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Kheirollahi A, Sadeghi S, Orandi S, Moayedi K, Khajeh K, Khoobi M, Golestani A. Chondroitinase as a therapeutic enzyme: Prospects and challenges. Enzyme Microb Technol 2024; 172:110348. [PMID: 37898093 DOI: 10.1016/j.enzmictec.2023.110348] [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: 05/22/2023] [Revised: 09/28/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
The chondroitinases (Chase) are bacterial lyases that specifically digest chondroitin sulfate and/or dermatan sulfate glycosaminoglycans via a β-elimination reaction and generate unsaturated disaccharides. In recent decades, these enzymes have attracted the attention of many researchers due to their potential applications in various aspects of medicine from the treatment of spinal cord injury to use as an analytical tool. In spite of this diverse spectrum, the application of Chase is faced with several limitations and challenges such as thermal instability and lack of a suitable delivery system. In the current review, we address potential therapeutic applications of Chase with emphasis on the challenges ahead. Then, we summarize the latest achievements to overcome the problems by considering the studies carried out in the field of enzyme engineering, drug delivery, and combination-based therapy.
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Affiliation(s)
- Asma Kheirollahi
- Department of Comparative Biosciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Solmaz Sadeghi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Orandi
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiana Moayedi
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Mehdi Khoobi
- Department of Radiopharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Golestani
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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2
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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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3
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Mesdaghi S, Price RM, Madine J, Rigden DJ. Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space. J Struct Biol 2023; 215:108010. [PMID: 37544372 DOI: 10.1016/j.jsb.2023.108010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/19/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Repeat proteins are common in all domains of life and exhibit a wide range of functions. One class of repeat protein contains solenoid folds where the repeating unit consists of β-strands separated by tight turns. β-solenoids have distinguishing structural features such as handedness, twist, oligomerisation state, coil shape and size which give rise to their diversity. Characterised β-solenoid repeat proteins are known to form regions in bacterial and viral virulence factors, antifreeze proteins and functional amyloids. For many of these proteins, the experimental structure has not been solved, as they are difficult to crystallise or model. Here we use various deep learning-based structure-modelling methods to discover novel predicted β-solenoids, perform structural database searches to mine further structural neighbours and relate their predicted structure to possible functions. We find both eukaryotic and prokaryotic adhesins, confirming a known functional linkage between adhesin function and the β-solenoid fold. We further identify exceptionally long, flat β-solenoid folds as possible structures of mucin tandem repeat regions and unprecedentedly small β-solenoid structures. Additionally, we characterise a novel β-solenoid coil shape, the FapC Greek key β-solenoid as well as plausible complexes between it and other proteins involved in Pseudomonas functional amyloid fibres.
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Affiliation(s)
- Shahram Mesdaghi
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom; Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Rebecca M Price
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Jillian Madine
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom.
| | - Daniel J Rigden
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom.
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Wang J, Liu Z, Pan X, Wang N, Li L, Du Y, Li J, Li M. Structural and Biochemical Analysis Reveals Catalytic Mechanism of Fucoidan Lyase from Flavobacterium sp. SA-0082. Mar Drugs 2022; 20:md20080533. [PMID: 36005536 PMCID: PMC9410043 DOI: 10.3390/md20080533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Fucoidans represent a type of polyanionic fucose-containing sulfated polysaccharides (FCSPs) that are cleaved by fucoidan-degrading enzymes, producing low-molecular-weight fucoidans with multiple biological activities suitable for pharmacological use. Most of the reported fucoidan-degrading enzymes are glycoside hydrolases, which have been well studied for their structures and catalytic mechanisms. Little is known, however, about the rarer fucoidan lyases, primarily due to the lack of structural information. FdlA from Flavobacterium sp. SA-0082 is an endo-type fucoidan-degrading enzyme that cleaves the sulfated fuco-glucuronomannan (SFGM) through a lytic mechanism. Here, we report nine crystal structures of the catalytic N-terminal domain of FdlA (FdlA-NTD), in both its wild type (WT) and mutant forms, at resolutions ranging from 1.30 to 2.25 Å. We show that the FdlA-NTD adopts a right-handed parallel β-helix fold, and possesses a substrate binding site composed of a long groove and a unique alkaline pocket. Our structural, biochemical, and enzymological analyses strongly suggest that FdlA-NTD utilizes catalytic residues different from other β-helix polysaccharide lyases, potentially representing a novel polysaccharide lyase family.
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Affiliation(s)
- Juanjuan Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zebin Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- College of Life Science, Capital Normal University, Beijing 100101, China
| | - Xiaowei Pan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, Capital Normal University, Beijing 100101, China
| | - Ning Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Legong Li
- College of Life Science, Capital Normal University, Beijing 100101, China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Correspondence: (J.L.); (M.L.)
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (J.L.); (M.L.)
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5
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Mou M, Hu Q, Li H, Long L, Li Z, Du X, Jiang Z, Ni H, Zhu Y. Characterization of a Thermostable and Surfactant-Tolerant Chondroitinase B from a Marine Bacterium Microbulbifer sp. ALW1. Int J Mol Sci 2022; 23:5008. [PMID: 35563396 PMCID: PMC9103228 DOI: 10.3390/ijms23095008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 02/05/2023] Open
Abstract
Chondroitinase plays an important role in structural and functional studies of chondroitin sulfate (CS). In this study, a new member of chondroitinase B of PL6 family, namely ChSase B6, was cloned from marine bacterium Microbulbifer sp. ALW1 and subjected to enzymatic and structural characterization. The recombinant ChSase B6 showed optimum activity at 40 °C and pH 8.0, with enzyme kinetic parameters of Km and Vmax against chondroitin sulfate B (CSB) to be 7.85 µg/mL and 1.21 U/mg, respectively. ChSase B6 demonstrated thermostability under 60 °C for 2 h with about 50% residual activity and good pH stability under 4.0-10.0 for 1 h with above 60% residual activity. In addition, ChSase B6 displayed excellent stability against the surfactants including Tween-20, Tween-80, Trion X-100, and CTAB. The degradation products of ChSase B6-treated CSB exhibited improved antioxidant ability as a hydroxyl radical scavenger. Structural analysis and site-directed mutagenesis suggested that the conserved residues Lys248 and Arg269 were important for the activity of ChSase B6. Characterization, structure, and molecular dynamics simulation of ChSase B6 provided a guide for further tailoring for its industrial application for chondroitin sulfate bioresource development.
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Affiliation(s)
- Mingjing Mou
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
| | - Qingsong Hu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
| | - Hebin Li
- Department of Pharmacy, Xiamen Medical College, Xiamen 361023, China;
| | - Liufei Long
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
| | - Xiping Du
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; (M.M.); (Q.H.); (L.L.); (Z.L.); (X.D.); (Z.J.); (H.N.)
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6
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Wang M, Chen L, Lou Z, Yuan X, Pan G, Ren X, Wang P. Cloning and Characterization of a Novel Alginate Lyase from Paenibacillus sp. LJ-23. Mar Drugs 2022; 20:md20010066. [PMID: 35049921 PMCID: PMC8780880 DOI: 10.3390/md20010066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/01/2023] Open
Abstract
As a low molecular weight alginate, alginate oligosaccharides (AOS) exhibit improved water solubility, better bioavailability, and comprehensive health benefits. In addition, their biocompatibility, biodegradability, non-toxicity, non-immunogenicity, and gelling capability make them an excellent biomaterial with a dual curative effect when applied in a drug delivery system. In this paper, a novel alginate lyase, Algpt, was cloned and characterized from a marine bacterium, Paenibacillus sp. LJ-23. The purified enzyme was composed of 387 amino acid residues, and had a molecular weight of 42.8 kDa. The optimal pH of Algpt was 7.0 and the optimal temperature was 45 °C. The analysis of the conserved domain and the prediction of the three-dimensional structure indicated that Algpt was a novel alginate lyase. The dominant degradation products of Algpt on alginate were AOS dimer to octamer, depending on the incubation time, which demonstrated that Algpt degraded alginate in an endolytic manner. In addition, Algpt was a salt-independent and thermo-tolerant alginate lyase. Its high stability and wide adaptability endow Algpt with great application potential for the efficient preparation of AOS with different sizes and AOS-based products.
