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Li J, Peng C, Mao A, Zhong M, Hu Z. An overview of microbial enzymatic approaches for pectin degradation. Int J Biol Macromol 2024; 254:127804. [PMID: 37913880 DOI: 10.1016/j.ijbiomac.2023.127804] [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: 09/01/2023] [Revised: 10/21/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and β-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many α-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.
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Affiliation(s)
- Jin Li
- College of Life Sciences, China West Normal University, Nanchong 637002, China; Department of Biology, College of Science, Shantou University, Shantou 515063, China.
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Aihua Mao
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Mingqi Zhong
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou 515063, China.
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Pandey S, Berger BW, Acharya R. Structural Analyses of Substrate-pH Activity Pairing Observed across Diverse Polysaccharide Lyases. Biochemistry 2023; 62:2775-2790. [PMID: 37620757 DOI: 10.1021/acs.biochem.3c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Anionic polysaccharides found in nature are functionally and structurally diverse, and so are the polysaccharide lyases (PLs) that catalyze their degradation. Atomic superposition of various PL folds according to their cleavable substrate structure confirms the occurrence of structural convergence at PL active sites. This suggests that various PL folds have emerged to cleave a particular class of anionic polysaccharide during the course of evolution. Whereas the structural and mechanistic similarity of PL active site has been highlighted in earlier studies, a detailed understanding regarding functional properties of this catalytic convergence remains an open question, especially the role of extrinsic factors such as pH in the context of substrate binding and catalysis. Our earlier structural and functional work on pH directed multisubstrate specificity of Smlt1473 inspired us to regroup PLs according to substrate type to analyze the pH dependence of their catalytic activity. Interestingly, we find that particular groups of substrates are cleaved in a particular pH range (acidic/neutral/basic) irrespective of PL fold, boosting the idea of functional convergence as well. On the basis of this observation, we set out to define structurally and computationally the key constituents of an active site among PL families. This study delineates the structural determinants of conserved "substrate-pH activity pairing" within and between PL families.
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Affiliation(s)
- Shubhant Pandey
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050 Odisha, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094 Maharashtra, India
| | - Bryan W Berger
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Rudresh Acharya
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050 Odisha, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094 Maharashtra, India
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Hugouvieux-Cotte-Pattat N, Pédron J, Van Gijsegem F. Insight into biodiversity of the recently rearranged genus Dickeya. FRONTIERS IN PLANT SCIENCE 2023; 14:1168480. [PMID: 37409305 PMCID: PMC10319131 DOI: 10.3389/fpls.2023.1168480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
The genus Dickeya includes plant pathogenic bacteria attacking a wide range of crops and ornamentals as well as a few environmental isolates from water. Defined on the basis of six species in 2005, this genus now includes 12 recognized species. Despite the description of several new species in recent years, the diversity of the genus Dickeya is not yet fully explored. Many strains have been analyzed for species causing diseases on economically important crops, such as for the potato pathogens D. dianthicola and D. solani. In contrast, only a few strains have been characterized for species of environmental origin or isolated from plants in understudied countries. To gain insights in the Dickeya diversity, recent extensive analyzes were performed on environmental isolates and poorly characterized strains from old collections. Phylogenetic and phenotypic analyzes led to the reclassification of D. paradisiaca (containing strains from tropical or subtropical regions) in the new genus, Musicola, the identification of three water species D. aquatica, D. lacustris and D. undicola, the description of a new species D. poaceaphila including Australian strains isolated from grasses, and the characterization of the new species D. oryzae and D. parazeae, resulting from the subdivision of the species D. zeae. Traits distinguishing each new species were identified from genomic and phenotypic comparisons. The high heterogeneity observed in some species, notably for D. zeae, indicates that additional species still need to be defined. The objective of this study was to clarify the present taxonomy of the genus Dickeya and to reassign the correct species to several Dickeya strains isolated before the current classification.
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Affiliation(s)
| | - Jacques Pédron
- Institute of Ecology and Environmental Sciences, Sorbonne University, CNRS, INRAE, Paris, France
| | - Frédérique Van Gijsegem
- Institute of Ecology and Environmental Sciences, Sorbonne University, CNRS, INRAE, Paris, France
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4
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Rhamnogalacturonan Endolyase Family 4 Enzymes: An Update on Their Importance in the Fruit Ripening Process. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fruit ripening is a process that produces fruit with top sensory qualities that are ideal for consumption. For the plant, the final objective is seed dispersal. One of the fruit characteristics observed by consumers is texture, which is related to the ripening and softening of the fruit. Controlled and orchestrated events occur to regulate the expression of genes involved in disassembling and solubilizing the cell wall. Studies have shown that changes in pectins are closely related to the loss of firmness and fruit softening. For this reason, studying the mechanisms and enzymes that act on pectins could help to elucidate the molecular events that occur in the fruit. This paper provides a review of the enzyme rhamnogalacturonan endolyase (RGL; EC 4.2.2.23), which is responsible for cleavage of the pectin rhamnogalacturonan I (RGL-I) between rhamnose (Rha) and galacturonic acid (GalA) through the mechanism of β-elimination during fruit ripening. RGL promotes the loosening and weakening of the cell wall and exposes the backbone of the polysaccharide to the action of other enzymes. Investigations into RGL and its relationship with fruit ripening have reliably demonstrated that this enzyme has an important role in this process.
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Itoh T. Structures and functions of carbohydrate-active enzymes of chitinolytic bacteria Paenibacillus sp. str. FPU-7. Biosci Biotechnol Biochem 2021; 85:1314-1323. [PMID: 33792636 DOI: 10.1093/bbb/zbab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/22/2021] [Indexed: 11/14/2022]
Abstract
Chitin and its derivatives have valuable potential applications in various fields that include medicine, agriculture, and food industries. Paenibacillus sp. str. FPU-7 is one of the most potent chitin-degrading bacteria identified. This review introduces the chitin degradation system of P. str. FPU-7. In addition to extracellular chitinases, P. str. FPU-7 uses a unique multimodular chitinase (ChiW) to hydrolyze chitin to oligosaccharides on the cell surface. Chitin oligosaccharides are converted to N-acetyl-d-glucosamine by β-N-acetylhexosaminidase (PsNagA) in the cytosol. The functions and structures of ChiW and PsNagA are also summarized. The genome sequence of P. str. FPU-7 provides opportunities to acquire novel enzymes. Genome mining has identified a novel alginate lyase, PsAly. The functions and structure of PsAly are reviewed. These findings will inform further improvement of the sustainable conversion of polysaccharides to functional materials.
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
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Zheng L, Xu Y, Li Q, Zhu B. Pectinolytic lyases: a comprehensive review of sources, category, property, structure, and catalytic mechanism of pectate lyases and pectin lyases. BIORESOUR BIOPROCESS 2021; 8:79. [PMID: 38650254 PMCID: PMC10992409 DOI: 10.1186/s40643-021-00432-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/16/2021] [Indexed: 12/22/2022] Open
Abstract
Pectate lyases and pectin lyases have essential roles in various biotechnological applications, such as textile industry, paper making, pectic wastewater pretreatment, juice clarification and oil extraction. They can effectively cleave the α-1,4-glycosidic bond of pectin molecules back bone by β-elimination reaction to produce pectin oligosaccharides. In this way, it will not generate highly toxic methanol and has the advantages of good enzymatic selectivity, less by-products, mild reaction conditions and high efficiency. However, numerous researches have been done for several decades; there are still no comprehensive reviews to summarize the recent advances of pectate lyases and pectin lyases. This review tries to fill this gap by providing all relevant information, including the substrate, origin, biochemical properties, sequence analysis, mode of action, the three-dimensional structure and catalytic mechanism.
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Affiliation(s)
- Ling Zheng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Yinxiao Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Qian Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816, P. R. China.
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Sabbadin F, Urresti S, Henrissat B, Avrova AO, Welsh LRJ, Lindley PJ, Csukai M, Squires JN, Walton PH, Davies GJ, Bruce NC, Whisson SC, McQueen-Mason SJ. Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes. Science 2021; 373:774-779. [PMID: 34385392 DOI: 10.1126/science.abj1342] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/06/2021] [Indexed: 01/19/2023]
Abstract
The oomycete Phytophthora infestans is a damaging crop pathogen and a model organism to study plant-pathogen interactions. We report the discovery of a family of copper-dependent lytic polysaccharide monooxygenases (LPMOs) in plant pathogenic oomycetes and its role in plant infection by P. infestans We show that LPMO-encoding genes are up-regulated early during infection and that the secreted enzymes oxidatively cleave the backbone of pectin, a charged polysaccharide in the plant cell wall. The crystal structure of the most abundant of these LPMOs sheds light on its ability to recognize and degrade pectin, and silencing the encoding gene in P. infestans inhibits infection of potato, indicating a role in host penetration. The identification of LPMOs as virulence factors in pathogenic oomycetes opens up opportunities in crop protection and food security.
