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Lansky S, Salama R, Biarnés X, Shwartstein O, Schneidman-Duhovny D, Planas A, Shoham Y, Shoham G. Integrative structure determination reveals functional global flexibility for an ultra-multimodular arabinanase. Commun Biol 2022; 5:465. [PMID: 35577850 PMCID: PMC9110388 DOI: 10.1038/s42003-022-03054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/15/2021] [Indexed: 11/08/2022] Open
Abstract
AbnA is an extracellular GH43 α-L-arabinanase from Geobacillus stearothermophilus, a key bacterial enzyme in the degradation and utilization of arabinan. We present herein its full-length crystal structure, revealing the only ultra-multimodular architecture and the largest structure to be reported so far within the GH43 family. Additionally, the structure of AbnA appears to contain two domains belonging to new uncharacterized carbohydrate-binding module (CBM) families. Three crystallographic conformational states are determined for AbnA, and this conformational flexibility is thoroughly investigated further using the "integrative structure determination" approach, integrating molecular dynamics, metadynamics, normal mode analysis, small angle X-ray scattering, dynamic light scattering, cross-linking, and kinetic experiments to reveal large functional conformational changes for AbnA, involving up to ~100 Å movement in the relative positions of its domains. The integrative structure determination approach demonstrated here may apply also to the conformational study of other ultra-multimodular proteins of diverse functions and structures.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion, Haifa, 3200, Israel
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, 08017, Spain
| | - Omer Shwartstein
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, 08017, Spain
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion, Haifa, 3200, Israel.
| | - Gil Shoham
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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2
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Sichert A, Cordero OX. Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology. Front Microbiol 2021; 12:705082. [PMID: 34690949 PMCID: PMC8531407 DOI: 10.3389/fmicb.2021.705082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.
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Computational Analysis of Thermal Adaptation in Extremophilic Chitinases: The Achilles' Heel in Protein Structure and Industrial Utilization. Molecules 2021; 26:molecules26030707. [PMID: 33572971 PMCID: PMC7866400 DOI: 10.3390/molecules26030707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/24/2021] [Accepted: 01/24/2021] [Indexed: 11/28/2022] Open
Abstract
Understanding protein stability is critical for the application of enzymes in biotechnological processes. The structural basis for the stability of thermally adapted chitinases has not yet been examined. In this study, the amino acid sequences and X-ray structures of psychrophilic, mesophilic, and hyperthermophilic chitinases were analyzed using computational and molecular dynamics (MD) simulation methods. From the findings, the key features associated with higher stability in mesophilic and thermophilic chitinases were fewer and/or shorter loops, oligomerization, and less flexible surface regions. No consistent trends were observed between stability and amino acid composition, structural features, or electrostatic interactions. Instead, unique elements affecting stability were identified in different chitinases. Notably, hyperthermostable chitinase had a much shorter surface loop compared to psychrophilic and mesophilic homologs, implying that the extended floppy surface region in cold-adapted and mesophilic chitinases may have acted as a “weak link” from where unfolding was initiated. MD simulations confirmed that the prevalence and flexibility of the loops adjacent to the active site were greater in low-temperature-adapted chitinases and may have led to the occlusion of the active site at higher temperatures compared to their thermostable homologs. Following this, loop “hot spots” for stabilizing and destabilizing mutations were also identified. This information is not only useful for the elucidation of the structure–stability relationship, but will be crucial for designing and engineering chitinases to have enhanced thermoactivity and to withstand harsh industrial processing conditions