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Violot S, Galisson F, Carrique L, Jugnarain V, Conchou L, Robert X, Thureau A, Helbert W, Aghajari N, Ballut L. Exploring molecular determinants of polysaccharide Lyase family 6-1 enzyme activity. Glycobiology 2021; 31:1557-1570. [PMID: 34245266 DOI: 10.1093/glycob/cwab073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/14/2022] Open
Abstract
The Polysaccharide Lyase Family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exo-lyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirm that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform which can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.
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Affiliation(s)
- Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Frédéric Galisson
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Loïc Carrique
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Vinesh Jugnarain
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Léa Conchou
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | | | - William Helbert
- Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Grenoble Alpes, CNRS, 38000 Grenoble, France
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
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Li Q, Zheng L, Guo Z, Tang T, Zhu B. Alginate degrading enzymes: an updated comprehensive review of the structure, catalytic mechanism, modification method and applications of alginate lyases. Crit Rev Biotechnol 2021; 41:953-968. [PMID: 34015998 DOI: 10.1080/07388551.2021.1898330] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Alginate, a kind of linear acidic polysaccharide, consists of α-L-guluronate (G) and β-D-mannuronate (M). Both alginate and its degradation products (alginate oligosaccharides) possess abundant biological activities such as antioxidant activity, antitumor activity, and antimicrobial activity. Therefore, alginate and alginate oligosaccharides have great value in food, pharmaceutical, and agricultural fields. Alginate lyase can degrade alginate into alginate oligosaccharides via the β-elimination reaction. It plays an important role in marine carbon recycling and the deep utilization of brown algae. Elucidating the structural features of alginate lyase can improve our knowledge of its catalytic mechanisms. With the development of structural analysis techniques, increasing numbers of alginate lyases have been characterized at the structural level. Hence, it is essential and helpful to summarize and discuss the up-to-date findings. In this review, we have summarized progress on the structural features and the catalytic mechanisms of alginate lyases. Furthermore, the molecular modification strategies and the applications of alginate lyases have also been discussed. This comprehensive information should be helpful to expand the applications of alginate lyases.
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Affiliation(s)
- Qian Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ling Zheng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zilong Guo
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Tiancheng Tang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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Wang B, Dong S, Li FL, Ma XQ. Structural basis for the exolytic activity of polysaccharide lyase family 6 alginate lyase BcAlyPL6 from human gut microbe Bacteroides clarus. Biochem Biophys Res Commun 2021; 547:111-117. [PMID: 33610038 DOI: 10.1016/j.bbrc.2021.02.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
Alginate is the structural polysaccharide of the cell wall of brown algae, which is an important carbon source for marine life. The depolymerization of alginate is dependent on alginate lyases. Recent studies showed that the alginate utilization ability had been obtained by human gut microbes. In contrast to the great number of studies on alginate lyases from marine/soil organisms, studies on alginate lyases from gut microbes are still limited. Here, the structure of a polysaccharide lyase family 6 (PL6) alginate lyase from human gut microbe Bacteroides clarus was solved by X-ray crystallography, which represents the cluster of two-domain PL6 alginate lyases from Bacteroidetes. Similar with the two-domain alginate lyase AlyGC originated from marine bacterium, both the N terminal domain (NTD) and C terminal domain (CTD) of BcAlyPL6 show right-handed parallel β-helix fold. However, unlike AlyGC, which forms a homodimer, BcAlyPL6 functions as a monomer. Biochemical analysis indicates that the substrate binding affinity is mainly contributed by the NTD while the CTD of BcAlyPL6 is involved in the formation of -1 subsite, which is essential for substrate turnover rate. Furthermore, CTD is involved in shaping a closed catalytic pocket, and deletion of it leads to increased activity towards highly polymerized substrate. Structure comparison of PL6 family alginate lyases implies that the linkers of two-domain alginate lyases might have evolutionary relationship with the N/C terminal extension of single-domain lyases.
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Affiliation(s)
- Bing Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Sheng Dong
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China.
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10
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Song G, Sun J, Zhao M, Wang Z, Gong Q, Yu W. Cloning and characterization of two chondroitin sulfate ABC lyases from Edwardsiella tarda LMG2793. Enzyme Microb Technol 2020; 143:109701. [PMID: 33375969 DOI: 10.1016/j.enzmictec.2020.109701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 11/29/2022]
Abstract
Chondroitinase ABC can be used to prepare chondroitin sulfate (CS) oligosaccharides efficiently and environmentally. It also promotes nerve recovery through enzymatic degradation of glycosaminoglycan chains in damaged nerve tissue. In this study, two new chondroitin sulfate ABC lyases were expressed and characterized from Edwardsiella tarda LMG2793, with molecular weight of 116.8 kDa and 115.9 kDa, respectively. Two lyases ChABC I and ChABC II belonged to the polysaccharide lyase (PL) family 8. ChABC I and ChABC II showed enzyme activity towards chondroitin sulfate A (CS-A), CS-B, CS-C and CS-D, but had no activity towards hyaluronan (HA). The optimal temperature for ChABC I to exhibit the highest activity against CS-A was 40 °C and the optimal pH was 7.0. ChABC II showed the highest activity to CS-A at optimal temperature of 40 °C and pH of 9.0. ChABC I and ChABC II were stable at 37 °C and remained about 90 % of activity after incubation at 37 °C for 3 h. Many metal ions had no effect on the activity of ChABC I and ChABC II. These properties were beneficial to their further basic research and application. ChABC I was an endo-type enzyme while ChABC II was an exo-type enzyme. A group of amino acids were selected for further study by evaluating the sequence homology with other CS degradation lyases. Mutagenesis studies speculated that the catalytic residues in ChABC I were His522, Tyr529 and Arg581. The catalytic residues of ChABC II were His498, Tyr505 and Arg558. This work will contribute to the structural and functional characterization of biomedically relevant CS and promote the application of CS lyase in further basic research and therapeutics.
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Affiliation(s)
- Guanrui Song
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, PR China; Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China
| | - Junhao Sun
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, PR China; Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China
| | - Mingliu Zhao
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, PR China; Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China
| | - Zheng Wang
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, PR China; Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China
| | - Qianhong Gong
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, PR China; Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China.
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, PR China; Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao, 266003, PR China.
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11
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Dharani SR, Srinivasan R, Sarath R, Ramya M. Recent progress on engineering microbial alginate lyases towards their versatile role in biotechnological applications. Folia Microbiol (Praha) 2020; 65:937-954. [DOI: 10.1007/s12223-020-00802-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
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12
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Biopolymer Extracted from Anadenanthera colubrina (Red Angico Gum) Exerts Therapeutic Potential in Mice: Antidiarrheal Activity and Safety Assessment. Pharmaceuticals (Basel) 2020; 13:ph13010017. [PMID: 31963683 PMCID: PMC7168896 DOI: 10.3390/ph13010017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Anadenanthera colubrina var. cebil (Griseb.) Altschul (Fabaceae family), commonly known as the red angico tree, is a medicinal plant found throughout Brazil’s semi-arid area. In this study, a chemical analysis was performed to investigate the antidiarrheal activity and safety profile of red angico gum (RAG), a biopolymer extracted from the trunk exudate of A. colubrina. Upon FT-IR spectroscopy, RAG showed bands in the regions of 1608 cm−1, 1368 cm−1, and 1029 cm−1, which relate to the vibration of O–H water molecules, deformation vibration of C-O bands, and vibration of the polysaccharide C-O band, respectively, all of which are relevant to glycosidic bonds. The peak molar mass of RAG was 1.89 × 105 g/mol, with the zeta potential indicating electronegativity. RAG demonstrated high yield and solubility with a low degree of impurity. Pre-treatment with RAG reduced the total diarrheal stool and enteropooling. RAG also enhanced Na+/K+-ATPase activity and reduced gastrointestinal transit, and thereby inhibited intestinal smooth muscle contractions. Enzyme-Linked Immunosorbent Assay (ELISA) demonstrated that RAG can interact with GM1 receptors and can also reduce E. coli-induced diarrhea in vivo. Moreover, RAG did not induce any signs of toxicity in mice. These results suggest that RAG is a possible candidate for the treatment of diarrheal diseases.