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Affiliation(s)
- Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
| | - Saioa Urresti
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Anna O Avrova
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Lydia R J Welsh
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter J Lindley
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Michael Csukai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Julie N Squires
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Paul H Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Gideon J Davies
- Department of Chemistry, University of York, York YO10 5DD, UK
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Stephen C Whisson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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Structural basis of catalysis and substrate recognition by the NAD(H)-dependent α-d-glucuronidase from the glycoside hydrolase family 4. Biochem J 2021; 478:943-959. [PMID: 33565573 DOI: 10.1042/bcj20200824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022]
Abstract
Members of the glycoside hydrolase family 4 (GH4) employ an unusual glycosidic bond cleavage mechanism utilizing NAD(H) and a divalent metal ion, under reducing conditions. These enzymes act upon a diverse range of glycosides, and unlike most other GH families, homologs here are known to accommodate both α- and β-anomeric specificities within the same active site. Here, we report the catalytic properties and the crystal structures of TmAgu4B, an α-d-glucuronidase from the hyperthermophile Thermotoga maritima. The structures in three different states include the apo form, the NADH bound holo form, and the ternary complex with NADH and the reaction product d-glucuronic acid, at 2.15, 1.97 and 1.85 Å resolutions, respectively. These structures reveal the step-wise route of conformational changes required in the active site to achieve the catalytically competent state, and illustrate the direct role of residues that determine the reaction mechanism. Furthermore, a structural transition of a helical region in the active site to a turn geometry resulting in the rearrangement of a unique arginine residue governs the exclusive glucopyranosiduronic acid recognition in TmAgu4B. Mutational studies show that modifications of the glycone binding site geometry lead to catalytic failure and indicate overlapping roles of specific residues in catalysis and substrate recognition. The data highlight hitherto unreported molecular features and associated active site dynamics that determine the structure-function relationships within the unique GH4 family.
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Wang D, Wang J, Zeng R, Wu J, Michael SV, Qu W. The degradation activities for three seaweed polysaccharides of Shewanella sp. WPAGA9 isolated from deep-sea sediments. J Basic Microbiol 2021; 61:406-418. [PMID: 33729617 DOI: 10.1002/jobm.202000728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/03/2021] [Accepted: 03/01/2021] [Indexed: 11/06/2022]
Abstract
Seaweed oligosaccharides possess great bioactivities. However, different microbial strains are required to degrade multiple polysaccharides due to their limited biodegradability, thereby increasing the cost and complexity of production. Shewanella sp. WPAGA9 was isolated from deep-sea sediments in this study. According to the genomic and biochemical analyses, the extracellular fermentation broth of WPAGA9 had versatile degradation abilities for three typical seaweed polysaccharides including agar, carrageenan, and alginate. The maximum enzyme activities of the extracellular fermentation broth of WPAGA9 were 71.63, 76.4, and 735.13 U/ml for the degradation of agar, alginate, and carrageenan, respectively. Moreover, multiple seaweed oligosaccharides can be produced by the extracellular fermentation broth of WPAGA9 under similar optimum conditions. Therefore, WPAGA9 can simultaneously degrade three types of seaweed polysaccharides under similar conditions, thereby greatly reducing the production cost of seaweed oligosaccharides. This finding indicates that Shewanella sp. WPAGA9 is an ideal biochemical tool for producing multiple active seaweed oligosaccharides at low costs and is also an important participant in the carbon cycle process of the deep-sea environment.
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Affiliation(s)
- Dingquan Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Runying Zeng
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen, China
| | - Jie Wu
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen, China
| | - Shija V Michael
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Sugiura H, Nagase A, Oiki S, Mikami B, Watanabe D, Hashimoto W. Bacterial inducible expression of plant cell wall-binding protein YesO through conflict between Glycine max and saprophytic Bacillus subtilis. Sci Rep 2020; 10:18691. [PMID: 33122638 PMCID: PMC7596534 DOI: 10.1038/s41598-020-75359-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/07/2020] [Indexed: 01/22/2023] Open
Abstract
Saprophytic bacteria and plants compete for limited nutrient sources. Bacillus subtilis grows well on steamed soybeans Glycine max to produce the fermented food, natto. Here we focus on bacterial responses in conflict between B. subtilis and G. max. B. subtilis cells maintained high growth rates specifically on non-germinating, dead soybean seeds. On the other hand, viable soybean seeds with germinating capability attenuated the initial growth of B. subtilis. Thus, B. subtilis cells may trigger saprophytic growth in response to the physiological status of G. max. Scanning electron microscope observation indicated that B. subtilis cells on steamed soybeans undergo morphological changes to form apertures, demonstrating cell remodeling during saprophytic growth. Further, transcriptomic analysis of B. subtilis revealed upregulation of the gene cluster, yesOPQR, in colonies growing on steamed soybeans. Recombinant YesO protein, a putative, solute-binding protein for the ATP-binding cassette transporter system, exhibited an affinity for pectin-derived oligosaccharide from plant cell wall. The crystal structure of YesO, in complex with the pectin oligosaccharide, was determined at 1.58 Å resolution. This study expands our knowledge of defensive and offensive strategies in interspecies competition, which may be promising targets for crop protection and fermented food production.
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Affiliation(s)
- Haruka Sugiura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ayumi Nagase
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Sayoko Oiki
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Daisuke Watanabe
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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Wu P, Yang S, Zhan Z, Zhang G. Origins and features of pectate lyases and their applications in industry. Appl Microbiol Biotechnol 2020; 104:7247-7260. [PMID: 32666183 DOI: 10.1007/s00253-020-10769-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/12/2020] [Accepted: 07/02/2020] [Indexed: 11/25/2022]
Abstract
Pectate lyase treatment can be an alternative strategy of the chemical processing, which causes severe environmental pollution, and has been broadly studied and applied for diverse industrial applications including textile industry, beverage industry, pulp processing, pectic wastewater pretreatment, and oil extraction. This review gave a brief description of the origins, enzymatic characterizations, structure, and applications of pectate lyases (Pels). Most of the reported pectate lyases are originated from microorganisms with a small number of them from plants and animals. Due to the diverse environments that these microorganisms exist, Pels present diversified features, especially for the range of optimal pH and temperature. The diversified biochemical properties of Pels define their applications in different industries, and the applications of alkaline Pels on cotton bioscouring and ramie degumming in textile industry were focused in this review. This review also discussed the perspectives of the development and applications of Pels. KEY POINTS: • The first review on pectate lyase focusing on biotechnological applications. • Origins, features, structures, applications of pectate lyases reviewed. • Applications of alkaline Pels in textile industry demonstrated. • Perspectives on future development and applications of Pels discussed.
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Affiliation(s)
- Pan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Wuhan Sunhy Biology Co., Ltd., Wuhan, 430206, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Zhichun Zhan
- Wuhan Sunhy Biology Co., Ltd., Wuhan, 430206, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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12
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Qiao L, Yang X, Xie R, Du C, Chi Y, Zhang J, Wang P. Efficient production of ulvan lyase from Ulva prolifera by Catenovulum sp. LP based on stage-controlled fermentation strategy. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Chen CC, Dai L, Ma L, Guo RT. Enzymatic degradation of plant biomass and synthetic polymers. Nat Rev Chem 2020; 4:114-126. [PMID: 37128024 DOI: 10.1038/s41570-020-0163-6] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2020] [Indexed: 12/17/2022]
Abstract
Plant biomass is an abundant renewable resource on Earth. Microorganisms harvest energy from plant material by means of complex enzymatic systems that efficiently degrade natural polymers. Intriguingly, microorganisms have evolved to exploit these ancient mechanisms to also decompose synthetic plastic polymers. In this Review, we summarize the mechanisms by which they decompose non-starch plant biomass and the six major types of synthetic plastics. We focus on the structural features of the enzymes that contribute to substrate recognition and then describe the catalytic mechanisms of polymer metabolism. An understanding of these natural biocatalysts is valuable if we are to exploit their potential for the degradation of synthetic polymers.
