alignments showed that the derived protein BglG shared 45.7% identities with reviewed β-glucosidases in the UniProtKB/Swiss-Prot database. Functional characterization of the β-glucosidase BglG indicated that BglG was a 468 aa protein with a molecular weight of 53.2 kDa. The BglG showed the highest activity in pH 7.0 at 35 °C and exhibited consistently high levels of activity within low temperatures ranging from 5 to 35 °C. The BglG appeared to be a psychrophilic enzyme. The values of Km, Vmax, kcat, and kcat/Km of recombinant BglG toward ρNPG were 1.1 mM, 1.4 µg/mL/min, 12.7 s−1, and 11.5 mM/s, respectively. The specific enzyme activity of BglG was 12.14 U/mg. The metal ion of Ca2+ and Fe3+ could stimulate the activity of BglG, whereas Mn2+ inhibited the activity. The cold-adapted β-glucosidase BglG displayed remarkable biochemical properties, making it a potential candidate for future industrial applications.
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10
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Henrissat B, Garron ML. How a Glycoside Hydrolase Recognizes a Helical Polyglucan. Structure 2019; 25:1319-1321. [PMID: 28877502 DOI: 10.1016/j.str.2017.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Similarly to other biopolymers, linear polysaccharides can form double- or triple-helical structures. How enzymes recognize and manage this quaternary structure is an unresolved question. In this issue of Structure, Pluvinage et al. (2017) shed light on the structural complementarity between family GH81 glycoside hydrolase and the quaternary structure of their polysaccharide substrates.
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Affiliation(s)
- Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France; INRA, USC 1408 AFMB, F-13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marie-Line Garron
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France; INRA, USC 1408 AFMB, F-13288 Marseille, France.
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11
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Wu Q, Dou X, Wang Q, Guan Z, Cai Y, Liao X. Isolation of β-1,3-Glucanase-Producing Microorganisms from Poria cocos Cultivation Soil via Molecular Biology. Molecules 2018; 23:molecules23071555. [PMID: 29954113 PMCID: PMC6100237 DOI: 10.3390/molecules23071555] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 11/26/2022] Open
Abstract
β-1,3-Glucanase is considered as a useful enzymatic tool for β-1,3-glucan degradation to produce (1→3)-linked β-glucan oligosaccharides with pharmacological activity properties. To validly isolate β-1,3-glucanase-producing microorganisms, the soil of Wolfiporia extensa, considered an environment rich in β-1,3-glucan-degrading microorganisms, was subjected to high throughput sequencing. The results demonstrated that the genera Streptomyces (1.90%) and Arthrobacter (0.78%) belonging to the order Actinomycetales (8.64%) in the phylum Actinobacteria (18.64%) were observed in soil for P. cocos cultivation (FTL1). Actinomycetes were considered as the candidates for isolation of glucan-degrading microorganisms. Out of 58 isolates, only 11 exhibited β-1,3-glucan-degrading activity. The isolate SYBCQL belonging to the genus Kitasatospora with β-1,3-glucan-degrading activity was found and reported for the first time and the isolate SYBC17 displayed the highest yield (1.02 U/mg) among the isolates. To check the β-1,3-glucanase contribution to β-1,3-glucan-degrading activity, two genes, 17-W and 17-Q, encoding β-1,3-glucanase in SYBC17 and one gene QLK1 in SYBCQL were cloned and expressed for verification at the molecular level. Our findings collectively showed that the isolates able to secrete β-1,3-glucanase could be obtained with the assistance of high-throughput sequencing and genes expression analysis. These methods provided technical support for isolating β-1,3-glucanase-producing microorganisms.
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Affiliation(s)
- Qiulan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Xin Dou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Qi Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Zhengbing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Xiangru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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12
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Qin Z, Yang D, You X, Liu Y, Hu S, Yan Q, Yang S, Jiang Z. The recognition mechanism of triple-helical β-1,3-glucan by a β-1,3-glucanase. Chem Commun (Camb) 2018; 53:9368-9371. [PMID: 28787048 DOI: 10.1039/c7cc03330c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
β-1,3-Glucan is one of the most abundant polysaccharides in fungi. Recognition of β-1,3-glucan occurs in both hydrolysis by glycoside hydrolases and immunological recognition. Our study provides a novel structural account of how glycoside hydrolase recognizes and hydrolyzes substrates in a triple-helical form and presents a general structural basis of β-1,3-glucan recognition.