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13
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Stender EGP, Dybdahl Andersen C, Fredslund F, Holck J, Solberg A, Teze D, Peters GHJ, Christensen BE, Aachmann FL, Welner DH, Svensson B. Structural and functional aspects of mannuronic acid-specific PL6 alginate lyase from the human gut microbe Bacteroides cellulosilyticus. J Biol Chem 2019; 294:17915-17930. [PMID: 31530640 PMCID: PMC6879350 DOI: 10.1074/jbc.ra119.010206] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/16/2019] [Indexed: 01/28/2023] Open
Abstract
Alginate is a linear polysaccharide from brown algae consisting of 1,4-linked β-d-mannuronic acid (M) and α-l-guluronic acid (G) arranged in M, G, and mixed MG blocks. Alginate was assumed to be indigestible in humans, but bacteria isolated from fecal samples can utilize alginate. Moreover, genomes of some human gut microbiome-associated bacteria encode putative alginate-degrading enzymes. Here, we genome-mined a polysaccharide lyase family 6 alginate lyase from the gut bacterium Bacteroides cellulosilyticus (BcelPL6). The structure of recombinant BcelPL6 was solved by X-ray crystallography to 1.3 Å resolution, revealing a single-domain, monomeric parallel β-helix containing a 10-step asparagine ladder characteristic of alginate-converting parallel β-helix enzymes. Substitutions of the conserved catalytic site residues Lys-249, Arg-270, and His-271 resulted in activity loss. However, imidazole restored the activity of BcelPL6-H271N to 2.5% that of the native enzyme. Molecular docking oriented tetra-mannuronic acid for syn attack correlated with M specificity. Using biochemical analyses, we found that BcelPL6 initially releases unsaturated oligosaccharides of a degree of polymerization of 2-7 from alginate and polyM, which were further degraded to di- and trisaccharides. Unlike other PL6 members, BcelPL6 had low activity on polyMG and none on polyG. Surprisingly, polyG increased BcelPL6 activity on alginate 7-fold. LC-electrospray ionization-MS quantification of products and lack of activity on NaBH4-reduced octa-mannuronic acid indicated that BcelPL6 is an endolyase that further degrades the oligosaccharide products with an intact reducing end. We anticipate that our results advance predictions of the specificity and mode of action of PL6 enzymes.
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Affiliation(s)
- Emil G P Stender
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christian Dybdahl Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Folmer Fredslund
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Amalie Solberg
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Bjørn E Christensen
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Ditte H Welner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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14
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Chondroitin Sulfate-Degrading Enzymes as Tools for the Development of New Pharmaceuticals. Catalysts 2019. [DOI: 10.3390/catal9040322] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chondroitin sulfates are linear anionic sulfated polysaccharides found in biological tissues, mainly within the extracellular matrix, which are degraded and altered by specific lyases depending on specific time points. These polysaccharides have recently acquired relevance in the pharmaceutical industry due to their interesting therapeutic applications. As a consequence, chondroitin sulfate (CS) lyases have been widely investigated as tools for the development of new pharmaceuticals based on these polysaccharides. This review focuses on the major breakthrough represented by chondroitin sulfate-degrading enzymes and their structures and mechanisms of function in addition to their major applications.
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15
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Yamaguchi Y, Yamamoto H, Tobisawa Y, Irie F. TMEM2: A missing link in hyaluronan catabolism identified? Matrix Biol 2018; 78-79:139-146. [PMID: 29601864 DOI: 10.1016/j.matbio.2018.03.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/17/2018] [Accepted: 03/25/2018] [Indexed: 12/20/2022]
Abstract
Hyaluronan (HA) is a glycosaminoglycan (GAG) composed of repeating disaccharide units of glucuronic acid and N-acetylglucosamine. HA is an extremely long, unbranched polymer, which often exceeds 106 Da and sometimes reaches 107 Da. A feature that epitomizes HA is its rapid turnover; one-third of the total body HA is turned over daily. The current model of HA catabolism postulates that high-molecular weight HA in the extracellular space is first cleaved into smaller fragments by a hyaluronidase(s) that resides at the cell surface, followed by internalization of fragments and their degradation into monosaccharides in lysosomes. Over the last decade, considerable research has shown that the HYAL family of hyaluronidases plays significant roles in HA catabolism. Nonetheless, the identity of a hyaluronidase responsible for the initial step of HA cleavage on the cell surface remains elusive, as biochemical and enzymological properties of HYAL proteins are not entirely consistent with those expected of cell surface hyaluronidases. Recent identification of transmembrane 2 (TMEM2) as a cell surface protein that possesses potent hyaluronidase activity suggests that it may be the "missing" cell surface hyaluronidase, and that novel models of HA catabolism should include this protein.
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Affiliation(s)
- Yu Yamaguchi
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Hayato Yamamoto
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yuki Tobisawa
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fumitoshi Irie
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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16
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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: 68] [Impact Index Per Article: 11.3] [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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17
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Roterman I, Banach M, Konieczny L. Towards the design of anti-amyloid short peptide helices. Bioinformation 2018; 14:1-7. [PMID: 29497253 PMCID: PMC5818643 DOI: 10.6026/97320630014001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/25/2018] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Abstract
A set of short peptide sequences susceptible to fibrillar aggregation produces sequneces capable of arresting elongation of amyloid fibrils. The "stop" signals are short helices customized for each individual target. Such a helix should exhibit high amphiphilicity, with differing conditions present on each side (one side should be highly hydrophilic to enable water to interact with the aggregate, while the other side must retain a local distribution of hydrophobicity which matches that of the terminal portion of the fibril). The emergence and elongation of fibrillary forms resulting from linear propagation of local hydrophobicity peaks is shown using the fuzzy oil drop model.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Lazarza 16, 31-530 Krakow, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Lazarza 16, 31-530 Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Kopernika 7, 31-034 Krakow, Poland
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18
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Roterman I, Banach M, Konieczny L. Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments. Pharmaceuticals (Basel) 2017; 10:E89. [PMID: 29144442 PMCID: PMC5748646 DOI: 10.3390/ph10040089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/02/2017] [Accepted: 11/13/2017] [Indexed: 11/17/2022] Open
Abstract
Amyloids characterized by unbounded growth of fibrillar structures cause many pathological processes. Such unbounded propagation is due to the presence of a propagating hydrophobicity field around the fibril's main axis, preventing its closure (unlike in globular proteins). Interestingly, similar fragments, commonly referred to as solenoids, are present in many naturally occurring proteins, where their propagation is arrested by suitably located "stopper" fragments. In this work, we analyze the distribution of hydrophobicity in solenoids and in their corresponding "stoppers" from the point of view of the fuzzy oil drop model (called FOD in this paper). This model characterizes the unique linear propagation of local hydrophobicity in the solenoid fragment and allows us to pinpoint "stopper" sequences, where local hydrophobicity quite closely resembles conditions encountered in globular proteins. Consequently, such fragments perform their function by mediating entropically advantageous contact with the water environment. We discuss examples of amyloid-like structures in solenoids, with particular attention to "stop" segments present in properly folded proteins found in living organisms.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, 31-530 Krakow, Poland.
