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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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Hajam IA, Katiki M, McNally R, Lázaro-Díez M, Kolar S, Chatterjee A, Gonzalez C, Paulchakrabarti M, Choudhury B, Caldera JR, Desmond T, Tsai CM, Du X, Li H, Murali R, Liu GY. Functional divergence of a bacterial enzyme promotes healthy or acneic skin. Nat Commun 2023; 14:8061. [PMID: 38052825 PMCID: PMC10697930 DOI: 10.1038/s41467-023-43833-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
Acne is a dermatologic disease with a strong pathologic association with human commensal Cutibacterium acnes. Conspicuously, certain C. acnes phylotypes are associated with acne, whereas others are associated with healthy skin. Here we investigate if the evolution of a C. acnes enzyme contributes to health or acne. Two hyaluronidase variants exclusively expressed by C. acnes strains, HylA and HylB, demonstrate remarkable clinical correlation with acne or health. We show that HylA is strongly pro-inflammatory, and HylB is modestly anti-inflammatory in a murine (female) acne model. Structural and phylogenic studies suggest that the enzymes evolved from a common hyaluronidase that acquired distinct enzymatic activity. Health-associated HylB degrades hyaluronic acid (HA) exclusively to HA disaccharides leading to reduced inflammation, whereas HylA generates large-sized HA fragments that drive robust TLR2-dependent pathology. Replacing an amino acid, Serine to Glycine near the HylA catalytic site enhances the enzymatic activity of HylA and produces an HA degradation pattern intermediate to HylA and HylB. Selective targeting of HylA using peptide vaccine or inhibitors alleviates acne pathology. We suggest that the functional divergence of HylA and HylB is a major driving force behind C. acnes health- and acne- phenotype and propose targeting of HylA as an approach for acne therapy.
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Affiliation(s)
- Irshad A Hajam
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Madhusudhanarao Katiki
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Randall McNally
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Vault Pharma Inc., 570 Westwood Plaza, Los Angeles, CA, 90025, USA
| | - María Lázaro-Díez
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- AIDS Research Institute (IrsiCaixa). VIRus Immune Escape and VACcine Design (VIRIEVAC) Universitary Hospital German Trias i Pujol Crta Canyet s/n 08916, Badalona, Barcelona, Spain
| | - Stacey Kolar
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Pharmacology at Armata Pharmaceuticals, Inc., Marina del Rey, CA, 90292, USA
| | - Avradip Chatterjee
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Cesia Gonzalez
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | | | - Biswa Choudhury
- GlycoAnalytics Core, University of California San Diego, San Diego, CA, 92093, USA
| | - J R Caldera
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Pathology & Laboratory Medicine, UCLA Health & David Geffen School of Medicine, Los Angeles, CA, 90095, USA
| | - Trieu Desmond
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
- School of Pharmacy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Chih-Ming Tsai
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Xin Du
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - George Y Liu
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA.
- Division of Infectious Diseases, Rady Children's Hospital, San Diego, CA, 92123, USA.
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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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Gardini C, Boccardi G, Guerrini M, Kellenbach E, Lunenburg M, van der Meer JY, Naggi A, Urso E. Quantitative 2D 1H, 13C HSQC NMR Spectroscopy for the Determination of Chondroitin Sulfate and Dermatan Sulfate Content in Danaparoid Sodium. Thromb Haemost 2023; 123:856-866. [PMID: 37094794 DOI: 10.1055/s-0043-1768225] [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: 04/26/2023]
Abstract
OBJECTIVE Danaparoid sodium is a biopolymeric complex drug composed of the most abundant heparan sulfate (HS) followed in descending order by dermatan sulfate (DS) and chondroitin sulfate (CS). This composite nature explains its peculiar antithrombotic and anticoagulant properties and make it particularly advantageous when the risk of heparin-induced thrombocytopenia occurs. A specific control of the danaparoid composition is required by the Ph. Eur. The monograph includes the CS and DS limit contents and describes the method for their quantification through selective enzymatic degradations. MATERIALS AND METHODS In this study, a quantitative two-dimensional nuclear magnetic resonance (NMR) method is proposed as a new method suitable for CS and DS quantification. Statistical comparison of the results provided by the analysis of a series of danaparoid samples with both NMR and enzymatic methods highlights a small systematic difference, likely derived from lyase-resistant sequences bearing oxidized terminals. Some modified structures, whose survival to the enzymatic action was confirmed by mass spectrometry, can be detected and quantified by NMR. CONCLUSION AND RESULTS The proposed NMR method can serve for the determination of DS and CS contents, is an easy-to-apply method with no dependence from enzymes and standards, and provides extensive structural information on the overall glycosaminoglycans mixture.