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14
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Kanungo A, Bag BP. Structural insights into the molecular mechanisms of pectinolytic enzymes. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42485-019-00027-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7. Sci Rep 2019; 9:14870. [PMID: 31619701 PMCID: PMC6796002 DOI: 10.1038/s41598-019-51006-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/23/2019] [Indexed: 02/07/2023] Open
Abstract
A novel alginate lyase, PsAly, with a molecular mass of 33 kDa and whose amino acid sequence shares no significant similarity to other known proteins, was biochemically and structurally characterised from Paenibacillus sp. str. FPU-7. The maximum PsAly activity was obtained at 65 °C, with an optimum pH of pH 7-7.5. The activity was enhanced by divalent cations, such as Mg2+, Mn2+, or Co2+, and inhibited by a metal chelator, ethylenediaminetetraacetic acid. The reaction products indicated that PsAly is an endolytic enzyme with a preference for polymannuronate. Herein, we report a detailed crystal structure of PsAly at a resolution of 0.89 Å, which possesses a β-helix fold that creates a long cleft. The catalytic site was different from that of other polysaccharide lyases. Site-directed mutational analysis of conserved residues predicted Tyr184 and Lys221 as catalytic residues, abstracting from the C5 proton and providing a proton to the glycoside bond, respectively. One cation was found to bind to the bottom of the cleft and neutralise the carboxy group of the substrate, decreasing the pKa of the C5 proton to promote catalysis. Our study provides an insight into the structural basis for the catalysis of alginate lyases and β-helix polysaccharide lyases.
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Labourel A, Baslé A, Munoz-Munoz J, Ndeh D, Booth S, Nepogodiev SA, Field RA, Cartmell A. Structural and functional analyses of glycoside hydrolase 138 enzymes targeting chain A galacturonic acid in the complex pectin rhamnogalacturonan II. J Biol Chem 2019; 294:7711-7721. [PMID: 30877196 PMCID: PMC6514610 DOI: 10.1074/jbc.ra118.006626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiome. The selection pressures in this environment have spurred the evolution of a complex reservoir of microbial genes encoding carbohydrate-active enzymes (CAZymes). Previously, we have shown that the human gut bacterium Bacteroides thetaiotaomicron (Bt) can depolymerize the most structurally complex glycan, the plant pectin rhamnogalacturonan II (RGII), commonly found in the human diet. Previous investigation of the RGII-degrading apparatus in Bt identified BT0997 as a new CAZyme family, classified as glycoside hydrolase 138 (GH138). The mechanism of substrate recognition by GH138, however, remains unclear. Here, using synthetic substrates and biochemical assays, we show that BT0997 targets the d-galacturonic acid-α-1,2-l-rhamnose linkage in chain A of RGII and that it absolutely requires the presence of a second d-galacturonic acid side chain (linked β-1,3 to l-rhamnose) for activity. NMR analysis revealed that BT0997 operates through a double displacement retaining mechanism. We also report the crystal structure of a BT0997 homolog, BPA0997 from Bacteroides paurosaccharolyticus, in complex with ligands at 1.6 Å resolution. The structure disclosed that the enzyme comprises four domains, including a catalytic TIM (α/β)8 barrel. Characterization of several BT0997 variants identified Glu-294 and Glu-361 as the catalytic acid/base and nucleophile, respectively, and we observed a chloride ion close to the active site. The three-dimensional structure and bioinformatic analysis revealed that two arginines, Arg-332 and Arg-521, are key specificity determinants of BT0997 in targeting d-galacturonic acid residues. In summary, our study reports the first structural and mechanistic analyses of GH138 enzymes.
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Affiliation(s)
- Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Jose Munoz-Munoz
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Didier Ndeh
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Simon Booth
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Alan Cartmell
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and
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17
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Screening of a Novel Polysaccharide Lyase Family 10 Pectate Lyase from Paenibacillus polymyxa KF-1: Cloning, Expression and Characterization. Molecules 2018; 23:molecules23112774. [PMID: 30373112 PMCID: PMC6278402 DOI: 10.3390/molecules23112774] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/16/2018] [Accepted: 10/25/2018] [Indexed: 01/23/2023] Open
Abstract
Pectate lyase (EC 4.2.2.2) catalyzes the cleavage of α-1,4-glycosidic bonds of pectin polymers, and it has potential uses in the textile industry. In this study, a novel pectate lyase belonging to polysaccharide lyase family 10 was screened from the secreted enzyme extract of Paenibacillus polymyxa KF-1 and identified by liquid chromatography-MS/MS. The gene was cloned from P. polymyxa KF-1 genomic DNA and expressed in Escherichia coli. The recombinant enzyme PpPel10a had a predicted Mr of 45.2 kDa and pI of 9.41. Using polygalacturonic acid (PGA) as substrate, the optimal conditions for PpPel10a reaction were determined to be 50 °C and pH 9.0, respectively. The Km, vmax and kcat values of PpPel10a with PGA as substrate were 0.12 g/L, 289 μmol/min/mg, and 202.3 s−1, respectively. Recombinant PpPel10a degraded citrus pectin, producing unsaturated mono- and oligogalacturonic acids. PpPel10a reduced the viscosity of PGA, and weight loss of ramie (Boehmeria nivea) fibers was observed after treatment with the enzyme alone (22.5%) or the enzyme in combination with alkali (26.3%). This enzyme has potential for use in plant fiber processing.
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18
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Huang S, Makarem M, Kiemle SN, Zheng Y, He X, Ye D, Gomez EW, Gomez ED, Cosgrove DJ, Kim SH. Dehydration-induced physical strains of cellulose microfibrils in plant cell walls. Carbohydr Polym 2018; 197:337-348. [DOI: 10.1016/j.carbpol.2018.05.091] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/05/2018] [Accepted: 05/30/2018] [Indexed: 01/08/2023]
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19
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Belik AA, Silchenko AS, Kusaykin MI, Zvyagintseva TN, Ermakova SP. Alginate Lyases: Substrates, Structure, Properties, and Prospects of Application. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018040040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Periplasmic depolymerase provides insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides. Proc Natl Acad Sci U S A 2018; 115:E4870-E4879. [PMID: 29735649 PMCID: PMC6003464 DOI: 10.1073/pnas.1801336115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Capsules are critical virulence determinants for bacterial pathogens. They are composed of capsular polysaccharides (CPSs) with diverse structures, whose assembly on the cell surface is often powered by a conserved ABC transporter. Current capsule-assembly models include a contiguous trans-envelope channel directing nascent CPSs from the transporter to the cell surface. This conserved apparatus is an attractive target for antivirulence antimicrobial development. This work describes a CPS depolymerizing lyase enzyme found in the Burkholderiales and unique structural features that define its mechanism, CPS specificity, and evolution to function in the periplasm in a noncatabolic role. The activity of this enzyme provides evidence that CPS assembled in an ABC transporter-dependent system is exposed to periplasm during translocation to the cell surface. Capsules are surface layers of hydrated capsular polysaccharides (CPSs) produced by many bacteria. The human pathogen Salmonella enterica serovar Typhi produces “Vi antigen” CPS, which contributes to virulence. In a conserved strategy used by bacteria with diverse CPS structures, translocation of Vi antigen to the cell surface is driven by an ATP-binding cassette (ABC) transporter. These transporters are engaged in heterooligomeric complexes proposed to form an enclosed translocation conduit to the cell surface, allowing the transporter to power the entire process. We identified Vi antigen biosynthesis genetic loci in genera of the Burkholderiales, which are paradoxically distinguished from S. Typhi by encoding VexL, a predicted pectate lyase homolog. Biochemical analyses demonstrated that VexL is an unusual metal-independent endolyase with an acidic pH optimum that is specific for O-acetylated Vi antigen. A 1.22-Å crystal structure of the VexL-Vi antigen complex revealed features which distinguish common secreted catabolic pectate lyases from periplasmic VexL, which participates in cell-surface assembly. VexL possesses a right-handed parallel β-superhelix, of which one face forms an electropositive glycan-binding groove with an extensive hydrogen bonding network that includes Vi antigen acetyl groups and confers substrate specificity. VexL provided a probe to interrogate conserved features of the ABC transporter-dependent export model. When introduced into S. Typhi, VexL localized to the periplasm and degraded Vi antigen. In contrast, a cytosolic derivative had no effect unless export was disrupted. These data provide evidence that CPS assembled in ABC transporter-dependent systems is actually exposed to the periplasm during envelope translocation.