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, 31-530 Krakow, Poland.
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College, Jagiellonian University, 31-034 Krakow, Poland.
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19
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Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle. ENTROPY 2017. [DOI: 10.3390/e19040167] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Leódido ACM, Costa LE, Araújo TS, Costa DS, Sousa NA, Souza LK, Sousa FB, Filho MD, Vasconcelos DF, Silva FR, Nogueira KM, Araújo AR, Barros FCN, Freitas ALP, Medeiros JVR. Anti-diarrhoeal therapeutic potential and safety assessment of sulphated polysaccharide fraction from Gracilaria intermedia seaweed in mice. Int J Biol Macromol 2017; 97:34-45. [DOI: 10.1016/j.ijbiomac.2017.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/08/2016] [Accepted: 01/02/2017] [Indexed: 10/20/2022]
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21
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Xu F, Dong F, Wang P, Cao HY, Li CY, Li PY, Pang XH, Zhang YZ, Chen XL. Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6. J Biol Chem 2017; 292:4457-4468. [PMID: 28154171 DOI: 10.1074/jbc.m116.766030] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/15/2017] [Indexed: 01/27/2023] Open
Abstract
Alginate lyases that degrade alginate via a β-elimination reaction fall into seven polysaccharide lyase (PL) families. Although the structures and catalytic mechanisms of alginate lyases in the other PL families have been clarified, those in family PL6 have yet to be revealed. Here, the crystal structure of AlyGC, a PL6 alginate lyase from marine bacterium Glaciecola chathamensis S18K6T, was solved, and its catalytic mechanism was illustrated. AlyGC is a homodimeric enzyme and adopts a structure distinct from other alginate lyases. Each monomer contains a catalytic N-terminal domain and a functionally unknown C-terminal domain. A combined structural and mutational analysis using the structures of AlyGC and of an inactive mutant R241A in complex with an alginate tetrasaccharide indicates that conformational changes occur in AlyGC when a substrate is bound and that the two active centers in AlyGC may not bind substrates simultaneously. The C-terminal domain is shown to be essential for the dimerization and the catalytic activity of AlyGC. Residues Tyr130, Arg187, His242, Arg265, and Tyr304 in the active center are also important for the activity of AlyGC. In catalysis, Lys220 and Arg241 function as the Brønsted base and acid, respectively, and a Ca2+ in the active center neutralizes the negative charge of the C5 carboxyl group of the substrate. Finally, based on our data, we propose a metal ion-assisted catalytic mechanism of AlyGC for alginate cleavage with a state change mode, which provides a better understanding for polysaccharide lyases and alginate degradation.
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Affiliation(s)
- Fei Xu
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
| | - Fang Dong
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
| | - Peng Wang
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
| | - Hai-Yan Cao
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
| | - Chun-Yang Li
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
| | - Ping-Yi Li
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
| | - Xiu-Hua Pang
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
| | - Yu-Zhong Zhang
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and.,the Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Xiu-Lan Chen
- From the State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong University, Jinan 250100 and
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22
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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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23
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Mathieu S, Henrissat B, Labre F, Skjåk-Bræk G, Helbert W. Functional Exploration of the Polysaccharide Lyase Family PL6. PLoS One 2016; 11:e0159415. [PMID: 27438604 PMCID: PMC4954714 DOI: 10.1371/journal.pone.0159415] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/03/2016] [Indexed: 11/19/2022] Open
Abstract
Alginate, the main cell-wall polysaccharide of brown algae, is composed of two residues: mannuronic acid (M-residues) and, its C5-epimer, guluronic acid (G-residues). Alginate lyases define a class of enzymes that cleave the glycosidic bond of alginate by β-elimination. They are classified according to their ability to recognize the distribution of M- and G-residues and are named M-, G- or MG-lyases. In the CAZy database, alginate lyases have been grouped by sequence similarity into seven distinct polysaccharide lyase families. The polysaccharide lyase family PL6 is subdivided into three subfamilies. Subfamily PL6_1 includes three biochemically characterized enzymes (two alginate lyases and one dermatan sulfatase lyase). No characterized enzymes have been described in the two other subfamilies (PL6_2 and PL6_3). To improve the prediction of polysaccharide-lyase activity in the PL6 family, we re-examined the classification of the PL6 family and biochemically characterized a set of enzymes reflecting the diversity of the protein sequences. Our results show that subfamily PL6_1 includes two dermatan sulfates lyases and several alginate lyases that have various substrate specificities and modes of action. In contrast, subfamilies PL6_2 and PL6_3 were found to contain only endo-poly-MG-lyases.
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Affiliation(s)
- Sophie Mathieu
- CERMAV, CNRS and Grenoble Alpes Université, BP53, 38000, Grenoble, Cedex 9, France
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France
- INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Flavien Labre
- CERMAV, CNRS and Grenoble Alpes Université, BP53, 38000, Grenoble, Cedex 9, France
| | - Gudmund Skjåk-Bræk
- Department of Biotechnology, Norwegian University of Science and Technology, NTNU Sem Sælands vei 6–8, 7491, Trondheim, Norway
| | - William Helbert
- CERMAV, CNRS and Grenoble Alpes Université, BP53, 38000, Grenoble, Cedex 9, France
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24
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Zhu B, Yin H. Alginate lyase: Review of major sources and classification, properties, structure-function analysis and applications. Bioengineered 2015; 6:125-31. [PMID: 25831216 PMCID: PMC4601208 DOI: 10.1080/21655979.2015.1030543] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022] Open
Abstract
Alginate lyases catalyze the degradation of alginate, a complex copolymer of α-L-guluronate and its C5 epimer β-D-mannuronate. The enzymes have been isolated from various kinds of organisms with different substrate specificities, including algae, marine mollusks, marine and terrestrial bacteria, and some viruses and fungi. With the progress of structural biology, many kinds of alginate lyases of different polysaccharide lyases families have been characterized by obtaining crystal structures, and the catalytic mechanism has also been elucidated. Combined with various studies, we summarized the source, classification and properties of the alginate lyases from different polysaccharide lyases families. The relationship between substrate specificity and protein sequence was also investigated.
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Affiliation(s)
- Benwei Zhu
- Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian, PR China
- University of Chinese Academy of Sciences; Beijing, PR China
| | - Heng Yin
- Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian, PR China
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25
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Hashimoto W, Maruyama Y, Nakamichi Y, Mikami B, Murata K. Crystal structure of Pedobacter heparinus heparin lyase Hep III with the active site in a deep cleft. Biochemistry 2014; 53:777-86. [PMID: 24437462 DOI: 10.1021/bi4012463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pedobacter heparinus (formerly known as Flavobacterium heparinum) is a typical glycosaminoglycan-degrading bacterium that produces three heparin lyases, Hep I, Hep II, and Hep III, which act on heparins with 1,4-glycoside bonds between uronate and amino sugar residues. Being different from Hep I and Hep II, Hep III is specific for heparan sulfate. Here we describe the crystal structure of Hep III with the active site located in a deep cleft. The X-ray crystallographic structure of Hep III was determined at 2.20 Å resolution using single-wavelength anomalous diffraction. This enzyme comprised an N-terminal α/α-barrel domain and a C-terminal antiparallel β-sheet domain as its basic scaffold. Overall structures of Hep II and Hep III were similar, although Hep III exhibited an open form compared with the closed form of Hep II. Superimposition of Hep III and heparin tetrasaccharide-bound Hep II suggested that an active site of Hep III was located in the deep cleft at the interface between its two domains. Three mutants (N240A, Y294F, and H424A) with mutations at the active site had significantly reduced enzyme activity. This is the first report of the structure-function relationship of P. heparinus Hep III.