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Affiliation(s)
- Cristina Gardini
- C.A.T. Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni" S.r.l., Milano, Italy
| | - Giovanni Boccardi
- Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", Milano, Italy
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", Milano, Italy
| | | | | | | | - Annamaria Naggi
- Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", Milano, Italy
| | - Elena Urso
- Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", Milano, Italy
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The structures and applications of microbial chondroitin AC lyase. World J Microbiol Biotechnol 2022; 38:199. [PMID: 35996038 DOI: 10.1007/s11274-022-03395-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/16/2022] [Indexed: 10/15/2022]
Abstract
As an important glycosaminoglycan hydrolase, chondroitin lyases can hydrolyze chondroitin sulfate (CS) and release disaccharides and oligosaccharides. They are further divided into chondroitin AC, ABC, and B lyases according to their spatial structure and substrate specificity. Chondroitin AC lyase can hydrolyze chondroitin sulfate A (CS-A), chondroitin sulfate C (CS-C), and hyaluronic acid (HA), making it an essential biocatalyst for the preparation of low molecular weight chondroitin sulfate, analysis of the structure of the chondroitin sulfate, treatment of spinal cord injury, and purification of heparin. This paper provides an overview of reported chondroitin AC lyases, including their properties and the challenges faced in industrial applications. Up to now, although many attempts have been adopted to improve the enzyme properties, the most important factors are still the low activity and stability. The relations between the stability of the enzyme and the spatial structure were also summarized and discussed. Also perspectives for remodeling the enzymes with protein engineering are included.
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6
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Zhou LJ, Guo LB, Wei W, Lv ZX, Zhang YW. A Novel Chondroitin AC Lyase With Broad Substrate Specificity From Pedobacter rhizosphaerae: Cloning, Expression, and Characterization. Front Bioeng Biotechnol 2022; 9:808872. [PMID: 35004658 PMCID: PMC8733870 DOI: 10.3389/fbioe.2021.808872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/03/2021] [Indexed: 12/01/2022] Open
Abstract
Chondroitin AC lyase (ChSaseAC) is one of the essential polysaccharides lyases in low molecular chondroitin sulfate production. In this work, a novel PrChSaseAC from Pedobacter rhizosphaerae was successfully cloned, expressed in Escherichia coli. After optimizing the induction, the recombinant PrChSaseAC could be expressed efficiently at 0.1 mM IPTG, 25°C, and 12 h induction. Then, it was purified with Ni-NTA affinity chromatography. The characterization of the purified PrChSaseAC showed that it had high specific activity and good storage stability, which would favor the production of low molecular weight chondroitin sulfate. It also displayed activity toward chondroitin sulfate C and hyaluronic acid. PrChSaseAC had the highest activity at pH 7.5, 37°C, 10 mM Ca2+, and 5 mg/ml of chondroitin sulfate A. Molecular docking of substrate and enzyme showed the interactions between the enzyme and substrate; it revealed that the enzyme showed high activity to CS-A and hyaluronic acid, but lower activity to CS-C attributed to the structure of the binding pocket. The high stability and specific activity of the enzyme will benefit the industrial production or clinical treatment.
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Affiliation(s)
- Li-Jian Zhou
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, China
| | - Li-Bin Guo
- School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Wei Wei
- School of Pharmacy, Jiangsu University, Zhenjiang, China.,Zhongshiduqing Biotechnology Co. Ltd., Heze, China
| | - Zhi-Xiang Lv
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, China
| | - Ye-Wang Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang, China
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7
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Rodrigues DT, Peterson L, de Oliveira LB, Sosa-Gómez DR, Ribeiro BM, Ardisson-Araújo DM. Characterization of a novel alphabaculovirus isolated from the Southern armyworm, Spodoptera eridania (Cramer, 1782) (Lepidoptera: Noctuidae) and the evolution of odv-e66, a bacterium-acquired baculoviral chondroitinase gene. Genomics 2020; 112:3903-3914. [DOI: 10.1016/j.ygeno.2020.06.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/24/2020] [Accepted: 06/28/2020] [Indexed: 11/16/2022]
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8
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Zhang Z, Su H, Wang X, Tang L, Hu J, Yu W, Han F. Cloning and characterization of a novel chondroitinase ABC categorized into a new subfamily of polysaccharide lyase family 8. Int J Biol Macromol 2020; 164:3762-3770. [PMID: 32871123 DOI: 10.1016/j.ijbiomac.2020.08.210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
Chondroitinases degrade chondroitin sulfate (CS) into oligosaccharides, of which the biological activities have vital roles in various fields. Some chondroitinases in polysaccharide lyase family 8 (PL8) have been classified into four subfamilies (PL8_1, PL8_2, PL8_3, and PL8_4) based on their sequence similarity and substrate specificities. In this study, a gene, vpa_0049, was cloned from marine bacterium Vibrio sp. QY108. The encoded protein, Vpa_0049, did not belong to the four existing subfamilies in PL8 based on phylogenetic analysis. Vpa_0049 could degrade various glycosaminoglycans (CS-A, CS-B, CS-C, CS-D, and HA) into unsaturated disaccharides in an endolytic manner, which was different from PL8 lyases of four existing subfamilies. The maximum activity of Vpa_0049 on different glycosaminoglycan substrates appeared at 30-37 °C and pH 7.0-8.0 in the presence of NaCl. Vpa_0049 showed approximately 50% of maximum activity towards CS-B and HA at 0 °C. It was stable in alkaline conditions (pH 8.0-10.6) and 0-30 °C. Our study provides a new broad-substrate chondroitinase and presents an in-depth understanding of PL8.