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21
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Xu F, Wang P, Zhang YZ, Chen XL. Diversity of Three-Dimensional Structures and Catalytic Mechanisms of Alginate Lyases. Appl Environ Microbiol 2018; 84:e02040-17. [PMID: 29150496 PMCID: PMC5772247 DOI: 10.1128/aem.02040-17] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alginate is a linear polysaccharide produced mainly by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units, β-d-mannuronate (M) and its C-5 epimer α-l-guluronate (G). Alginate lyases are polysaccharide lyases (PL) that degrade alginate via a β-elimination reaction. These enzymes play an important role in marine carbon recycling and also have widespread industrial applications. So far, more than 1,774 alginate lyase sequences have been identified and are distributed into 7 PL families. In this review, the folds, conformational changes during catalysis, and catalytic mechanisms of alginate lyases are described. Thus far, structures for 15 alginate lyases have been solved and are divided into 3 fold classes: the β-jelly roll class (PL7, -14, and -18), the (α/α)n toroid class (PL5, -15, and -17), and the β-helix fold (PL6). These enzymes adopt two different mechanisms for catalysis, and three kinds of conformational changes occur during this process. Moreover, common features in the structures, conformational changes, and catalytic mechanisms are summarized, providing a comprehensive understanding on alginate lyases.
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Affiliation(s)
- Fei Xu
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Peng Wang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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22
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Qin HM, Xu P, Guo Q, Cheng X, Gao D, Sun D, Zhu Z, Lu F. Biochemical characterization of a novel ulvan lyase from Pseudoalteromonas sp. strain PLSV. RSC Adv 2018; 8:2610-2615. [PMID: 35541464 PMCID: PMC9077492 DOI: 10.1039/c7ra12294b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/29/2017] [Indexed: 11/21/2022] Open
Abstract
Ulvans, complex polysaccharides found in the ulvales (green seaweed) cell wall, contain predominantly 3-sulfated rhamnose (Rha3S) linked to either d-glucuronic acid, l-iduronic acid or d-xylose. The ulvan lyase endolytically cleaves the glycoside bond between Rha3S and uronic acid via a β-elimination mechanism. Ulvan lyase has been identified as belonging to the polysaccharide lyase family PL24 or PL25 in the carbohydrate active enzymes database, in which fewer members have been characterized. We present the cloning and characterization of a novel ulvan lyase from Pseudoalteromonas sp. strain PLSV (PsPL). The enzymes were heterologously expressed in Escherichia coli BL21 (DE3) and purified as the His-tag fusion protein using affinity chromatography, ion-exchange chromatography and size-exclusion chromatography. The degradation products were determined by thin-layer chromatography (TLC), liquid chromatography-mass spectrometry (LC-MS) to be mainly disaccharides and tetrasaccharides. Ulvan lyase provides an example of degrading ulvales into oligosaccharides. Arg265, His152 and Tyr249 were considered to serve as catalytic residues based on PsPL structural model analysis. Ulvans, complex polysaccharides found in the ulvales (green seaweed) cell wall, contain predominantly 3-sulfated rhamnose (Rha3S) linked to either d-glucuronic acid, l-iduronic acid or d-xylose.![]()
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Affiliation(s)
- Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- China
- Tianjin Key Laboratory of Industrial Microbiology
- China
| | - Panpan Xu
- College of Biotechnology
- Tianjin University of Science and Technology
- China
| | - Qianqian Guo
- College of Biotechnology
- Tianjin University of Science and Technology
- China
| | - Xiaotao Cheng
- College of Biotechnology
- Tianjin University of Science and Technology
- China
| | - Dengke Gao
- College of Biotechnology
- Tianjin University of Science and Technology
- China
| | - Dengyue Sun
- College of Biotechnology
- Tianjin University of Science and Technology
- China
| | - Zhangliang Zhu
- College of Biotechnology
- Tianjin University of Science and Technology
- China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- China
- Tianjin Key Laboratory of Industrial Microbiology
- China
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23
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Munoz-Munoz J, Cartmell A, Terrapon N, Baslé A, Henrissat B, Gilbert HJ. An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins. J Biol Chem 2017. [PMID: 28637865 DOI: 10.1074/jbc.m117.794578] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta, and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the l-rhamnose-α1,4-d-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Δ4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-β-l-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (α/α)6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the β-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.
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Affiliation(s)
- José Munoz-Munoz
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alan Cartmell
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France.,the USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France, and.,the Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
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24
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Ulaganathan T, Boniecki MT, Foran E, Buravenkov V, Mizrachi N, Banin E, Helbert W, Cygler M. New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture. ACS Chem Biol 2017; 12:1269-1280. [PMID: 28290654 DOI: 10.1021/acschembio.7b00126] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ulvan is a complex sulfated polysaccharide biosynthesized by green seaweed and contains predominantly rhamnose, xylose, and uronic acid sugars. Ulvan-degrading enzymes have only recently been identified and added to the CAZy ( www.cazy.org ) database as family PL24, but neither their structure nor catalytic mechanism(s) are yet known. Several homologous, new ulvan lyases, have been discovered in Pseudoalteromonas sp. strain PLSV, Alteromonas LOR, and Nonlabens ulvanivorans, defining a new family PL25, with the lyase encoded by the gene PLSV_3936 being one of them. This enzyme cleaves the glycosidic bond between 3-sulfated rhamnose (R3S) and glucuronic acid (GlcA) or iduronic acid (IdoA) via a β-elimination mechanism. We report the crystal structure of PLSV_3936 and its complex with a tetrasaccharide substrate. PLSV_3936 folds into a seven-bladed β-propeller, with each blade consisting of four antiparallel β-strands. Sequence conservation analysis identified a highly conserved region lining at one end of a deep crevice on the protein surface. The putative active site was identified by mutagenesis and activity measurements. Crystal structure of the enzyme with a bound tetrasaccharide substrate confirmed the identity of base and acid residues and allowed determination of the catalytic mechanism and also the identification of residues neutralizing the uronic acid carboxylic group. The PLSV_3936 structure provides an example of a convergent evolution among polysaccharide lyases toward a common active site architecture embedded in distinct folds.
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Affiliation(s)
| | - Michal T. Boniecki
- Department
of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Elizabeth Foran
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Vitaliy Buravenkov
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Naama Mizrachi
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Ehud Banin
- Institute
for Nanotechnology and Advanced Materials and Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - William Helbert
- Recherches
sur les Macromolécules Végétales, UPR-CNRS 5301, Université Joseph Fourier, and Institut de Chimie Moléculaire de Grenoble, ICMG, FR-CNRS
2607, Grenoble, France
| | - Miroslaw Cygler
- Department
of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
- Department
of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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25
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An Improved Kinetic Assay for the Characterization of Metal-Dependent Pectate Lyases. Methods Mol Biol 2017. [PMID: 28417359 DOI: 10.1007/978-1-4939-6899-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Pectate lyases are a subset of polysaccharide lyases (PLs) that specifically utilize a metal dependent β-elimination mechanism to cleave glyosidic bonds in homogalacturonan (HG; α-D-1,4-galacturonic acid). Most commonly, PLs harness calcium for catalysis; however, some PL families (e.g., PL2 and PL22) display preferences for transitional metals. Deploying alternative metals during β-elimination is correlated with signature coordination pocket chemistry, and is reflective of the evolution, functional specialization, and cellular location of PL activity. Here we describe an optimized method for the analysis of metal-dependent polysaccharide lyases (PLs). We use an endolytic PL2 from Yersinia enterocolitica (YePL2A) as example to demonstrate how altering the catalytic metal within the reaction can modulate PL kinetics.
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26
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Zhou Z, Liu Y, Chang Z, Wang H, Leier A, Marquez-Lago TT, Ma Y, Li J, Song J. Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming. Appl Microbiol Biotechnol 2016; 101:2919-2929. [PMID: 28028551 DOI: 10.1007/s00253-016-7994-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/26/2016] [Accepted: 11/05/2016] [Indexed: 11/27/2022]
Abstract
Biotechnological applications of microbial pectate lyases (Pels) in plant fiber processing are promising, eco-friendly substitutes for conventional chemical degumming processes. However, to potentiate the enzymes' use for industrial applications, resolving the molecular structure to elucidate catalytic mechanisms becomes necessary. In this manuscript, we report the high resolution (1.45 Å) crystal structure of pectate lyase (pelN) from Paenibacillus sp. 0602 in apo form. Through sequence alignment and structural superposition with other members of the polysaccharide lyase (PL) family 1 (PL1), we determined that pelN shares the characteristic right-handed β-helix and is structurally similar to other members of the PL1 family, while exhibiting key differences in terms of catalytic and substrate binding residues. Then, based on information from structure alignments with other PLs, we engineered a novel pelN. Our rational design yielded a pelN mutant with a temperature for enzymatic activity optimally shifted from 67.5 to 60 °C. Most importantly, this pelN mutant displayed both higher specific activity and ramie fiber degumming ability when compared with the wild-type enzyme. Altogether, our rational design method shows great potential for industrial applications. Moreover, we expect the reported high-resolution crystal structure to provide a solid foundation for future rational, structure-based engineering of genetically enhanced pelNs.