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Affiliation(s)
- Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University , Uji, Kyoto 611-0011, Japan
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Fernandes CL, Escouto GB, Verli H. Structural glycobiology of heparinase II from Pedobacter heparinus. J Biomol Struct Dyn 2013; 32:1092-102. [PMID: 23808670 DOI: 10.1080/07391102.2013.809604] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four systems were simulated, encompassing nonglycosylated hepII without structural ions, nonglycosylated hepII with Zn(2+), nonglycosylated hepII with Ca(2+), and glycosylated hepII with Zn(2+). The obtained data suggest a role for Zn(2+) in modulating the protein flexibility at specific loop regions. Such flexibility pattern is not properly maintained in the absence of such structural ion or when the ion is replaced by Ca(2+). Still, semiempirical calculations suggest more favorable interactions with Zn(2+). These events correlate with the experimentally reported inhibitory effect of calcium over hepII. Additionally, the glycan chain seems able to promote an additional stabilization on hepII dynamics. Taken together, these results improve our understanding of the structural and dynamical features of hepII, as well as atomic-level comprehension of previous experimental data.
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Affiliation(s)
- Cláudia L Fernandes
- a Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Av Bento Gonçalves, 9500, CP 15005, Porto , Alegre , 91500-970 , Brazil
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27
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Bhat AH, Mondal H, Chauhan JS, Raghava GPS, Methi A, Rao A. ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins. Nucleic Acids Res 2011; 40:D388-93. [PMID: 22039152 PMCID: PMC3245024 DOI: 10.1093/nar/gkr911] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
ProGlycProt (http://www.proglycprot.org/) is an open access, manually curated, comprehensive repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). To facilitate maximum information at one point, the database is arranged under two sections: (i) ProCGP-the main data section consisting of 95 entries with experimentally characterized glycosites and (ii) ProUGP-a supplementary data section containing 245 entries with experimentally identified glycosylation but uncharacterized glycosites. Every entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. Interestingly, ProGlycProt contains as many as 174 entries for which information is unavailable or the characterized glycosites are unannotated in Swiss-Prot release 2011_07. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology.
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Affiliation(s)
- Aadil H Bhat
- Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research, Rajasthan, India
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28
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Shaya D, Zhao W, Garron ML, Xiao Z, Cui Q, Zhang Z, Sulea T, Linhardt RJ, Cygler M. Catalytic mechanism of heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate. J Biol Chem 2010; 285:20051-61. [PMID: 20404324 PMCID: PMC2888417 DOI: 10.1074/jbc.m110.101071] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 03/10/2010] [Indexed: 11/06/2022] Open
Abstract
Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Recently, we determined the crystal structure of HepII from Pedobacter heparinus (previously known as Flavobacterium heparinum) in complex with a heparin disaccharide product, and identified the location of its active site. Here we present the structure of HepII complexed with a heparan sulfate disaccharide product, proving that the same binding/active site is responsible for the degradation of both uronic acid epimers containing substrates. The key enzymatic step involves removal of a proton from the C5 carbon (a chiral center) of the uronic acid, posing a topological challenge to abstract the proton from either side of the ring in a single active site. We have identified three potential active site residues equidistant from C5 and located on both sides of the uronate product and determined their role in catalysis using a set of defined tetrasaccharide substrates. HepII H202A/Y257A mutant lost activity for both substrates and we determined its crystal structure complexed with a heparan sulfate-derived tetrasaccharide. Based on kinetic characterization of various mutants and the structure of the enzyme-substrate complex we propose residues participating in catalysis and their specific roles.
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Affiliation(s)
- David Shaya
- From the Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Wenjing Zhao
- the Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Biotech 4005, Troy, New York 12180-3590, and
| | - Marie-Line Garron
- From the Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Zhongping Xiao
- the Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Biotech 4005, Troy, New York 12180-3590, and
| | - Qizhi Cui
- the Biotechnology Research Institute, NRC, Montréal, Québec H4P 2R2, Canada
| | - Zhenqing Zhang
- the Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Biotech 4005, Troy, New York 12180-3590, and
| | - Traian Sulea
- the Biotechnology Research Institute, NRC, Montréal, Québec H4P 2R2, Canada
| | - Robert J. Linhardt
- the Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Biotech 4005, Troy, New York 12180-3590, and
| | - Miroslaw Cygler
- From the Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
- the Biotechnology Research Institute, NRC, Montréal, Québec H4P 2R2, Canada
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29
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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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30
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Sattelle BM, Shakeri J, Roberts IS, Almond A. A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation. Carbohydr Res 2009; 345:291-302. [PMID: 20022001 PMCID: PMC3098369 DOI: 10.1016/j.carres.2009.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 11/06/2009] [Accepted: 11/10/2009] [Indexed: 11/26/2022]
Abstract
The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-structure at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without (15)N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the beta(1-->3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the beta(1-->3) psi dihedral (as previously predicted by simulation), while the beta(1-->4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties.
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Affiliation(s)
- Benedict M Sattelle
- Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN, UK
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31
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Han C, Spring S, Lapidus A, Del Rio TG, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Saunders E, Chertkov O, Brettin T, Göker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci 2009; 1:54-62. [PMID: 21304637 PMCID: PMC3035210 DOI: 10.4056/sigs.22138] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum ‘Bacteroidetes’. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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32
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Min T, Vedadi M, Watson DC, Wasney GA, Munger C, Cygler M, Matte A, Young NM. Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes. Biochemistry 2009; 48:3057-67. [PMID: 19236052 DOI: 10.1021/bi802195d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PEB3 is a glycoprotein adhesin from Campylobacter jejuni whose structure suggested a role in transport. We have investigated potential ligands for PEB3 and characterized their binding properties using biophysical methods in solution and by X-ray crystallography. A thermal aggregation assay of PEB3 with a library of physiological compounds identified three possible ligands [3-phosphoglycerate (3-PG), phosphoenolpyruvate (PEP), and aconitate], which stabilized wild-type PEB3 but did not stabilize either a PEB3 form containing two mutations at the ligand-binding site, T138A/S139A, or a second PEB3 mutant, K135E, at a site approximately 14 A away. Fluorescence titration experiments and cocrystal structures with various ligands were used to characterize the binding of 3-PG, PEP, and phosphate to PEB3. Further, a C. jejuni growth experiment in minimal medium supplemented with 3-PG showed that this molecule enhances the growth of wild-type C. jejuni, but not of the PEB3 mutants. Crystallographic analysis of PEB3 complexes revealed that the Ser171-Gln180 region in the presence of 3-PG or other phosphates is helical and similar to those of other transport proteins, but it is nonhelical when citrate is bound. The K135E mutation resulted in expression of a more highly glycosylated form of PEB3 in vivo, and its crystal structure showed the conformation of the first two residues of the glycan. On the basis of our findings, we suggest that PEB3 is a transport protein that may function in utilization of 3-PG or other phosphate-containing molecules from the host.