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Affiliation(s)
- Zhelun Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao 266003, PR China; Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, 5 Yushan Road, Qingdao 266003, PR China; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, PR China
| | - Hang Su
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao 266003, PR China; Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, 5 Yushan Road, Qingdao 266003, PR China; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, PR China
| | - Xiaoyi Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao 266003, PR China; Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, 5 Yushan Road, Qingdao 266003, PR China; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, PR China
| | - Luyao Tang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao 266003, PR China; Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, 5 Yushan Road, Qingdao 266003, PR China; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, PR China
| | - Jingyang Hu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao 266003, PR China; Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, 5 Yushan Road, Qingdao 266003, PR China; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, PR China
| | - Wengong Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao 266003, PR China; Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, 5 Yushan Road, Qingdao 266003, PR China; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, PR China
| | - Feng Han
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, 5 Yushan Road, Qingdao 266003, PR China; Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, 5 Yushan Road, Qingdao 266003, PR China; School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, PR China..
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9
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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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10
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Jensen PF, Kadziola A, Comamala G, Segura DR, Anderson L, Poulsen JCN, Rasmussen KK, Agarwal S, Sainathan RK, Monrad RN, Svendsen A, Nielsen JE, Lo Leggio L, Rand KD. Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity. Cell Chem Biol 2019; 26:191-202.e6. [DOI: 10.1016/j.chembiol.2018.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/14/2018] [Accepted: 10/19/2018] [Indexed: 10/27/2022]
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11
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Li Y, Zhou Z, Chen Z. High-level production of ChSase ABC I by co-expressing molecular chaperones in Escherichia coli. Int J Biol Macromol 2018; 119:779-784. [DOI: 10.1016/j.ijbiomac.2018.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/18/2022]
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12
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Rani A, Dhillon A, Sharma K, Goyal A. Insights into the structural characteristics and substrate binding analysis of chondroitin AC lyase (PsPL8A) from Pedobacter saltans. Int J Biol Macromol 2018; 109:980-991. [PMID: 29155196 DOI: 10.1016/j.ijbiomac.2017.11.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/12/2017] [Accepted: 11/13/2017] [Indexed: 10/18/2022]
Abstract
The structure of chondroitin AC lyase (PsPL8A) of family 8 polysaccharide lyase was characterized. Modeled PsPL8A structure showed, it contains N-terminal (α/α)6 incomplete toroidal fold and a layered β sandwich structure at C-terminal. Ramchandran plot displayed 98.5% residues in favoured and 1.2% in generously allowed region. Secondary structure of PsPL8A by CD revealed 27.31% α helices 22.7% β sheets and 49.9% random coils. Protein melting study showed, PsPL8A completely unfolds at 60°C. SAXS analysis showed, PsPL8A is fully folded in solution form. The ab initio derived dummy model of PsPL8A superposed well with its modeled structure excluding some α-helices and loop region. Structural superposition and docking analysis showed, N153, W105, H203, Y208, Y212, R266 and E349 were involved in catalysis. Mutants N153A, H203A, Y212F, R266A and E349A created by SDM revealed no residual activity. Isothermal titration calorimetry analysis of Y212F and H203A with C4S polysaccharide, showed moderate binding by Y212F (Ka=9.56±3.81×105) and no binding with H203A, showing active contribution of Y212 in substrate binding. Residues Y212 and H203 or R266 might act as general base and general acid respectively. Residues N153 and E349 are likely contributing in charge neutralization and stabilizing enolate anion intermediate during β-elimination.
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Affiliation(s)
- Aruna Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Dhillon
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kedar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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13
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Peng C, Wang Q, Wang S, Wang W, Jiao R, Han W, Li F. A chondroitin sulfate and hyaluronic acid lyase with poor activity to glucuronyl 4,6- O-disulfated N-acetylgalactosamine (E-type)-containing structures. J Biol Chem 2018; 293:4230-4243. [PMID: 29414785 DOI: 10.1074/jbc.ra117.001238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/16/2018] [Indexed: 11/06/2022] Open
Abstract
GlcUAβ1-3GalNAc(4S,6S) (E unit)-rich domains have been shown to play key roles in various biological functions of chondroitin sulfate (CS). However, an enzyme that can specifically isolate such domains through the selective digestion of other domains in polysaccharides has not yet been reported. Here, we identified a glycosaminoglycan lyase from a marine bacterium Vibrio sp. FC509. This enzyme efficiently degraded hyaluronic acid (HA) and CS variants, but not E unit-rich CS-E, into unsaturated disaccharides; therefore, we designated this enzyme a CS-E-resisted HA/CS lyase (HCLase Er). We isolated a series of resistant oligosaccharides from the final product of a low-sulfated CS-E exhaustively digested by HCLase Er and found that the E units were dramatically accumulate in these resistant oligosaccharides. By determining the structures of several resistant tetrasaccharides, we observed that all of them possessed a Δ4,5HexUAα1-3GalNAc(4S,6S) at their non-reducing ends, indicating that the disulfation of GalNAc abrogates HCLase Er activity on the β1-4 linkage between the E unit and the following disaccharide. Δ4,5HexUAα1-3GalNAc(4S,6S)β1-4GlcUAβ1-3GalNAc(4S,6S) was most strongly resistant to HCLase Er. To our knowledge, this study is the first reporting a glycosaminoglycan lyase specifically inhibited by both 4-O- and 6-O-sulfation of GalNAc. Site-directed and truncation mutagenesis experiments indicated that HCLase Er may use a general acid-base catalysis mechanism and that an extra domain (Gly739-Gln796) is critical for its activity. This enzyme will be a useful tool for structural analyses and for preparing bioactive oligosaccharides of HA and CS variants, particularly from E unit-rich CS chains.