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Affiliation(s)
- Zhanping Zhou
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yang Liu
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhenying Chang
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huilin Wang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - André Leier
- Isaac Newton Institute for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Tatiana T Marquez-Lago
- Isaac Newton Institute for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Yanhe Ma
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jian Li
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Jiangning Song
- National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, 3800, Australia.
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27
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Ma G, Zhu W, Liu Y. QM/MM studies on the calcium-assisted β-elimination mechanism of pectate lyase from bacillus subtilis. Proteins 2016; 84:1606-1615. [DOI: 10.1002/prot.25103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/06/2016] [Accepted: 07/15/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Guangcai Ma
- Key Laboratory of Colloid and Interface Chemistry; Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University; Shandong Jinan 250100 China
| | - Wenyou Zhu
- Key Laboratory of Colloid and Interface Chemistry; Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University; Shandong Jinan 250100 China
- College of Chemistry and Chemical Engineering; Xuzhou Institute of Technology; Xuzhou Jiangsu 221111 China
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry; Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University; Shandong Jinan 250100 China
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28
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Nguyen SG, Kim J, Guevarra RB, Lee JH, Kim E, Kim SI, Unno T. Laminarin favorably modulates gut microbiota in mice fed a high-fat diet. Food Funct 2016; 7:4193-4201. [DOI: 10.1039/c6fo00929h] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We investigated the anti-obesity effects of the potential prebiotic, laminarin, on mice fed a high-fat diet.
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Affiliation(s)
- Son G. Nguyen
- Faculty of Biotechnology
- College of Applied Life Science
- SARI
- Jeju National University
- Jeju 63243
| | - Jungman Kim
- Faculty of Biotechnology
- College of Applied Life Science
- SARI
- Jeju National University
- Jeju 63243
| | - Robin B. Guevarra
- Faculty of Biotechnology
- College of Applied Life Science
- SARI
- Jeju National University
- Jeju 63243
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry
- Chonbuk National University
- Jeonju 561-756
- Republic of Korea
| | - Eungpil Kim
- Marine Biotechnology Research Center
- Jellanam-do
- South Korea
| | - Su-il Kim
- Marine Biotechnology Research Center
- Jellanam-do
- South Korea
| | - Tatsuya Unno
- Faculty of Biotechnology
- College of Applied Life Science
- SARI
- Jeju National University
- Jeju 63243
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29
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Ali S, Søndergaard CR, Teixeira S, Pickersgill RW. Structural insights into the loss of catalytic competence in pectate lyase activity at low pH. FEBS Lett 2015; 589:3242-6. [PMID: 26420545 DOI: 10.1016/j.febslet.2015.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 09/20/2015] [Indexed: 10/23/2022]
Abstract
Pectate lyase, a family 1 polysaccharide lyase, catalyses cleavage of the α-1,4 linkage of the polysaccharide homogalacturonan via an anti β-elimination reaction. In the Michaelis complex two calcium ions bind between the C6 carboxylate of the d-galacturonate residue and enzyme aspartates at the active centre (+1 subsite), they withdraw electrons acidifying the C5 proton facilitating its abstraction by the catalytic arginine. Here we show that activity is lost at low pH because protonation of aspartates results in the loss of the two catalytic calcium-ions causing a profound failure to correctly organise the Michaelis complex.
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Affiliation(s)
- Salyha Ali
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; School of Biological and Chemical Sciences, Queen Mary University of London, Department of Chemistry & Biochemistry, Mile End Road, London E1 4NS, United Kingdom
| | | | - Susana Teixeira
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Queen Mary University of London, Department of Chemistry & Biochemistry, Mile End Road, London E1 4NS, United Kingdom.
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30
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McLean R, Hobbs JK, Suits MD, Tuomivaara ST, Jones DR, Boraston AB, Abbott DW. Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2. J Biol Chem 2015; 290:21231-43. [PMID: 26160170 DOI: 10.1074/jbc.m115.664847] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Indexed: 11/06/2022] Open
Abstract
Family 2 polysaccharide lyases (PL2s) preferentially catalyze the β-elimination of homogalacturonan using transition metals as catalytic cofactors. PL2 is divided into two subfamilies that have been generally associated with secretion, Mg(2+) dependence, and endolysis (subfamily 1) and with intracellular localization, Mn(2+) dependence, and exolysis (subfamily 2). When present within a genome, PL2 genes are typically found as tandem copies, which suggests that they provide complementary activities at different stages along a catabolic cascade. This relationship most likely evolved by gene duplication and functional divergence (i.e. neofunctionalization). Although the molecular basis of subfamily 1 endolytic activity is understood, the adaptations within the active site of subfamily 2 enzymes that contribute to exolysis have not been determined. In order to investigate this relationship, we have conducted a comparative enzymatic analysis of enzymes dispersed within the PL2 phylogenetic tree and elucidated the structure of VvPL2 from Vibrio vulnificus YJ016, which represents a transitional member between subfamiles 1 and 2. In addition, we have used ancestral sequence reconstruction to functionally investigate the segregated evolutionary history of PL2 progenitor enzymes and illuminate the molecular evolution of exolysis. This study highlights that ancestral sequence reconstruction in combination with the comparative analysis of contemporary and resurrected enzymes holds promise for elucidating the origins and activities of other carbohydrate active enzyme families and the biological significance of cryptic metabolic pathways, such as pectinolysis within the zoonotic marine pathogen V. vulnificus.
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Affiliation(s)
- Richard McLean
- From the Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - Joanne K Hobbs
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - Michael D Suits
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada, the Department of Chemistry and Biochemistry, Wilfred Laurier University, Waterloo, Ontario N2L 3C5, Canada, and
| | - Sami T Tuomivaara
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Darryl R Jones
- From the Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - Alisdair B Boraston
- the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
| | - D Wade Abbott
- From the Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada,
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31
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Hugouvieux-Cotte-Pattat N, Condemine G, Shevchik VE. Bacterial pectate lyases, structural and functional diversity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:427-40. [PMID: 25646533 DOI: 10.1111/1758-2229.12166] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Pectate lyases are enzymes involved in plant cell wall degradation. They cleave pectin using a β-elimination mechanism, specific for acidic polysaccharides. They are mainly produced by plant pathogens and plant-associated organisms, and only rarely by animals. Pectate lyases are also commonly produced in the bacterial world, either by bacteria living in close proximity with plants or by gut bacteria that find plant material in the digestive tract of their hosts. The role of pectate lyases is essential for plant pathogens, such as Dickeya dadantii, that use a set of pectate lyases as their main virulence factor. Symbiotic bacteria produce their own pectate lyases, but they also induce plant pectate lyases to initiate the symbiosis. Pectin degradation products may act as signals affecting the plant–bacteria interactions. Bacterial pectate lyases are also essential for using the pectin of dead or living plants as a carbon source for growth. In the animal gut, Bacteroides pectate lyases degrade the pectin of ingested food, and this is particularly important for herbivores that depend on their microflora for the digestion of pectin. Some human pathogens, such as Yersinia enterocolitica, produce a few intracellular pectate lyases that can facilitate their growth in the presence of highly pectinolytic bacteria, at the plant surface, in the soil or in the animal gut.
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32
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Garron ML, Cygler M. Uronic polysaccharide degrading enzymes. Curr Opin Struct Biol 2014; 28:87-95. [PMID: 25156747 DOI: 10.1016/j.sbi.2014.07.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/24/2014] [Accepted: 07/30/2014] [Indexed: 12/13/2022]
Abstract
In the past several years progress has been made in the field of structure and function of polysaccharide lyases (PLs). The number of classified polysaccharide lyase families has increased to 23 and more detailed analysis has allowed the identification of more closely related subfamilies, leading to stronger correlation between each subfamily and a unique substrate. The number of as yet unclassified polysaccharide lyases has also increased and we expect that sequencing projects will allow many of these unclassified sequences to emerge as new families. The progress in structural analysis of PLs has led to having at least one representative structure for each of the families and for two unclassified enzymes. The newly determined structures have folds observed previously in other PL families and their catalytic mechanisms follow either metal-assisted or Tyr/His mechanisms characteristic for other PL enzymes. Comparison of PLs with glycoside hydrolases (GHs) shows several folds common to both classes but only for the β-helix fold is there strong indication of divergent evolution from a common ancestor. Analysis of bacterial genomes identified gene clusters containing multiple polysaccharide cleaving enzymes, the Polysaccharides Utilization Loci (PULs), and their gene complement suggests that they are organized to process completely a specific polysaccharide.