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Affiliation(s)
- Tongpil Min
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
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33
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Prabhakar V, Capila I, Soundararajan V, Raman R, Sasisekharan R. Recombinant expression, purification, and biochemical characterization of chondroitinase ABC II from Proteus vulgaris. J Biol Chem 2009; 284:974-82. [PMID: 18849565 PMCID: PMC2613618 DOI: 10.1074/jbc.m806630200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 09/29/2008] [Indexed: 11/06/2022] Open
Abstract
Chondroitin lyases (or chondroitinases) are a family of enzymes that depolymerize chondroitin sulfate (CS) and dermatan sulfate (DS) galactosaminoglycans, which have gained prominence as important players in central nervous system biology. Two distinct chondroitinase ABC enzymes, cABCI and cABCII, were identified in Proteus vulgaris. Recently, cABCI was cloned, recombinantly expressed, and extensively characterized structurally and biochemically. This study focuses on recombinant expression, purification, biochemical characterization, and understanding the structure-function relationship of cABCII. The biochemical parameters for optimal activity and kinetic parameters associated with processing of various CS and DS substrates were determined. The profile of products formed by action of cABCII on different substrates was compared with product profile of cABCI. A homology-based structural model of cABCII and its complexes with CS oligosaccharides was constructed. This structural model provided molecular insights into the experimentally observed differences in the product profile of cABCII as compared with that of cABCI. The critical active site residues involved in the catalytic activity of cABCII identified based on the structural model were validated using site-directed mutagenesis and kinetic characterization of the mutants. The development of such a contaminant-free cABCII enzyme provides additional tools to decode the biologically important structure-function relationship of CS and DS galactosaminoglycans and offers novel therapeutic strategies for recovery after central nervous system injury.
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Affiliation(s)
- Vikas Prabhakar
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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34
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Shaya D, Hahn BS, Park NY, Sim JS, Kim YS, Cygler M. Characterization of Chondroitin Sulfate Lyase ABC from Bacteroides thetaiotaomicron WAL2926. Biochemistry 2008; 47:6650-61. [DOI: 10.1021/bi800353g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Shaya
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Bum-Soo Hahn
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Nam Young Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Joon-Soo Sim
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Yeong Shik Kim
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
| | - Miroslaw Cygler
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada, National Institute of Agricultural Biotechnology, 225 Seodun-Dong, Suwon 441-707, South Korea, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 151-742, South Korea, and Biotechnology Research Institute, NRC, 6100 Royalmount Avenue, Montréal, Québec, Canada H4P 2R2
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35
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Shaya D, Hahn BS, Bjerkan TM, Kim WS, Park NY, Sim JS, Kim YS, Cygler M. Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid. Glycobiology 2008; 18:270-7. [PMID: 18227125 DOI: 10.1093/glycob/cwn002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Enzymes have evolved as catalysts with high degrees of stereospecificity. When both enantiomers are biologically important, enzymes with two different folds usually catalyze reactions with the individual enantiomers. In rare cases a single enzyme can process both enantiomers efficiently, but no molecular basis for such catalysis has been established. The family of bacterial chondroitin lyases ABC comprises such enzymes. They can degrade both chondroitin sulfate (CS) and dermatan sulfate (DS) glycosaminoglycans at the nonreducing end of either glucuronic acid (CS) or its epimer iduronic acid (DS) by a beta-elimination mechanism, which commences with the removal of the C-5 proton from the uronic acid. Two other structural folds evolved to perform these reactions in an epimer-specific fashion: (alpha/alpha)(5) for CS (chondroitin lyases AC) and beta-helix for DS (chondroitin lyases B); their catalytic mechanisms have been established at the molecular level. The structure of chondroitinase ABC from Proteus vulgaris showed surprising similarity to chondroitinase AC, including the presence of a Tyr-His-Glu-Arg catalytic tetrad, which provided a possible mechanism for CS degradation but not for DS degradation. We determined the structure of a distantly related Bacteroides thetaiotaomicron chondroitinase ABC to identify additional structurally conserved residues potentially involved in catalysis. We found a conserved cluster located approximately 12 A from the catalytic tetrad. We demonstrate that a histidine in this cluster is essential for catalysis of DS but not CS. The enzyme utilizes a single substrate-binding site while having two partially overlapping active sites catalyzing the respective reactions. The spatial separation of the two sets of residues suggests a substrate-induced conformational change that brings all catalytically essential residues close together.
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Affiliation(s)
- D Shaya
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
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36
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Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K. A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller. J Biol Chem 2007; 282:37134-45. [PMID: 17947240 DOI: 10.1074/jbc.m704663200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rhamnogalacturonan (RG) lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls. An extracellular RG lyase YesW from saprophytic Bacillus subtilis is a member of polysaccharide lyase family 11 and cleaves glycoside bonds in polygalacturonan as well as RG type-I through a beta-elimination reaction. Crystal structures of YesW and its complex with galacturonan disaccharide, a reaction product analogue, were determined at 1.4 and 2.5 A resolutions with final R-factors of 16.4% and 16.6%, respectively. The enzyme is composed of an eight-bladed beta-propeller with a deep cleft in the center as a basic scaffold, and its structural fold has not been seen in polysaccharide lyases analyzed thus far. Structural analysis of the disaccharide-bound YesW and a site-directed mutagenesis study suggested that Arg-452 and Lys-535 stabilize the carboxyl group of the acidic polysaccharide molecule and Tyr-595 makes a stack interaction with the sugar pyranose ring. In addition to amino acid residues binding to the disaccharide, one calcium ion, which is coordinated by Asp-401, Glu-422, His-363, and His-399, may mediate the enzyme activity. This is, to our knowledge, the first report of a new structural category with a beta-propeller fold in polysaccharide lyases and provides structural insights into substrate binding by RG lyase.
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Affiliation(s)
- Akihito Ochiai
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
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37
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Imberty A, Lortat-Jacob H, Pérez S. Structural view of glycosaminoglycan–protein interactions. Carbohydr Res 2007; 342:430-9. [PMID: 17229412 DOI: 10.1016/j.carres.2006.12.019] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 12/15/2006] [Accepted: 12/18/2006] [Indexed: 01/28/2023]
Abstract
The essential role of protein-glycosaminoglycan interactions in the regulation of various physiological processes has been recognized for several decades but it is only recently that the molecular basis underlying such interactions has emerged. The different methodologies to elucidate the three-dimensional features of glycosaminoglycans along with the interactions with proteins cover high resolution NMR spectroscopy, X-ray crystallography, molecular modeling, and hydrodynamic measurements. The structural results that have accumulated have been organized in databases that allow rapid searching with entries related either to the type of glycosaminoglycan or the type of protein. Finally, three selected examples enlightening the complexity of the nature of the interactions occurring between proteins and glycosaminoglycans are given. The example of interactions between heparin and antithrombin III illustrates how such a complex mechanism as the regulation of blood coagulation by a specific pentasaccharide can be dissected through the combined use of dedicated carbohydrate chemistry and structural glycobiology. The second example deals with the study of complexes between chemokines and heparin, and shows how multimolecular complexes of proteins can be organized in space throughout the action of glycosaminoglycans. Again, the synthesis of chemical mimetics offers an unexpected route to the development of novel glycotherapeutics. Finally, the area of enzymes/glycosaminoglycans complexes is briefly covered to realize the limited knowledge that we have for such an important class of biomacromolecular complexes.
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Affiliation(s)
- Anne Imberty
- CERMAV-CNRS (affiliated with Université Joseph Fourier), BP 53, F-38041 Grenoble, France.
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38
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Prabhakar V, Capila I, Raman R, Srinivasan A, Bosques CJ, Pojasek K, Wrick MA, Sasisekharan R. The catalytic machinery of chondroitinase ABC I utilizes a calcium coordination strategy to optimally process dermatan sulfate. Biochemistry 2006; 45:11130-9. [PMID: 16964974 DOI: 10.1021/bi0605484] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chondroitinases are bacterial lyases that specifically cleave chondroitin sulfate and/or dermatan sulfate glycosaminoglycans. One of these enzymes, chondroitinase ABC I from Proteus vulgaris, has the broadest substrate specificity and has been widely used to depolymerize these glycosaminoglycans. Biochemical and structural studies to investigate the active site of chondroitinase ABC I have provided important insights into the catalytic amino acids. In this study, we demonstrate that calcium, a divalent ion, preferentially increases the activity of chondroitinase ABC I toward dermatan versus chondroitin substrates in a concentration-dependent manner. Through biochemical and biophysical investigations, we have established that chondroitinase ABC I binds calcium. Experiments using terbium, a fluorescent calcium analogue, confirm the specificity of this interaction. On the basis of theoretical structural models of the enzyme-substrate complexes, specific amino acids that could potentially play a role in calcium coordination were identified. These amino acids were investigated through site-directed mutagenesis studies and kinetic assays to identify possible mechanisms for calcium-mediated processing of the dermatan substrate in the active site of the enzyme.