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Affiliation(s)
- Chune Peng
- From the National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, and State Key Laboratory of Microbial Technology, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Qingbin Wang
- From the National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, and State Key Laboratory of Microbial Technology, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Shumin Wang
- From the National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, and State Key Laboratory of Microbial Technology, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Wenshuang Wang
- From the National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, and State Key Laboratory of Microbial Technology, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Runmiao Jiao
- From the National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, and State Key Laboratory of Microbial Technology, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Wenjun Han
- From the National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, and State Key Laboratory of Microbial Technology, Shandong University, 27 South Shanda Road, Jinan 250100, China
| | - Fuchuan Li
- From the National Glycoengineering Research Center, Shandong Provincial Key Laboratory of Carbohydrate Chemistry and Glycobiology, and State Key Laboratory of Microbial Technology, Shandong University, 27 South Shanda Road, Jinan 250100, China
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14
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New insights into the action of bacterial chondroitinase AC I and hyaluronidase on hyaluronic acid. Carbohydr Polym 2017; 158:85-92. [DOI: 10.1016/j.carbpol.2016.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 01/22/2023]
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15
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Expression, purification and characterization of GAPDH-ChSase ABC I from Proteus vulgaris in Escherichia coli. Protein Expr Purif 2016; 128:36-41. [DOI: 10.1016/j.pep.2016.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 11/18/2022]
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16
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A new member of family 8 polysaccharide lyase chondroitin AC lyase ( Ps PL8A) from Pedobacter saltans displays endo- and exo-lytic catalysis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Ulaganathan T, Shi R, Yao D, Gu RX, Garron ML, Cherney M, Tieleman DP, Sterner E, Li G, Li L, Linhardt RJ, Cygler M. Conformational flexibility of PL12 family heparinases: structure and substrate specificity of heparinase III from Bacteroides thetaiotaomicron (BT4657). Glycobiology 2016; 27:176-187. [PMID: 27621378 DOI: 10.1093/glycob/cww096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 01/19/2023] Open
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides comprised of disaccharide repeat units, a hexuronic acid, glucuronic acid or iduronic acid, linked to a hexosamine, N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine. GAGs undergo further modification such as epimerization and sulfation. These polysaccharides are abundant in the extracellular matrix and connective tissues. GAGs function in stabilization of the fibrillar extracellular matrix, control of hydration, regulation of tissue, organism development by controlling cell cycle, cell behavior and differentiation. Niche adapted bacteria express enzymes called polysaccharide lyases (PL), which degrade GAGs for their nutrient content. PL have been classified into 24 sequence-related families. Comparison of 3D structures of the prototypic members of these families allowed identification of distant evolutionary relationships between lyases that were unrecognized at the sequence level, and identified occurrences of convergent evolution. We have characterized structurally and enzymatically heparinase III from Bacteroides thetaiotaomicron (BtHepIII; gene BT4657), which is classified within the PL12 family. BtHepIII is a 72.5 kDa protein. We present the X-ray structures of two crystal forms of BtHepIII at resolution 1.8 and 2.4 Å. BtHepIII contains two domains, the N-terminal α-helical domain forming a toroid and the C-terminal β-sheet domain. Comparison with recently determined structures of two other heparinases from the same PL12 family allowed us to identify structural flexibility in the arrangement of the domains indicating open-close movement. Based on comparison with other GAG lyases, we identified Tyr301 as the main catalytic residue and confirmed this by site-directed mutagenesis. We have characterized substrate preference of BtHepIII toward sulfate-poor heparan sulfate substrate.