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Affiliation(s)
- Zhen Qin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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13
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Kumagai Y, Okuyama M, Kimura A. Heat treatment of curdlan enhances the enzymatic production of biologically active β-(1,3)-glucan oligosaccharides. Carbohydr Polym 2016; 146:396-401. [DOI: 10.1016/j.carbpol.2016.03.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/20/2022]
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14
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Liu M, Duan L, Wang M, Zeng H, Liu X, Qiu D. Crystal Structure Analysis and the Identification of Distinctive Functional Regions of the Protein Elicitor Mohrip2. FRONTIERS IN PLANT SCIENCE 2016; 7:1103. [PMID: 27507984 PMCID: PMC4960229 DOI: 10.3389/fpls.2016.01103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/12/2016] [Indexed: 05/31/2023]
Abstract
The protein elicitor MoHrip2, which was extracted from Magnaporthe oryzae as an exocrine protein, triggers the tobacco immune system and enhances blast resistance in rice. However, the detailed mechanisms by which MoHrip2 acts as an elicitor remain unclear. Here, we investigated the structure of MoHrip2 to elucidate its functions based on molecular structure. The three-dimensional structure of MoHrip2 was obtained. Overall, the crystal structure formed a β-barrel structure and showed high similarity to the pathogenesis-related (PR) thaumatin superfamily protein thaumatin-like xylanase inhibitor (TL-XI). To investigate the functional regions responsible for MoHrip2 elicitor activities, the full length and eight truncated proteins were expressed in Escherichia coli and were evaluated for elicitor activity in tobacco. Biological function analysis showed that MoHrip2 triggered the defense system against Botrytis cinerea in tobacco. Moreover, only MoHrip2M14 and other fragments containing the 14 amino acids residues in the middle region of the protein showed the elicitor activity of inducing a hypersensitive response and resistance related pathways, which were similar to that of full-length MoHrip2. These results revealed that the central 14 amino acid residues were essential for anti-pathogenic activity.
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Affiliation(s)
- Mengjie Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection – Chinese Academy of Agricultural SciencesBeijing, China
| | - Liangwei Duan
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Meifang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection – Chinese Academy of Agricultural SciencesBeijing, China
| | - Hongmei Zeng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection – Chinese Academy of Agricultural SciencesBeijing, China
| | - Xinqi Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Dewen Qiu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection – Chinese Academy of Agricultural SciencesBeijing, China
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15
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Oda M, Tanabe Y, Noda M, Inaba S, Krayukhina E, Fukada H, Uchiyama S. Structural and binding properties of laminarin revealed by analytical ultracentrifugation and calorimetric analyses. Carbohydr Res 2016; 431:33-8. [PMID: 27267066 DOI: 10.1016/j.carres.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
One of the β-1,3-glucans, laminarin, has been widely used as a substrate for enzymes including endo-1,3-β-glucanase. To obtain quantitative information about the molecular interaction between laminarin and endo-1,3-β-glucanase, the structural properties of laminarin should be determined. The results from pioneering work using analytical ultracentrifugation for carbohydrate analysis showed that laminarin from Laminaria digitata predominantly exists as a single-chain species with approximately 5% of triple-helical species. Differential scanning calorimetry experiments did not show a peak assignable to the transition from triple-helix to single-chain, supporting the notion that a large proportion of laminarin is the single-chain species. The interaction of laminarin with an inactive variant of endo-1,3-β-glucanase from Cellulosimicrobium cellulans, E119A, was quantitatively analyzed using isothermal titration calorimetry. The binding was enthalpically driven and the binding affinity was approximately 10(6) M(-1). The results from binding stoichiometric analysis indicated that on average, E119A binds to laminarin in a 2:1 ratio. This seems to be reasonable, because laminarin mainly exists as a monomer, the apparent molecular mass of laminarin is 3.6 kDa, and E119A would have substrate-binding subsites corresponding to 6 glucose units. The analytical ultracentrifugation experiments could detect different complex species of laminarin and endo-1,3-β-glucanase.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.
| | - Yoichi Tanabe
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Masanori Noda
- U-Medico Inc., 1-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satomi Inaba
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | | | - Harumi Fukada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Susumu Uchiyama
- U-Medico Inc., 1-1, Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Engineering, Osaka University, 1-1, Yamadaoka, Suita, Osaka 565-0871, Japan
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16
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Sultana R, Tanneeru K, Kumar ABR, Guruprasad L. Prediction of Certain Well-Characterized Domains of Known Functions within the PE and PPE Proteins of Mycobacteria. PLoS One 2016; 11:e0146786. [PMID: 26891364 PMCID: PMC4758615 DOI: 10.1371/journal.pone.0146786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022] Open
Abstract
The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We have therefore used bioinformatics tools to characterize the structure and function of these proteins. We selected representative members of the PE and PPE protein family by phylogeny analysis and using structure-based sequence annotation identified ten well-characterized protein domains of known function. Some of these domains were observed to be common to all mycobacterial species and some were species specific.