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Affiliation(s)
- Marie-Line Garron
- Aix-Marseille University, AFMB UMR7257, 163 Avenue de Luminy, 13288 Marseille, France; CNRS, AFMB UMR7257, 163 Avenue de Luminy, 13288 Marseille, France
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada.
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33
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Hung JE, Fogle EJ, Garg N, Chekan JR, Nair SK, van der Donk WA. Chemical rescue and inhibition studies to determine the role of Arg301 in phosphite dehydrogenase. PLoS One 2014; 9:e87134. [PMID: 24498026 PMCID: PMC3909101 DOI: 10.1371/journal.pone.0087134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/19/2013] [Indexed: 12/11/2022] Open
Abstract
Phosphite dehydrogenase (PTDH) catalyzes the NAD(+)-dependent oxidation of phosphite to phosphate. This reaction requires the deprotonation of a water nucleophile for attack on phosphite. A crystal structure was recently solved that identified Arg301 as a potential base given its proximity and orientation to the substrates and a water molecule within the active site. Mutants of this residue showed its importance for efficient catalysis, with about a 100-fold loss in k cat and substantially increased K m,phosphite for the Ala mutant (R301A). The 2.35 Å resolution crystal structure of the R301A mutant with NAD(+) bound shows that removal of the guanidine group renders the active site solvent exposed, suggesting the possibility of chemical rescue of activity. We show that the catalytic activity of this mutant is restored to near wild-type levels by the addition of exogenous guanidinium analogues; Brønsted analysis of the rates of chemical rescue suggests that protonation of the rescue reagent is complete in the transition state of the rate-limiting step. Kinetic isotope effects on the reaction in the presence of rescue agents show that hydride transfer remains at least partially rate-limiting, and inhibition experiments show that K i of sulfite with R301A is ∼400-fold increased compared to the parent enzyme, similar to the increase in K m for phosphite in this mutant. The results of our experiments indicate that Arg301 plays an important role in phosphite binding as well as catalysis, but that it is not likely to act as an active site base.
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Affiliation(s)
- John E. Hung
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Emily J. Fogle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Neha Garg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jonathan R. Chekan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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34
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Abstract
Over the sixty years since Koshland initially formulated the classical mechanisms for retaining and inverting glycosidases, researchers have assembled a large body of supporting evidence and have documented variations of these mechanisms. Recently, however, researchers have uncovered a number of completely distinct mechanisms for enzymatic cleavage of glycosides involving elimination and/or hydration steps. In family GH4 and GH109 glycosidases, the reaction proceeds via transient NAD(+)-mediated oxidation at C3, thereby acidifying the proton at C2 and allowing for elimination across the C1-C2 bond. Subsequent Michael-type addition of water followed by reduction at C3 generates the hydrolyzed product. Enzymes employing this mechanism can hydrolyze thioglycosides as well as both anomers of activated substrates. Sialidases employ a conventional retaining mechanism in which a tyrosine functions as the nucleophile, but in some cases researchers have observed off-path elimination end products. These reactions occur via the normal covalent intermediate, but instead of an attack by water on the anomeric center, the catalytic acid/base residue abstracts an adjacent proton. These enzymes can also catalyze hydration of the enol ether via the reverse pathway. Reactions of α-(1,4)-glucan lyases also proceed through a covalent intermediate with subsequent abstraction of an adjacent proton to give elimination. However, in this case, the departing carboxylate "nucleophile" serves as the base in a concerted but asynchronous syn-elimination process. These enzymes perform only elimination reactions. Polysaccharide lyases, which act on uronic acid-containing substrates, also catalyze only elimination reactions. Substrate binding neutralizes the charge on the carboxylate, which allows for abstraction of the proton on C5 and leads to an elimination reaction via an E1cb mechanism. These enzymes can also cleave thioglycosides, albeit slowly. The unsaturated product of polysaccharide lyases can then serve as a substrate for a hydration reaction carried out by unsaturated glucuronyl hydrolases. This hydration is initiated by protonation at C4 and proceeds in a Markovnikov fashion rather than undergoing a Michael-type addition, giving a hemiketal at C5. This hemiketal then undergoes a rearrangement that results in cleavage of the anomeric bond. These enzymes can also hydrolyze thioglycosides efficiently and slowly turn over substrates with inverted anomeric configuration. The mechanisms discussed in this Account proceed through transition states that involve either positive or negative charges, unlike the exclusively cationic transition states of the classical Koshland retaining and inverting glycosidases. In addition, the distribution of this charge throughout the substrate can vary substantially. The nature of these mechanisms and their transition states means that any inhibitors or inactivators of these unusual enzymes probably differ from those presently used for Koshland retaining or inverting glycosidases.
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Affiliation(s)
- Seino A. K. Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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35
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Huo L, Davis I, Chen L, Liu A. The power of two: arginine 51 and arginine 239* from a neighboring subunit are essential for catalysis in α-amino-β-carboxymuconate-epsilon-semialdehyde decarboxylase. J Biol Chem 2013; 288:30862-71. [PMID: 24019523 DOI: 10.1074/jbc.m113.496869] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although the crystal structure of α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase from Pseudomonas fluorescens was solved as a dimer, this enzyme is a mixture of monomer, dimer, and higher order structures in solution. In this work, we found that the dimeric state, not the monomeric state, is the functionally active form. Two conserved arginine residues are present in the active site: Arg-51 and an intruding Arg-239* from the neighboring subunit. In this study, they were each mutated to alanine and lysine, and all four mutants were catalytically inactive. The mutants were also incapable of accommodating pyridine-2,6-dicarboxylic acid, a competitive inhibitor of the native enzyme, suggesting that the two Arg residues are involved in substrate binding. It was also observed that the decarboxylase activity was partially recovered in a heterodimer hybridization experiment when inactive R51(A/K) and R239(A/K) mutants were mixed together. Of the 20 crystal structures obtained from mixing inactive R51A and R239A homodimers that diffracted to a resolution lower than 3.00 Å, two structures are clearly R51A/R239A heterodimers and belong to the C2 space group. They were refined to 1.80 and 2.00 Å resolutions, respectively. Four of the remaining crystals are apparently single mutants and belong to the P42212 space group. In the heterodimer structures, one active site is shown to contain dual mutation of Ala-51 and Ala-239*, whereas the other contains the native Arg-51 and Arg-239* residues, identical to the wild-type structure. Thus, these observations provide the foundation for a molecular mechanism by which the oligomerization state of α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase could regulate the enzyme activity.
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Affiliation(s)
- Lu Huo
- From the Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
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36
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Suits MD, Boraston AB. Structure of the Streptococcus pneumoniae surface protein and adhesin PfbA. PLoS One 2013; 8:e67190. [PMID: 23894284 PMCID: PMC3718772 DOI: 10.1371/journal.pone.0067190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/16/2013] [Indexed: 12/29/2022] Open
Abstract
PfbA (plasmin- and fibronectin-binding protein A) is an extracellular Streptococcus pneumoniae cell-wall attached surface protein that binds to fibronectin, plasmin, and plasminogen. Here we present a structural analysis of the surface exposed domains of PfbA using a combined approach of X-ray crystallography and small-angle X-ray scattering (SAXS). The crystal structure of the PfbA core domain, here called PfbAβ, determined to 2.28 Å resolution revealed an elongated 12-stranded parallel β-helix fold, which structure-based comparisons reveal is most similar to proteins with carbohydrate modifying activity. A notable feature of the PfbAβ is an extensive cleft on one face of the protein with electrochemical and spatial features that are analogous to structurally similar carbohydrate-active enzymes utilizing this feature for substrate accommodation. Though this cleft displays a combination of basic amino acid residues and solvent exposed aromatic amino acids that are distinct features for recognition of carbohydrates, no obvious arrangement of amino acid side chains that would constitute catalytic machinery is evident. The pseudo-atomic SAXS model of a larger fragment of PfbA suggests that it has a relatively well-ordered structure with the N-terminal and core domains of PfbA adopting an extend organization and reveals a novel structural class of surface exposed pneumococcal matrix molecule adhesins.