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Affiliation(s)
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO, and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec City, QC G1V 0A6, Canada
| | - Deqiang Yao
- National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China
| | - Ruo-Xu Gu
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada H4P 2R2, Canada
| | - Marie-Line Garron
- the Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Aix-Marseille University, F-13288 Marseille, France, the INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France
| | - Maia Cherney
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Saskatchewan, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada H4P 2R2, Canada
| | - Eric Sterner
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Guoyun Li
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lingyun Li
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Saskatchewan, Canada
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18
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Gene deletion strategy to examine the involvement of the two chondroitin lyases in Flavobacterium columnare virulence. Appl Environ Microbiol 2015; 81:7394-402. [PMID: 26253667 DOI: 10.1128/aem.01586-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/06/2015] [Indexed: 11/20/2022] Open
Abstract
Flavobacterium columnare is an important bacterial pathogen of freshwater fish that causes high mortality of infected fish and heavy economic losses in aquaculture. The pathogenesis of this bacterium is poorly understood, in part due to the lack of efficient methods for genetic manipulation. In this study, a gene deletion strategy was developed and used to determine the relationship between the production of chondroitin lyases and virulence. The F. johnsoniae ompA promoter (PompA) was fused to sacB to construct a counterselectable marker for F. columnare. F. columnare carrying PompA-sacB failed to grow on media containing 10% sucrose. A suicide vector carrying PompA-sacB was constructed, and a gene deletion strategy was developed. Using this approach, the chondroitin lyase-encoding genes, cslA and cslB, were deleted. The ΔcslA and ΔcslB mutants were both partially deficient in digestion of chondroitin sulfate A, whereas a double mutant (ΔcslA ΔcslB) was completely deficient in chondroitin lyase activity. Cells of F. columnare wild-type strain G4 and of the chondroitin lyase-deficient ΔcslA ΔcslB mutant exhibited similar levels of virulence toward grass carp in single-strain infections. Coinfections, however, revealed a competitive advantage for the wild type over the chondroitin lyase mutant. The results indicate that chondroitin lyases are not essential virulence factors of F. columnare but may contribute to the ability of the pathogen to compete and cause disease in natural infections. The gene deletion method developed in this study may be employed to investigate the virulence factors of this bacterium and may have wide application in many other members of the phylum Bacteroidetes.
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19
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Kale V, Friðjónsson Ó, Jónsson JÓ, Kristinsson HG, Ómarsdóttir S, Hreggviðsson GÓ. Chondroitin Lyase from a Marine Arthrobacter sp. MAT3885 for the Production of Chondroitin Sulfate Disaccharides. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:479-492. [PMID: 25912370 DOI: 10.1007/s10126-015-9629-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Chondroitin sulfate (CS) saccharides from cartilage tissues have potential application in medicine or as dietary supplements due to their therapeutic bioactivities. Studies have shown that depolymerized CS saccharides may display enhanced bioactivity. The objective of this study was to isolate a CS-degrading enzyme for an efficient production of CS oligo- or disaccharides. CS-degrading bacteria from marine environments were enriched using in situ artificial support colonization containing CS from shark cartilage as substrate. Subsequently, an Arthrobacter species (strain MAT3885) efficiently degrading CS was isolated from a CS enrichment culture. The genomic DNA from strain MAT3885 was pyro-sequenced by using the 454 FLX sequencing technology. Following assembly and annotation, an orf, annotated as family 8 polysaccharide lyase genes, was identified, encoding an amino acid sequence with a similarity to CS lyases according to NCBI blastX. The gene, designated choA1, was cloned in Escherichia coli and expressed downstream of and in frame with the E. coli malE gene for obtaining a high yield of soluble recombinant protein. Applying a dual-tag system (MalE-Smt3-ChoA1), the MalE domain was separated from ChoA1 with proteolytic cleavage using Ulp1 protease. ChoA1 was defined as an AC-type enzyme as it degraded chondroitin sulfate A, C, and hyaluronic acid. The optimum activity of the enzyme was at pH 5.5-7.5 and 40 °C, running a 10-min reaction. The native enzyme was estimated to be a monomer. As the recombinant chondroitin sulfate lyase (designated as ChoA1R) degraded chondroitin sulfate efficiently compared to a benchmark enzyme, it may be used for the production of chondroitin sulfate disaccharides for the food industry or health-promoting products.
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Affiliation(s)
- Varsha Kale
- Matís, Vínlandsleið 12, 113, Reykjavík, Iceland
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20
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Study the effect of His-tag on chondroitinase ABC I based on characterization of enzyme. Int J Biol Macromol 2015; 78:96-101. [DOI: 10.1016/j.ijbiomac.2015.03.068] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 03/21/2015] [Accepted: 03/26/2015] [Indexed: 11/22/2022]
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21
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Chen Z, Li Y, Feng Y, Chen L, Yuan Q. Enzyme activity enhancement of chondroitinase ABC I from Proteus vulgaris by site-directed mutagenesis. RSC Adv 2015. [DOI: 10.1039/c5ra15220h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Arg660 was found as a new active site and Asn795Ala and Trp818Ala mutants showed higher activities than the wild type based on molecular docking simulation analysis for the first time.
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Affiliation(s)
- Zhenya Chen
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Ye Li
- Department of Biotechnology
- Beijing Polytechnic
- Beijing 100029
- China
| | - Yue Feng
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Liang Chen
- Department of Biotechnology
- Beijing Polytechnic
- Beijing 100029
- China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
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22
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Djukic M, Brzuszkiewicz E, Fünfhaus A, Voss J, Gollnow K, Poppinga L, Liesegang H, Garcia-Gonzalez E, Genersch E, Daniel R. How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae. PLoS One 2014; 9:e90914. [PMID: 24599066 PMCID: PMC3944939 DOI: 10.1371/journal.pone.0090914] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/05/2014] [Indexed: 12/20/2022] Open
Abstract
Paenibacillus larvae, a Gram positive bacterial pathogen, causes American Foulbrood (AFB), which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of P. larvae, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of P. larvae strain DSM 25430 (genotype ERIC II) consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of P. larvae strain DSM 25719 (genotype ERIC I) comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.