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Affiliation(s)
- Vikas Prabhakar
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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39
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Itoh T, Hashimoto W, Mikami B, Murata K. Crystal Structure of Unsaturated Glucuronyl Hydrolase Complexed with Substrate. J Biol Chem 2006; 281:29807-16. [PMID: 16893885 DOI: 10.1074/jbc.m604975200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Unsaturated glucuronyl hydrolase (UGL), which is a member of glycoside hydrolase family GH-88, is a bacterial enzyme that degrades mammalian glycosaminoglycans and bacterial biofilms. The enzyme, which acts on unsaturated oligosaccharides with an alpha-glycoside bond produced by microbial polysaccharide lyases responsible for bacterial invasion of host cells, was believed to release 4-deoxy-l-threo-5-hexosulose-uronate (unsaturated glucuronic acid, or DeltaGlcA) and saccharide with a new nonreducing terminus by hydrolyzing the glycosidic bond. We detail the crystal structures of wild-type inactive mutant UGL of Bacillus sp. GL1 and its complex with a substrate (unsaturated chondroitin disaccharide), identify active site residues, and postulate a reaction mechanism catalyzed by UGL that triggers the hydration of the vinyl ether group in DeltaGlcA, based on the structural analysis of the enzyme-substrate complex and biochemical analysis. The proposed catalytic mechanism of UGL is a novel case among known glycosidases. Under the proposed mechanism, Asp-149 acts as a general acid and base catalyst to protonate the DeltaGlcA C4 atom and to deprotonate the water molecule. The deprotonated water molecule attacks the DeltaGlcA C5 atom to yield unstable hemiketal; this is followed by spontaneous conversion to an aldehyde (4-deoxy-l-threo-5-hexosulose-uronate) and saccharide through hemiacetal formation and cleavage of the glycosidic bond. UGL is the first clarified alpha(6)/alpha(6)-barrel enzyme using aspartic acid as the general acid/base catalyst.
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Affiliation(s)
- Takafumi Itoh
- Division of Applied Life Sciences and Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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Sasisekharan R, Raman R, Prabhakar V. GLYCOMICS APPROACH TO STRUCTURE-FUNCTION RELATIONSHIPS OF GLYCOSAMINOGLYCANS. Annu Rev Biomed Eng 2006; 8:181-231. [PMID: 16834555 DOI: 10.1146/annurev.bioeng.8.061505.095745] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Extracellular modulation of phenotype is an emerging paradigm in this current postgenomics age of molecular and cell biology. Glycosaminoglycans (GAGs) are primary components of the cell surface and the cell-extracellular matrix (ECM) interface. Advances in the technology to analyze GAGs and in whole-organism genetics have led to a dramatic increase in the known important biological role of these complex polysaccharides. Owing to their ubiquitous distribution at the cell-ECM interface, GAGs interact with numerous proteins and modulate their activity, thus impinging on fundamental biological processes such as cell growth and development. Many recent reviews have captured important aspects of GAG structure and biosynthesis, GAG-protein interactions, and GAG biology. GAG research is currently at a stage where there is a need for an integrated systems or glycomics approach, which involves an integration of all of the above concepts to define their structure-function relationships. Focusing on heparin/heparan (HSGAGs) and chondroitin/dermatan sulfate (CSGAGs), this review highlights the important aspects of GAGs and summarizes these aspects in the context of taking a glycomics approach that integrates the different technologies to define structure-function relationships of GAGs.
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Affiliation(s)
- Ram Sasisekharan
- Biological Engineering Division, Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Rye CS, Matte A, Cygler M, Withers SG. An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase. Chembiochem 2006; 7:631-7. [PMID: 16521140 DOI: 10.1002/cbic.200500428] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chondroitin AC lyase from Flavobacterium heparinum catalyses the degradation of chondroitin by an anionic E1cb elimination mechanism that involves proton abstraction from C5 of glucuronic acid. The lyase also carries out efficient proton transfer to a sugar nitronate anion, which was designed originally as an inhibitor of the enzyme, with a second-order rate constant of kcat/Km=2.7x10(6) M(-1) s(-); this is very similar to that of the natural chondroitin substrate (kcat/Km=1.3x10(6) M(-1) s(-1)). Studies with this nitronate should therefore provide insight into the proton-transfer step (general base catalysis) within this mechanism. Indeed, the Tyr234Phe mutant of the enzyme was essentially inactive with the natural substrate and correspondingly did not catalyse proton transfer to the nitronate, thereby implicating this residue as the general base catalyst. Parallel studies designed to identify the acid catalyst were carried out by using a substrate with a 2,4-dinitrophenol leaving group that needs no acid assistance for departure. These results are consistent with Tyr234 also playing the role of acid catalyst. Not only do these studies confirm the suspected role of Tyr234, but also they validate a new methodology for identification of acid/base catalysts in lyases and epimerases of this type. In addition a structural and mechanistic rationale is provided for different active-site acid/base configurations in syn and anti lyases.
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Affiliation(s)
- Carl S Rye
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
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42
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Langedijk JPM, Fuentes G, Boshuizen R, Bonvin AMJJ. Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in transmissible spongiform encephalopathies. J Mol Biol 2006; 360:907-20. [PMID: 16782127 DOI: 10.1016/j.jmb.2006.05.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 05/12/2006] [Accepted: 05/17/2006] [Indexed: 11/22/2022]
Abstract
In this study, a new beta-helical model is proposed that explains the species barrier and strain variation in transmissible spongiform encephalopathies. The left-handed beta-helix serves as a structural model that can explain the seeded growth characteristics of beta-sheet structure in PrP(Sc) fibrils. Molecular dynamics simulations demonstrate that the left-handed beta-helix is structurally more stable than the right-handed beta-helix, with a higher beta-sheet content during the simulation and a better distributed network of inter-strand backbone-backbone hydrogen bonds between parallel beta-strands of different rungs. Multiple sequence alignments and homology modelling of prion sequences with different rungs of left-handed beta-helices illustrate that the PrP region with the highest beta-helical propensity (residues 105-143) can fold in just two rungs of a left-handed beta-helix. Even if no other flanking sequence participates in the beta-helix, the two rungs of a beta-helix can give the growing fibril enough elevation to accommodate the rest of the PrP protein in a tight packing at the periphery of a trimeric beta-helix. The folding of beta-helices is driven by backbone-backbone hydrogen bonding and stacking of side-chains in adjacent rungs. The sequence and structure of the last rung at the fibril end with unprotected beta-sheet edges selects the sequence of a complementary rung and dictates the folding of the new rung with optimal backbone hydrogen bonding and side-chain stacking. An important side-chain stack that facilitates the beta-helical folding is between methionine residues 109 and 129, which explains their importance in the species barrier of prions. Because the PrP sequence is not evolutionarily optimised to fold in a beta-helix, and because the beta-helical fold shows very little sequence preference, alternative alignments are possible that result in a different rung able to select for an alternative complementary rung. A different top rung results in a new strain with different growth characteristics. Hence, in the present model, sequence variation and alternative alignments clarify the basis of the species barrier and strain specificity in PrP-based diseases.