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Secretory production in Escherichia coli of a GH46 chitosanase from Chromobacterium violaceum, suitable to generate antifungal chitooligosaccharides. Int J Biol Macromol 2020; 165:1482-1495. [PMID: 33017605 DOI: 10.1016/j.ijbiomac.2020.09.221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 01/23/2023]
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5
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Malecki PH, Bejger M, Rypniewski W, Vorgias CE. The Crystal Structure of a Streptomyces thermoviolaceus Thermophilic Chitinase Known for Its Refolding Efficiency. Int J Mol Sci 2020; 21:ijms21082892. [PMID: 32326166 PMCID: PMC7215727 DOI: 10.3390/ijms21082892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 12/27/2022] Open
Abstract
Analyzing the structure of proteins from extremophiles is a promising way to study the rules governing the protein structure, because such proteins are results of structural and functional optimization under well-defined conditions. Studying the structure of chitinases addresses an interesting aspect of enzymology, because chitin, while being the world’s second most abundant biopolymer, is also a recalcitrant substrate. The crystal structure of a thermostable chitinase from Streptomyces thermoviolaceus (StChi40) has been solved revealing a β/α-barrel (TIM-barrel) fold with an α+β insertion domain. This is the first chitinase structure of the multi-chitinase system of S. thermoviolaceus. The protein is also known to refold efficiently after thermal or chemical denaturation. StChi40 is structurally close to the catalytic domain of psychrophilic chitinase B from Arthrobacter TAD20. Differences are noted in comparison to the previously examined chitinases, particularly in the substrate-binding cleft. A comparison of the thermophilic enzyme with its psychrophilic homologue revealed structural features that could be attributed to StChi40’s thermal stability: compactness of the structure with trimmed surface loops and unique disulfide bridges, one of which is additionally stabilized by S–π interactions with aromatic rings. Uncharacteristically for thermophilic proteins, StChi40 has fewer salt bridges than its mesophilic and psychrophilic homologues.
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Affiliation(s)
- Piotr H. Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (P.H.M.); (M.B.)
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (P.H.M.); (M.B.)
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (P.H.M.); (M.B.)
- Correspondence:
| | - Constantinos E. Vorgias
- Department of Biology, Section of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Zografou, Greece;
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6
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Rutkiewicz M, Bujacz A, Wanarska M, Wierzbicka-Wos A, Cieslinski H. Active Site Architecture and Reaction Mechanism Determination of Cold Adapted β-d-galactosidase from Arthrobacter sp. 32cB. Int J Mol Sci 2019; 20:E4301. [PMID: 31484304 PMCID: PMC6747455 DOI: 10.3390/ijms20174301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/25/2019] [Accepted: 08/30/2019] [Indexed: 01/15/2023] Open
Abstract
ArthβDG is a dimeric, cold-adapted β-d-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its ArthβDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The ArthβDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The resulting three-dimensional structures of complexes: ArthβDG_E441Q/LACs and ArthβDG/IPTG (ligand bound in shallow mode) and structures of complexes ArthβDG_E441Q/LACd, ArthβDG/ONPG (ligands bound in deep mode), and galactose ArthβDG/GAL and their analysis enabled structural characterization of the hydrolysis reaction mechanism. Furthermore, comparative analysis with mesophilic analogs revealed the most striking differences in catalysis mechanisms. The key role in substrate transfer from shallow to deep binding mode involves rotation of the F581 side chain. It is worth noting that the 10-aa loop restricting access to the active site in mesophilic GH2 βDGs, in ArthβDG is moved outward. This facilitates access of substrate to active site. Such a permanent exposure of the entrance to the active site may be a key factor for improved turnover rate of the cold adapted enzyme and thus a structural feature related to its cold adaptation.