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Affiliation(s)
- Marvin Djukic
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Elzbieta Brzuszkiewicz
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anne Fünfhaus
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Jörn Voss
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Kathleen Gollnow
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lena Poppinga
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Eva Garcia-Gonzalez
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Elke Genersch
- Department for Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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23
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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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24
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Nazari-Robati M, Khajeh K, Aminian M, Mollania N, Golestani A. Enhancement of thermal stability of chondroitinase ABC I by site-directed mutagenesis: An insight from Ramachandran plot. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:479-86. [DOI: 10.1016/j.bbapap.2012.11.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Revised: 11/05/2012] [Accepted: 11/09/2012] [Indexed: 10/27/2022]
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25
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Mikami B, Ban M, Suzuki S, Yoon HJ, Miyake O, Yamasaki M, Ogura K, Maruyama Y, Hashimoto W, Murata K. Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1207-16. [PMID: 22948922 DOI: 10.1107/s090744491202495x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 05/31/2012] [Indexed: 11/11/2022]
Abstract
The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] were determined by X-ray crystallography at around 2.2 Å resolution together with the apo form of the H192A mutant. The final models of the complex forms, which comprised two monomers (of 353 amino-acid residues each), 268-287 water molecules and two tetrasaccharide substrates, had R factors of around 0.17. A large conformational change occurred in the position of the lid loop (residues 64-85) in holo H192A and Y246F compared with that in apo H192A. The lid loop migrated about 14 Å from an open form to a closed form to interact with the bound tetrasaccharide and a catalytic residue. The tetrasaccharide was bound in the active cleft at subsites -3 to +1 as a substrate form in which the glycosidic linkage to be cleaved existed between subsites -1 and +1. In particular, the O(η) atom of Tyr68 in the closed lid loop forms a hydrogen bond to the side chain of a presumed catalytic residue, O(η) of Tyr246, which acts both as an acid and a base catalyst in a syn mechanism.
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Affiliation(s)
- Bunzo Mikami
- Department of Applied Life Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.
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26
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Quantification of chondroitin sulfate and dermatan sulfate in danaparoid sodium by 1H NMR spectroscopy and PLS regression. Anal Bioanal Chem 2010; 399:629-34. [DOI: 10.1007/s00216-010-4193-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/31/2010] [Accepted: 09/02/2010] [Indexed: 10/19/2022]
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27
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Garron ML, Cygler M. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 2010; 20:1547-73. [PMID: 20805221 DOI: 10.1093/glycob/cwq122] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polysaccharide lyases (PLs) have been assigned to 21 families based on their sequences, with ~ 50 singletons awaiting further classification. For 19 of these families, the structure of at least one protein is known. In this review, we have analyzed the available structural information and show that presently known PL families belong to six general folds. Only two general catalytic mechanisms have been observed among these PLs: (1) metal-assisted neutralization of the acidic group of the sugar next to the cleaved bond, with, rather unusually, arginine or lysine playing the role of Brønsted base and (2) neutralization of the acidic group on the sugar by a close approach of an amino or acidic group forcing its protonation and Tyr or Tyr-His acting as the Brønsted base and acid.
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Affiliation(s)
- Marie-Line Garron
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
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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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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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Liquid chromatography-mass spectrometry to study chondroitin lyase action pattern. Anal Biochem 2008; 385:57-64. [PMID: 18992215 DOI: 10.1016/j.ab.2008.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 10/08/2008] [Accepted: 10/13/2008] [Indexed: 12/12/2022]
Abstract
Liquid chromatography-mass spectrometry was applied to determine the action pattern of different chondroitin lyases. Two commercial enzymes, chondroitinase ABC (Proteus vulgaris) and chondroitinase ACII (Arthrobacter aurescens), having action patterns previously determined by viscosimetry and gel electrophoresis were first examined. Next, the action patterns of recombinant lyases, chondroitinase ABC from Bacteroides thetaiotaomicron (expressed in Escherichia coli) and chondroitinase AC from Flavobacterium heparinum (expressed in its original host), were examined. Chondroitin sulfate A (CS-A, also known as chondroitin-4-sulfate) was used as the substrate for these four lyases. Aliquots taken at various time points were analyzed. The products of chondroitinase ABC (P. vulgaris) and chondroitinase AC (F. heparinum) contained unsaturated oligosaccharides of sizes ranging from disaccharide to decasaccharide, demonstrating that both are endolytic enzymes. The products afforded by chondroitinase ABC (B. thetaiotaomicron) and chondroitinase ACII (A. aurescens) contained primarily unsaturated disaccharide. These two exolytic enzymes showed different minor products, suggesting some subtle specificity differences between the actions of these two exolytic lyases on chondroitin sulfate A.