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Affiliation(s)
- Rafiya Sultana
- School of Chemistry, University of Hyderabad, Hyderabad, 500046, India
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17
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Bianchetti CM, Takasuka TE, Deutsch S, Udell HS, Yik EJ, Bergeman LF, Fox BG. Active site and laminarin binding in glycoside hydrolase family 55. J Biol Chem 2015; 290:11819-32. [PMID: 25752603 DOI: 10.1074/jbc.m114.623579] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 11/06/2022] Open
Abstract
The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.
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Affiliation(s)
- Christopher M Bianchetti
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, Wisconsin 54901
| | - Taichi E Takasuka
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, the Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Sam Deutsch
- the Joint Genome Institute, Walnut Creek, California 94598, and
| | - Hannah S Udell
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Eric J Yik
- the Department of Chemistry and Biochemistry, California State University-Fullerton, Fullerton, California 92831
| | - Lai F Bergeman
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Brian G Fox
- From the Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706,
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18
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Multiple rewards from a treasure trove of novel glycoside hydrolase and polysaccharide lyase structures: new folds, mechanistic details, and evolutionary relationships. Curr Opin Struct Biol 2013; 23:652-9. [DOI: 10.1016/j.sbi.2013.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/04/2013] [Accepted: 06/04/2013] [Indexed: 11/18/2022]
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19
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Zhou P, Chen Z, Yan Q, Yang S, Hilgenfeld R, Jiang Z. The structure of a glycoside hydrolase family 81 endo-β-1,3-glucanase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2027-38. [PMID: 24100321 DOI: 10.1107/s090744491301799x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 06/29/2013] [Indexed: 11/11/2022]
Abstract
Endo-β-1,3-glucanases catalyze the hydrolysis of β-1,3-glycosidic linkages in glucans. They are also responsible for rather diverse physiological functions such as carbon utilization, cell-wall organization and pathogen defence. Glycoside hydrolase (GH) family 81 mainly consists of β-1,3-glucanases from fungi, higher plants and bacteria. A novel GH family 81 β-1,3-glucanase gene (RmLam81A) from Rhizomucor miehei was expressed in Escherichia coli. Purified RmLam81A was crystallized and the structure was determined in two crystal forms (form I-free and form II-Se) at 2.3 and 2.0 Å resolution, respectively. Here, the crystal structure of a member of GH family 81 is reported for the first time. The structure of RmLam81A is greatly different from all endo-β-1,3-glucanase structures available in the Protein Data Bank. The overall structure of the RmLam81A monomer consists of an N-terminal β-sandwich domain, a C-terminal (α/α)6 domain and an additional domain between them. Glu553 and Glu557 are proposed to serve as the proton donor and basic catalyst, respectively, in a single-displacement mechanism. In addition, Tyr386, Tyr482 and Ser554 possibly contribute to both the position or the ionization state of the basic catalyst Glu557. The first crystal structure of a GH family 81 member will be helpful in the study of the GH family 81 proteins and endo-β-1,3-glucanases.
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Affiliation(s)
- Peng Zhou
- Department of Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
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20
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Wojtkowiak A, Witek K, Hennig J, Jaskolski M. Structures of an active-site mutant of a plant 1,3-β-glucanase in complex with oligosaccharide products of hydrolysis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 69:52-62. [PMID: 23275163 DOI: 10.1107/s0907444912042175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Accepted: 10/08/2012] [Indexed: 08/29/2023]
Abstract
Plant endo-1,3-β-glucanases are involved in important physiological processes such as defence mechanisms, cell division and flowering. They hydrolyze (1→3)-β-glucans, with very limited activity towards mixed (1→3,1→4)-β-glucans and branched (1→3,1→6)-β-glucans. Here, crystal structures of the potato (Solanum tuberosum) endo-1,3-β-glucanase GLUB20-2 with the nucleophilic Glu259 residue substituted by alanine (E259A) are reported. Despite this active-site mutation, the protein retained residual endoglucanase activity and when incubated in the crystallization buffer with a linear hexameric substrate derived from (1→3)-β-glucan (laminarahexose) cleaved it in two different ways, generating trisaccharides and tetrasaccharides, as confirmed by mass spectrometry. The trisaccharide (laminaratriose) shows higher binding affinity and was found to fully occupy the -1, -2 and -3 sites of the active-site cleft, even at a low molar excess of the substrate. At elevated substrate concentration the tetrasaccharide molecule (laminaratetrose) also occupies the active site, spanning the opposite sites +1, +2, +3 and +4 of the cleft. These are the first crystal structures of a plant glycoside hydrolase family 17 (GH17) member to reveal the protein-saccharide interactions and were determined at resolutions of 1.68 and 1.55 Å, respectively. The geometry of the active-site cleft clearly precludes any (1→4)-β-glucan topology at the subsites from -3 to +4 and could possibly accommodate β-1,6-branching only at subsites +1 and +2. The glucose units at subsites -1 and -2 interact with highly conserved protein residues. In contrast, subsites -3, +3 and +4 are variable, suggesting that the mode of glucose binding at these sites may vary between different plant endo-1,3-β-glucanases. Low substrate affinity is observed at subsites +1 and +2, as manifested by disorder of the glycosyl units there.