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Affiliation(s)
- Michael D. Suits
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
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37
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Hung JE, Fogle EJ, Christman HD, Johannes TW, Zhao H, Metcalf WW, van der Donk WA. Investigation of the role of Arg301 identified in the X-ray structure of phosphite dehydrogenase. Biochemistry 2012; 51:4254-62. [PMID: 22564138 PMCID: PMC3361975 DOI: 10.1021/bi201691w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Phosphite dehydrogenase (PTDH) from Pseudomonas
stutzeri catalyzes the nicotinamide adenine dinucleotide-dependent
oxidation
of phosphite to phosphate. The enzyme belongs to the family of d-hydroxy acid dehydrogenases (DHDHs). A search of the protein
databases uncovered many additional putative phosphite dehydrogenases.
The genes encoding four diverse candidates were cloned and expressed,
and the enzymes were purified and characterized. All oxidized phosphite
to phosphate and had similar kinetic parameters despite a low level
of pairwise sequence identity (39–72%). A recent crystal structure
identified Arg301 as a residue in the active site that has not been
investigated previously. Arg301 is fully conserved in the enzymes
shown here to be PTDHs, but the residue is not conserved in other
DHDHs. Kinetic analysis of site-directed mutants of this residue shows
that it is important for efficient catalysis, with an ∼100-fold
decrease in kcat and an almost 700-fold
increase in Km,phosphite for the R301A
mutant. Interestingly, the R301K mutant displayed a slightly higher kcat than the parent PTDH, and a more modest
increase in Km for phosphite (nearly 40-fold).
Given these results, Arg301 may be involved in the binding and orientation
of the phosphite substrate and/or play a catalytic role via electrostatic
interactions. Three other residues in the active site region that
are conserved in the PTDH orthologs but not DHDHs were identified
(Trp134, Tyr139, and Ser295). The importance of these residues was
also investigated by site-directed mutagenesis. All of the mutants
had kcat values similar to that of the
wild-type enzyme, indicating these residues are not important for
catalysis.
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Affiliation(s)
- John E Hung
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA
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38
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Blanc B, Mayfield JA, McDonald CA, Lukat-Rodgers GS, Rodgers KR, DuBois JL. Understanding how the distal environment directs reactivity in chlorite dismutase: spectroscopy and reactivity of Arg183 mutants. Biochemistry 2012; 51:1895-910. [PMID: 22313119 DOI: 10.1021/bi2017377] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chlorite dismutase from Dechloromonas aromatica (DaCld) catalyzes the highly efficient decomposition of chlorite to O(2) and chloride. Spectroscopic, equilibrium thermodynamic, and kinetic measurements have indicated that Cld has two pH sensitive moieties; one is the heme, and Arg183 in the distal heme pocket has been hypothesized to be the second. This active site residue has been examined by site-directed mutagenesis to understand the roles of positive charge and hydrogen bonding in O-O bond formation. Three Cld mutants, Arg183 to Lys (R183K), Arg183 to Gln (R183Q), and Arg183 to Ala (R183A), were investigated to determine their respective contributions to the decomposition of chlorite ion, the spin state and coordination states of their ferric and ferrous forms, their cyanide and imidazole binding affinities, and their reduction potentials. UV-visible and resonance Raman spectroscopies showed that DaCld(R183A) contains five-coordinate high-spin (5cHS) heme, the DaCld(R183Q) heme is a mixture of five-coordinate and six-coordinate high spin (5c/6cHS) heme, and DaCld(R183K) contains six-coordinate low-spin (6cLS) heme. In contrast to wild-type (WT) Cld, which exhibits pK(a) values of 6.5 and 8.7, all three ferric mutants exhibited pH-independent spectroscopic signatures and kinetic behaviors. Steady state kinetic parameters of the chlorite decomposition reaction catalyzed by the mutants suggest that in WT DaCld the pK(a) of 6.5 corresponds to a change in the availability of positive charge from the guanidinium group of Arg183 to the heme site. This could be due to either direct acid-base chemistry at the Arg183 side chain or a flexible Arg183 side chain that can access various orientations. Current evidence is most consistent with a conformational adjustment of Arg183. A properly oriented Arg183 is critical for the stabilization of anions in the distal pocket and for efficient catalysis.
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Affiliation(s)
- Béatrice Blanc
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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39
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Keenholtz RA, Rowland SJ, Boocock MR, Stark WM, Rice PA. Structural basis for catalytic activation of a serine recombinase. Structure 2011; 19:799-809. [PMID: 21645851 PMCID: PMC3238390 DOI: 10.1016/j.str.2011.03.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/17/2011] [Accepted: 03/22/2011] [Indexed: 12/01/2022]
Abstract
Sin resolvase is a site-specific serine recombinase that is normally controlled by a complex regulatory mechanism. A single mutation, Q115R, allows the enzyme to bypass the entire regulatory apparatus, such that no accessory proteins or DNA sites are required. Here, we present a 1.86 Å crystal structure of the Sin Q115R catalytic domain, in a tetrameric arrangement stabilized by an interaction between Arg115 residues on neighboring subunits. The subunits have undergone significant conformational changes from the inactive dimeric state previously reported. The structure provides a new high-resolution view of a serine recombinase active site that is apparently fully assembled, suggesting roles for the conserved active site residues. The structure also suggests how the dimer-tetramer transition is coupled to assembly of the active site. The tetramer is captured in a different rotational substate than that seen in previous hyperactive serine recombinase structures, and unbroken crossover site DNA can be readily modeled into its active sites.
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Affiliation(s)
- Ross A. Keenholtz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sally-J. Rowland
- Division of Molecular Genetics, FBLS, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Martin R. Boocock
- Division of Molecular Genetics, FBLS, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - W. Marshall Stark
- Division of Molecular Genetics, FBLS, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Phoebe A. Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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40
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Abstract
Carbohydrate-active enzymes face huge substrate diversity in a highly selective manner using only a limited number of available folds. They are therefore subjected to multiple divergent and convergent evolutionary events. This and their frequent modularity render their functional annotation in genomes difficult in a number of cases. In the present paper, a classification of polysaccharide lyases (the enzymes that cleave polysaccharides using an elimination instead of a hydrolytic mechanism) is shown thoroughly for the first time. Based on the analysis of a large panel of experimentally characterized polysaccharide lyases, we examined the correlation of various enzyme properties with the three levels of the classification: fold, family and subfamily. The resulting hierarchical classification, which should help annotate relevant genes in genomic efforts, is available and constantly updated at the Carbohydrate-Active Enzymes Database (http://www.cazy.org).
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41
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Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL, Larsen S, Leggio LL. Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus aculeatus. J Mol Biol 2010; 404:100-11. [DOI: 10.1016/j.jmb.2010.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/02/2010] [Accepted: 09/06/2010] [Indexed: 11/24/2022]
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42
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Abbott DW, Gilbert HJ, Boraston AB. The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination. J Biol Chem 2010; 285:39029-38. [PMID: 20851883 DOI: 10.1074/jbc.m110.153981] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Oligogalacturonate lyases (OGLs; now also classified as pectate lyase family 22) are cytoplasmic enzymes found in pectinolytic members of Enterobacteriaceae, such as the enteropathogen Yersinia enterocolitica. OGLs utilize a β-elimination mechanism to preferentially catalyze the conversion of saturated and unsaturated digalacturonate into monogalacturonate and the 4,5-unsaturated monogalacturonate-like molecule, 5-keto-4-deoxyuronate. To provide mechanistic insights into the specificity of this enzyme activity, we have characterized the OGL from Y. enterocolitica, YeOGL, on oligogalacturonides and determined its three-dimensional x-ray structure to 1.65 Å. The model contains a Mn(2+) atom in the active site, which is coordinated by three histidines, one glutamine, and an acetate ion. The acetate mimics the binding of the uronate group of galactourono-configured substrates. These findings, in combination with enzyme kinetics and metal supplementation assays, provide a framework for modeling the active site architecture of OGL. This enzyme appears to contain a histidine for the abstraction of the α-proton in the -1 subsite, a residue that is highly conserved throughout the OGL family and represents a unique catalytic base among pectic active lyases. In addition, we present a hypothesis for an emerging relationship observed between the cellular distribution of pectate lyase folding and the distinct metal coordination chemistries of pectate lyases.
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Affiliation(s)
- D Wade Abbott
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA.