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33
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Michaud P, Da Costa A, Courtois B, Courtois J. Polysaccharide Lyases: Recent Developments as Biotechnological Tools. Crit Rev Biotechnol 2008; 23:233-66. [PMID: 15224891 DOI: 10.1080/07388550390447043] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polysaccharide lyases, which are polysaccharide cleavage enzymes, act mainly on anionic polysaccharides. Produced by prokaryote and eukaryote organisms, these enzymes degrade (1,4) glycosidic bond by a beta elimination mechanism and have unsaturated oligosaccharides as major products. New polysaccharides are cleaved only by their specific polysaccharide lyases. From anionic polysaccharides controlled degradations, various biotechnological applications were investigated. This review catalogues the degradation of bacterial, plant and animal polysaccharides (neutral and anionic) by this family of carbohydrate acting enzymes.
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Affiliation(s)
- P Michaud
- Laboratoire des Glucides--LPMV, IUT/Génie Biologique, Université de Picardie Jules Verne, Avenue des Facultés, Le Bailly, 80025 Amiens Cedex, France.
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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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Crystal Structure of YihS in Complex with d-Mannose: Structural Annotation of Escherichia coli and Salmonella enterica yihS-encoded Proteins to an Aldose–Ketose Isomerase. J Mol Biol 2008; 377:1443-59. [DOI: 10.1016/j.jmb.2008.01.090] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 11/20/2022]
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36
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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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37
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Oliver DC, Paetzel M. Crystal structure of the major periplasmic domain of the bacterial membrane protein assembly facilitator YidC. J Biol Chem 2007; 283:5208-16. [PMID: 18093969 DOI: 10.1074/jbc.m708936200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The essential bacterial membrane protein YidC facilitates insertion and assembly of proteins destined for integration into the inner membrane. It has homologues in both mitochondria and chloroplasts. Here we report the crystal structure of the Escherichia coli YidC major periplasmic domain (YidCECP1) at 2.5A resolution. This domain is present in YidC from Gram-negative bacteria and is more than half the size of the full-length protein. The structure reveals that YidCECP1 is made up of a large twisted beta-sandwich protein fold with a C-terminal alpha-helix that packs against one face of the beta-sandwich. Our structure and sequence analysis reveals that the C-terminal alpha-helix and the beta-sheet that it lays against are the most conserved regions of the domain. The region corresponding to the C-terminal alpha-helix was previously shown to be important for the protein insertase function of YidC and is conserved in other YidC-like proteins. The structure reveals that a region of YidC that was previously shown to be involved in binding to SecF maps to one edge of the beta-sandwich. Electrostatic analysis of the molecular surface for this region of YidC reveals a predominantly charged surface and suggests that the SecF-YidC interaction may be electrostatic in nature. Interestingly, YidCECP1 has significant structural similarity to galactose mutarotase from Lactococcus lactis, suggesting that this domain may have another function besides its role in membrane protein assembly.
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Affiliation(s)
- David C Oliver
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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38
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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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39
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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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40
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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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41
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Akhtar MS, Krishnan MY, Bhakuni V. Insights into the Mechanism of Action of Hyaluronate Lyase. J Biol Chem 2006; 281:28336-44. [PMID: 16854993 DOI: 10.1074/jbc.m601165200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Hyaluronate lyases (HLs) cleave hyaluronan and certain other chondroitin/chondroitin sulfates. Although native HL from Streptococcus agalactiae is composed of four domains, it finally stabilizes after autocatalytic conversion as a 92-kDa enzyme composed of the N-terminal spacer, middle alpha-, and C-terminal domains. These three domains are independent folding/unfolding units of the enzyme. Comparative structural and functional studies using the enzyme and its various fragments/domains suggest a relatively insignificant role of the N-terminal spacer domain in the 92-kDa enzyme. Functional studies demonstrate that the alpha-domain is the catalytic domain. However, independently it has a maximum of only about 10% of the activity of the 92-kDa enzyme, whereas its complex with the C-terminal domain in vitro shows a significant enhancement (about 6-fold) in the activity. It has been previously proposed that the C-terminal domain modulates the enzymatic activity of HLs. In addition, one of the possible roles for calcium ions was suggested to induce conformational changes in the enzyme loops, making HL more suitable for catalysis. However, we observed that calcium ions do not interact with the enzyme, and its role actually is in modulating the hyaluronan conformation and not in the functional regulation of enzyme.