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Affiliation(s)
- Agnieszka Wojtkowiak
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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21
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Wojtkowiak A, Witek K, Hennig J, Jaskolski M. Two high-resolution structures of potato endo-1,3-β-glucanase reveal subdomain flexibility with implications for substrate binding. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:713-23. [PMID: 22683794 DOI: 10.1107/s090744491200995x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 03/06/2012] [Indexed: 11/11/2022]
Abstract
Endo-1,3-β-glucanases are widely distributed among bacteria, fungi and higher plants. They are responsible for hydrolysis of the glycosidic bond in specific polysaccharides with tracts of unsubstituted β-1,3-linked glucosyl residues. The plant enzymes belong to glycoside hydrolase family 17 (GH17) and are also members of class 2 of pathogenesis-related (PR) proteins. X-ray diffraction data were collected to 1.40 and 1.26 Å resolution from two crystals of endo-1,3-β-glucanase from Solanum tuberosum (potato, cultivar Désirée) which, despite having a similar packing framework, represented two separate crystal forms. In particular, they differed in the Matthews coefficient and are consequently referred to as higher density (HD; 1.40 Å resolution) and lower density (LD; 1.26 Å resolution) forms. The general fold of the protein resembles that of other known plant endo-1,3-β-glucanases and is defined by a (β/α)(8)-barrel with an additional subdomain built around the C-terminal half of the barrel. The structures revealed high flexibility of the subdomain, which forms part of the catalytic cleft. Comparison with structures of other GH17 endo-1,3-β-glucanases revealed differences in the arrangement of the secondary-structure elements in this region, which can be correlated with sequence variability and may suggest distinct substrate-binding patterns. The crystal structures revealed an unusual packing mode, clearly visible in the LD structure, caused by the presence of the C-terminal His(6) tag, which extends from the compact fold of the enzyme molecule and docks in the catalytic cleft of a neighbouring molecule. In this way, an infinite chain of His-tag-linked protein molecules is formed along the c direction.
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Affiliation(s)
- Agnieszka Wojtkowiak
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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22
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Jeng WY, Wang NC, Lin CT, Shyur LF, Wang AHJ. Crystal structures of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with inhibitors: essential residues for β-1,3- and β-1,4-glucan selection. J Biol Chem 2011; 286:45030-40. [PMID: 22065588 DOI: 10.1074/jbc.m111.271213] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Laminarinases hydrolyzing the β-1,3-linkage of glucans play essential roles in microbial saccharide degradation. Here we report the crystal structures at 1.65-1.82 Å resolution of the catalytic domain of laminarinase from the thermophile Thermotoga maritima with various space groups in the ligand-free form or in the presence of inhibitors gluconolactone and cetyltrimethylammonium. Ligands were bound at the cleft of the active site near an enclosure formed by Trp-232 and a flexible GASIG loop. A closed configuration at the active site cleft was observed in some molecules. The loop flexibility in the enzyme may contribute to the regulation of endo- or exo-activity of the enzyme and a preference to release laminaritrioses in long chain carbohydrate hydrolysis. Glu-137 and Glu-132 are proposed to serve as the proton donor and nucleophile, respectively, in the retaining catalysis of hydrolyzation. Calcium ions in the crystallization media are found to accelerate crystal growth. Comparison of laminarinase and endoglucanase structures revealed the subtle difference of key residues in the active site for the selection of β-1,3-glucan and β-1,4-glucan substrates, respectively. Arg-85 may be pivotal to β-1,3-glucan substrate selection. The similarity of the structures between the laminarinase catalytic domain and its carbohydrate-binding modules may have evolutionary relevance because of the similarities in their folds.
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Affiliation(s)
- Wen-Yih Jeng
- Institute of Biological Chemistry, Core Facility for Protein Production and X-ray Structural Analysis, Academia Sinica, Taipei 115, Taiwan
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23
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Shrestha KL, Liu SW, Huang CP, Wu HM, Wang WC, Li YK. Characterization and identification of essential residues of the glycoside hydrolase family 64 laminaripentaose-producing- -1, 3-glucanase. Protein Eng Des Sel 2011; 24:617-25. [DOI: 10.1093/protein/gzr031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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