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43
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Garron ML, Cygler M. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 2010; 20:1547-73. [PMID: 20805221 DOI: 10.1093/glycob/cwq122] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polysaccharide lyases (PLs) have been assigned to 21 families based on their sequences, with ~ 50 singletons awaiting further classification. For 19 of these families, the structure of at least one protein is known. In this review, we have analyzed the available structural information and show that presently known PL families belong to six general folds. Only two general catalytic mechanisms have been observed among these PLs: (1) metal-assisted neutralization of the acidic group of the sugar next to the cleaved bond, with, rather unusually, arginine or lysine playing the role of Brønsted base and (2) neutralization of the acidic group on the sugar by a close approach of an amino or acidic group forcing its protonation and Tyr or Tyr-His acting as the Brønsted base and acid.
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Affiliation(s)
- Marie-Line Garron
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
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44
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Basu S, Roy A, Ghosh A, Bera A, Chattopadhyay D, Chakrabarti K. Arg235 is an essential catalytic residue of Bacillus pumilus DKS1 pectate lyase to degum ramie fibre. Biodegradation 2010; 22:153-61. [DOI: 10.1007/s10532-010-9384-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 06/23/2010] [Indexed: 10/19/2022]
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45
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Thompson JE, Pourhossein M, Waterhouse A, Hudson T, Goldrick M, Derrick JP, Roberts IS. The K5 lyase KflA combines a viral tail spike structure with a bacterial polysaccharide lyase mechanism. J Biol Chem 2010; 285:23963-9. [PMID: 20519506 DOI: 10.1074/jbc.m110.127571] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
K5 lyase A (KflA) is a tail spike protein (TSP) encoded by a K5A coliphage, which cleaves K5 capsular polysaccharide, a glycosaminoglycan with the repeat unit [-4)-betaGlcA-(1,4)- alphaGlcNAc(1-], displayed on the surface of Escherichia coli K5 strains. The crystal structure of KflA reveals a trimeric arrangement, with each monomer containing a right-handed, single-stranded parallel beta-helix domain. Stable trimer formation by the intertwining of strands in the C-terminal domain, followed by proteolytic maturation, is likely to be catalyzed by an autochaperone as described for K1F endosialidase. The structure of KflA represents the first bacteriophage tail spike protein combining polysaccharide lyase activity with a single-stranded parallel beta-helix fold. We propose a catalytic site and mechanism representing convergence with the syn-beta-elimination site of heparinase II from Pedobacter heparinus.
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Affiliation(s)
- James E Thompson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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Gilbert HJ. The biochemistry and structural biology of plant cell wall deconstruction. PLANT PHYSIOLOGY 2010; 153:444-55. [PMID: 20406913 PMCID: PMC2879781 DOI: 10.1104/pp.110.156646] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 04/17/2010] [Indexed: 05/18/2023]
Affiliation(s)
- Harry J Gilbert
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA.
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Ochiai A, Yamasaki M, Mikami B, Hashimoto W, Murata K. Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens. J Biol Chem 2010; 285:24519-28. [PMID: 20507980 DOI: 10.1074/jbc.m110.125450] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alginate, a major component of the cell wall matrix in brown seaweeds, is degraded by alginate lyases through a beta-elimination reaction. Almost all alginate lyases act endolytically on substrate, thereby yielding unsaturated oligouronic acids having 4-deoxy-l-erythro-hex-4-enepyranosyluronic acid at the nonreducing end. In contrast, Agrobacterium tumefaciens alginate lyase Atu3025, a member of polysaccharide lyase family 15, acts on alginate polysaccharides and oligosaccharides exolytically and releases unsaturated monosaccharides from the substrate terminal. The crystal structures of Atu3025 and its inactive mutant in complex with alginate trisaccharide (H531A/DeltaGGG) were determined at 2.10- and 2.99-A resolutions with final R-factors of 18.3 and 19.9%, respectively, by x-ray crystallography. The enzyme is comprised of an alpha/alpha-barrel + anti-parallel beta-sheet as a basic scaffold, and its structural fold has not been seen in alginate lyases analyzed thus far. The structural analysis of H531A/DeltaGGG and subsequent site-directed mutagenesis studies proposed the enzyme reaction mechanism, with His(311) and Tyr(365) as the catalytic base and acid, respectively. Two structural determinants, i.e. a short alpha-helix in the central alpha/alpha-barrel domain and a conformational change at the interface between the central and C-terminal domains, are essential for the exolytic mode of action. This is, to our knowledge, the first report on the structure of the family 15 enzyme.
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Affiliation(s)
- Akihito Ochiai
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Seyedarabi A, To TT, Ali S, Hussain S, Fries M, Madsen R, Clausen MH, Teixteira S, Brocklehurst K, Pickersgill RW. Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase. Biochemistry 2010; 49:539-46. [PMID: 20000851 DOI: 10.1021/bi901503g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pectate lyases harness anti beta-elimination chemistry to cleave the alpha-1,4 linkage in the homogalacturonan region of plant cell wall pectin. We have studied the binding of five pectic oligosaccharides to Bacillus subtilis pectate lyase in crystals of the inactive enzyme in which the catalytic base is substituted with alanine (R279A). We discover that the three central subsites (-1, +1, and +2) have a profound preference for galacturonate but that the distal subsites can accommodate methylated galacturonate. It is reasonable to assume therefore that pectate lyase can cleave pectin with three consecutive galacturonate residues. The enzyme in the absence of substrate binds a single calcium ion, and we show that two additional calcium ions bind between enzyme and substrate carboxylates occupying the +1 subsite in the Michaelis complex. The substrate binds less intimately to the enzyme in a complex made with a catalytic base in place but in the absence of the calcium ions and an adjacent lysine. In this complex, the catalytic base is correctly positioned to abstract the C5 proton, but there are no calcium ions binding the carboxylate at the +1 subsite. It is clear, therefore, that the catalytic calcium ions and adjacent lysine promote catalysis by acidifying the alpha-proton, facilitating its abstraction by the base. There is also clear evidence that binding distorts the relaxed 2(1) or 3(1) helical conformation of the oligosaccharides in the region of the scissile bond.
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Affiliation(s)
- Arefeh Seyedarabi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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Konno N, Ishida T, Igarashi K, Fushinobu S, Habu N, Samejima M, Isogai A. Crystal structure of polysaccharide lyase family 20 endo-beta-1,4-glucuronan lyase from the filamentous fungus Trichoderma reesei. FEBS Lett 2009; 583:1323-6. [PMID: 19306878 DOI: 10.1016/j.febslet.2009.03.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 03/11/2009] [Accepted: 03/16/2009] [Indexed: 10/21/2022]
Abstract
The crystal structure of endo-beta-(1-->4)-glucuronan lyase from Trichoderma reesei (TrGL) has been determined at 1.8A resolution as the first three-dimensional structure of polysaccharide lyase (PL) family 20. TrGL has a typical beta-jelly roll fold, which is similar to glycoside hydrolase family 16 and PL7 enzymes. A calcium ion is bound to the site far from the cleft and appears to contribute to the stability. There are several completely conserved residues in the cleft. Possible catalytic residues are predicted based on structural comparison with PL7 alginate lyase A1-II'.
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Affiliation(s)
- Naotake Konno
- Department of Biomaterials, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Structural biology of pectin degradation by Enterobacteriaceae. Microbiol Mol Biol Rev 2008; 72:301-16, table of contents. [PMID: 18535148 DOI: 10.1128/mmbr.00038-07] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
SUMMARY Pectin is a structural polysaccharide that is integral for the stability of plant cell walls. During soft rot infection, secreted virulence factors from pectinolytic bacteria such as Erwinia spp. degrade pectin, resulting in characteristic plant cell necrosis and tissue maceration. Catabolism of pectin and its breakdown products by pectinolytic bacteria occurs within distinct cellular environments. This process initiates outside the cell, continues within the periplasmic space, and culminates in the cytoplasm. Although pectin utilization is well understood at the genetic and biochemical levels, an inclusive structural description of pectinases and pectin binding proteins by both extracellular and periplasmic enzymes has been lacking, especially following the recent characterization of several periplasmic components and protein-oligogalacturonide complexes. Here we provide a comprehensive analysis of the protein folds and mechanisms of pectate lyases, polygalacturonases, and carbohydrate esterases and the binding specificities of two periplasmic pectic binding proteins from Enterobacteriaceae. This review provides a structural understanding of the molecular determinants of pectin utilization and the mechanisms driving catabolite selectivity and flow through the pathway.
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