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Affiliation(s)
- Robert Stern
- Department of Pathology and Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, CA 94143-0511, USA
| | - Mark J. Jedrzejas
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
- To whom correspondence should be addressed: Children’s Hospital Oakland Research Institute, 5700 Martin Luther King, Jr. Way, Oakland, California 94609, USA, Phone: +1 510-450-7932, Fax +1 510-450-7914, e-mail: , Web: www.chori.org/investigators/jedrzejas.html
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Shaya D, Tocilj A, Li Y, Myette J, Venkataraman G, Sasisekharan R, Cygler M. Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product. J Biol Chem 2006; 281:15525-35. [PMID: 16565082 DOI: 10.1074/jbc.m512055200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heparinase II depolymerizes heparin and heparan sulfate glycosaminoglycans, yielding unsaturated oligosaccharide products through an elimination degradation mechanism. This enzyme cleaves the oligosaccharide chain on the nonreducing end of either glucuronic or iduronic acid, sharing this characteristic with a chondroitin ABC lyase. We have determined the first structure of a heparin-degrading lyase, that of heparinase II from Pedobacter heparinus (formerly Flavobacterium heparinum), in a ligand-free state at 2.15 A resolution and in complex with a disaccharide product of heparin degradation at 2.30 A resolution. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. Heparinase II shows overall structural similarities to the polysaccharide lyase family 8 (PL8) enzymes chondroitin AC lyase and hyaluronate lyase. In contrast to PL8 enzymes, however, heparinase II forms stable dimers, with the two active sites formed independently within each monomer. The structure of the N-terminal domain of heparinase II is also similar to that of alginate lyases from the PL5 family. A Zn2+ ion is bound within the central domain and plays an essential structural role in the stabilization of a loop forming one wall of the substrate-binding site. The disaccharide binds in a long, deep canyon formed at the top of the N-terminal domain and by loops extending from the central domain. Based on structural comparison with the lyases from the PL5 and PL8 families having bound substrates or products, the disaccharide found in heparinase II occupies the "+1" and "+2" subsites. The structure of the enzyme-product complex, combined with data from previously characterized mutations, allows us to propose a putative chemical mechanism of heparin and heparan-sulfate degradation.
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Affiliation(s)
- David Shaya
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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Gazit E. Mechanisms of amyloid fibril self-assembly and inhibition. Model short peptides as a key research tool. FEBS J 2006; 272:5971-8. [PMID: 16302962 DOI: 10.1111/j.1742-4658.2005.05022.x] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of amyloid fibrils is associated with various human medical disorders of unrelated origin. Recent research indicates that self-assembled amyloid fibrils are also involved in physiological processes in several micro-organisms. Yet, the molecular basis for the recognition and self-assembly processes mediating the formation of such structures from their soluble protein precursors is not fully understood. Short peptide models have provided novel insight into the mechanistic issues of amyloid formation, revealing that very short peptides (as short as a tetrapeptide) contain all the necessary molecular information for forming typical amyloid fibrils. A careful analysis of short peptides has not only facilitated the identification of molecular recognition modules that promote the interaction and self-assembly of fibrils but also revealed that aromatic interactions are important in many cases of amyloid formation. The realization of the role of aromatic moieties in fibril formation is currently being used to develop novel inhibitors that can serve as therapeutic agents to treat amyloid-associated disorders.
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Affiliation(s)
- Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.
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Prabhakar V, Raman R, Capila I, Bosques C, Pojasek K, Sasisekharan R. Biochemical characterization of the chondroitinase ABC I active site. Biochem J 2006; 390:395-405. [PMID: 16108757 PMCID: PMC1198919 DOI: 10.1042/bj20050532] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
cABC I (chondroitinase ABC I) from Proteus vulgaris is a GalAG (galactosaminoglycan) depolymerizing lyase that cleaves its substrates at the glycosidic bond via beta-elimination. cABC I cleaves a particularly broad range of GalAG substrates, including CS (chondroitin sulphate), DS (dermatan sulphate) and hyaluronic acid. We recently cloned and recombinantly expressed cABC I in Escherichia coli, and completed a preliminary biochemical characterization of the enzyme. In the present study, we have coupled site-directed mutagenesis of the recombinant cABC I with a structural model of the enzyme-substrate complex in order to investigate in detail the roles of active site amino acids in the catalytic action of the enzyme. The putative catalytic residues His-501, Tyr-508, Arg-560 and Glu-653 were probed systematically via mutagenesis. Assessment of these mutants in kinetic and end-point assays provided direct evidence on the catalytic roles of these active-site residues. The crystal structure of the native enzyme provided a framework for molecular docking of representative CS and DS substrates. This enabled us to construct recombinant enzyme-substrate structural complexes. These studies together provided structural insights into the effects of the mutations on the catalytic mechanism of cABC I and the differences in its processing of CS and DS substrates. All His-501 mutants were essentially inactive and thereby implicating this amino acid to play the critical role of proton abstraction during catalysis. The kinetic data for Glu-653 mutants indicated that it is involved in a hydrogen bonding network in the active site. The proximity of Tyr-508 to the glycosidic oxygen of the substrate at the site of cleavage suggested its potential role in protonating the leaving group. Arg-560 was proximal to the uronic acid C-5 proton, suggesting its possible role in the stabilization of the carbanion intermediate formed during catalysis.
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Affiliation(s)
- Vikas Prabhakar
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
| | - Rahul Raman
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
| | - Ishan Capila
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
| | - Carlos J. Bosques
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
| | - Kevin Pojasek
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
| | - Ram Sasisekharan
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A
- To whom correspondence should be addressed (email )
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Prabhakar V, Sasisekharan R. The biosynthesis and catabolism of galactosaminoglycans. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2006; 53:69-115. [PMID: 17239763 DOI: 10.1016/s1054-3589(05)53005-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Vikas Prabhakar
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Petit E, Delattre C, Papy-Garcia D, Michaud P. Chondroitin Sulfate Lyases: Applications in Analysis and Glycobiology. CHONDROITIN SULFATE: STRUCTURE, ROLE AND PHARMACOLOGICAL ACTIVITY 2006; 53:167-86. [PMID: 17239766 DOI: 10.1016/s1054-3589(05)53008-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Linhardt RJ, Avci FY, Toida T, Kim YS, Cygler M. CS lyases: structure, activity, and applications in analysis and the treatment of diseases. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2006; 53:187-215. [PMID: 17239767 PMCID: PMC4114251 DOI: 10.1016/s1054-3589(05)53009-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Robert J Linhardt
- Department of Chemistry and Chemical Biology, Biology and Chemical and Biological Engineering Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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50
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Abstract
Beta-rolls and beta-helices belong to a larger group of topologically similar proteins with solenoid folds: because their regular secondary structure elements are exclusively beta-strands, they are referred to as beta-solenoids. The number of beta-solenoids whose structures are known is now large enough to support a systematic analysis. Here we survey the distinguishing structural features of beta-solenoids, also documenting their notable diversity. Appraisal of these structures suggests a classification based on handedness, twist, oligomerization state, and coil shape. In addition, beta-solenoids are distinguished by the number of chains that wind around a common axis: the majority are single-stranded but there is a recently discovered subset of triple-stranded beta-solenoids. This survey has revealed some relationships of the amino acid sequences of beta-solenoids with their structures and functions-in particular, the repetitive character of the coil sequences and conformations that recur in tracts of tandem repeats. We have proposed the term beta-arc for the distinctive turns found in beta-solenoids and beta-arch for the corresponding strand-turn-strand motifs. The evolutionary mechanisms underlying these proteins are also discussed. This analysis has direct implications for sequence-based detection, structural prediction, and de novo design of other beta-solenoid proteins. The abundance of virulence factors, toxins and allergens among beta-solenoids, as well as commonalities of beta-solenoids with amyloid fibrils, imply that this class of folds may have a broader role in human diseases than was previously recognized. Thus, identification of genes with putative beta-solenoid domains promises to be a fertile direction in the search for viable targets in the development of new antibiotics and vaccines.
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Affiliation(s)
- Andrey V Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS FRE-2593, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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