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42
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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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43
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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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44
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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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45
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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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46
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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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Prabhakar V, Capila I, Bosques C, Pojasek K, Sasisekharan R. Chondroitinase ABC I from Proteus vulgaris: cloning, recombinant expression and active site identification. Biochem J 2005; 386:103-12. [PMID: 15691229 PMCID: PMC1134771 DOI: 10.1042/bj20041222] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GalAGs (galactosaminoglycans) are one subset of the GAG (glycosaminoglycan) family of chemically heterogeneous polysaccharides that are involved in a wide range of biological processes. These complex biomacromolecules are believed to be responsible for the inhibition of nerve regeneration following injury to the central nervous system. The enzymic degradation of GAG chains in damaged nervous tissue by cABC I (chondroitinase ABC I), a broad-specificity lyase that degrades GalAGs, promotes neural recovery. In the present paper, we report the subcloning of cABC I from Proteus vulgaris, and discuss a simple methodology for the recombinant expression and purification of this enzyme. The originally expressed cABC I clone resulted in an enzyme with negligible activity against a variety of GalAG substrates. Sequencing of the cABC I clone revealed four point mutations at issue with the electron-density data of the cABC I crystal structure. Site-directed mutagenesis produced a clone with restored GalAG-degrading function. We have characterized this enzyme biochemically, including an analysis of its substrate specificity. By coupling structural inspections of cABC I and an evaluation of sequence homology against other GAG-degrading lyases, a set of amino acids was chosen for further study. Mutagenesis studies of these residues resulted in the first experimental evidence of cABC I's active site. This work will facilitate the structure-function characterization of biomedically relevant GalAGs and further the development of therapeutics for nerve regeneration.
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Affiliation(s)
- Vikas Prabhakar
- 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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Maruyama Y, Hashimoto W, Mikami B, Murata K. Crystal Structure of Bacillus sp. GL1 Xanthan Lyase Complexed with a Substrate: Insights into the Enzyme Reaction Mechanism. J Mol Biol 2005; 350:974-86. [PMID: 15979090 DOI: 10.1016/j.jmb.2005.05.055] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2005] [Revised: 05/22/2005] [Accepted: 05/24/2005] [Indexed: 11/15/2022]
Abstract
Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8 (PL-8), acts exolytically on the side-chains of pentasaccharide-repeating polysaccharide xanthan and cleaves the glycosidic bond between glucuronic acid (GlcUA) and pyruvylated mannose (PyrMan) through a beta-elimination reaction. To clarify the enzyme reaction mechanism, i.e. its substrate recognition and catalytic reaction, we determined crystal structures of a mutant enzyme, N194A, in complexes with the product (PyrMan) and a substrate (pentasacharide) and in a ligand-free form at 1.8, 2.1, and 2.3A resolution. Based on the structures of the mutant in complexes with the product and substrate, we found that xanthan lyase recognized the PyrMan residue at subsite -1 and the GlcUA residue at +1 on the xanthan side-chain and underwent little interaction with the main chain of the polysaccharide. The structure of the mutant-substrate complex also showed that the hydroxyl group of Tyr255 was close to both the C-5 atom of the GlcUA residue and the oxygen atom of the glycosidic bond to be cleaved, suggesting that Tyr255 likely acts as a general base that extracts the proton from C-5 of the GlcUA residue and as a general acid that donates the proton to the glycosidic bond. A structural comparison of catalytic centers of PL-8 lyases indicated that the catalytic reaction mechanism is shared by all members of the family PL-8, while the substrate recognition mechanism differs.
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Affiliation(s)
- Yukie Maruyama
- Laboratory of Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Hanoulle X, Rollet E, Clantin B, Landrieu I, Odberg-Ferragut C, Lippens G, Bohin JP, Villeret V. Structural analysis of Escherichia coli OpgG, a protein required for the biosynthesis of osmoregulated periplasmic glucans. J Mol Biol 2004; 342:195-205. [PMID: 15313617 DOI: 10.1016/j.jmb.2004.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Revised: 07/06/2004] [Accepted: 07/06/2004] [Indexed: 11/17/2022]
Abstract
Osmoregulated periplasmic glucans (OPGs) G protein (OpgG) is required for OPGs biosynthesis. OPGs from Escherichia coli are branched glucans, with a backbone of beta-1,2 glucose units and with branches attached by beta-1,6 linkages. In Proteobacteria, OPGs are involved in osmoprotection, biofilm formation, virulence and resistance to antibiotics. Despite their important biological implications, enzymes synthesizing OPGs are poorly characterized. Here, we report the 2.5 A crystal structure of OpgG from E.coli. The structure was solved using a selenemethionine derivative of OpgG and the multiple anomalous diffraction method (MAD). The protein is composed of two beta-sandwich domains connected by one turn of 3(10) helix. The N-terminal domain (residues 22-388) displays a 25-stranded beta-sandwich fold found in several carbohydrate-related proteins. It exhibits a large cleft comprising many aromatic and acidic residues. This putative binding site shares some similarities with enzymes such as galactose mutarotase and glucodextranase, suggesting a potential catalytic role for this domain in OPG synthesis. On the other hand, the C-terminal domain (residues 401-512) has a seven-stranded immunoglobulin-like beta-sandwich fold, found in many proteins where it is mainly implicated in interactions with other molecules. The structural data suggest that OpgG is an OPG branching enzyme in which the catalytic activity is located in the large N-terminal domain and controlled via the smaller C-terminal domain.
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Affiliation(s)
- Xavier Hanoulle
- UMR 8525 CNRS, Institut de Biologie de Lille, Université de Lille II, 1 rue du Professeur Calmette, BP447, 59021, France.
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