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Affiliation(s)
- Maria Rutkiewicz
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Anna Bujacz
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland.
| | - Marta Wanarska
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Anna Wierzbicka-Wos
- Department of Microbiology, Faculty of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland
| | - Hubert Cieslinski
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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7
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Meier KK, Jones SM, Kaper T, Hansson H, Koetsier MJ, Karkehabadi S, Solomon EI, Sandgren M, Kelemen B. Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. Chem Rev 2018; 118:2593-2635. [PMID: 29155571 PMCID: PMC5982588 DOI: 10.1021/acs.chemrev.7b00421] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M. Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Martijn J. Koetsier
- DuPont Industrial Biosciences, Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Bradley Kelemen
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
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8
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Czjzek M, Ficko-Blean E. Probing the Complex Architecture of Multimodular Carbohydrate-Active Enzymes Using a Combination of Small Angle X-Ray Scattering and X-Ray Crystallography. Methods Mol Biol 2017; 1588:239-253. [PMID: 28417374 DOI: 10.1007/978-1-4939-6899-2_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The various modules in multimodular carbohydrate-active enzymes (CAZymes) may function in catalysis, carbohydrate binding, protein-protein interactions or as linkers. Here, we describe how combining the biophysical techniques of Small Angle X-ray Scattering (SAXS) and macromolecular X-ray crystallography (XRC) provides a powerful tool for examination into questions related to overall structural organization of ultra multimodular CAZymes.
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Affiliation(s)
- Mirjam Czjzek
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universite, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, Bretagne, France.
| | - Elizabeth Ficko-Blean
- UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universite, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, Bretagne, France.
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9
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Sheridan KJ, Lechner BE, Keeffe GO, Keller MA, Werner ER, Lindner H, Jones GW, Haas H, Doyle S. Ergothioneine Biosynthesis and Functionality in the Opportunistic Fungal Pathogen, Aspergillus fumigatus. Sci Rep 2016; 6:35306. [PMID: 27748436 PMCID: PMC5066259 DOI: 10.1038/srep35306] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/03/2016] [Indexed: 12/11/2022] Open
Abstract
Ergothioneine (EGT; 2-mercaptohistidine trimethylbetaine) is a trimethylated and sulphurised histidine derivative which exhibits antioxidant properties. Here we report that deletion of Aspergillus fumigatus egtA (AFUA_2G15650), which encodes a trimodular enzyme, abrogated EGT biosynthesis in this opportunistic pathogen. EGT biosynthetic deficiency in A. fumigatus significantly reduced resistance to elevated H2O2 and menadione, respectively, impaired gliotoxin production and resulted in attenuated conidiation. Quantitative proteomic analysis revealed substantial proteomic remodelling in ΔegtA compared to wild-type under both basal and ROS conditions, whereby the abundance of 290 proteins was altered. Specifically, the reciprocal differential abundance of cystathionine γ-synthase and β-lyase, respectively, influenced cystathionine availability to effect EGT biosynthesis. A combined deficiency in EGT biosynthesis and the oxidative stress response regulator Yap1, which led to extreme oxidative stress susceptibility, decreased resistance to heavy metals and production of the extracellular siderophore triacetylfusarinine C and increased accumulation of the intracellular siderophore ferricrocin. EGT dissipated H2O2 in vitro, and elevated intracellular GSH levels accompanied abrogation of EGT biosynthesis. EGT deficiency only decreased resistance to high H2O2 levels which suggests functionality as an auxiliary antioxidant, required for growth at elevated oxidative stress conditions. Combined, these data reveal new interactions between cellular redox homeostasis, secondary metabolism and metal ion homeostasis.
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Affiliation(s)
- Kevin J Sheridan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Grainne O' Keeffe
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Markus A Keller
- Division of Biological Chemistry, Biocenter, Medical University Innsbruck, Innrain 80/82, Austria
| | - Ernst R Werner
- Division of Biological Chemistry, Biocenter, Medical University Innsbruck, Innrain 80/82, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University Innsbruck, Innrain 80/82, Austria
| | - Gary W Jones
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Medical University Innsbruck, Innrain 80/82, Austria
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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10
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Fadel F, Zhao Y, Cousido-Siah A, Ruiz FX, Mitschler A, Podjarny A. X-Ray Crystal Structure of the Full Length Human Chitotriosidase (CHIT1) Reveals Features of Its Chitin Binding Domain. PLoS One 2016; 11:e0154190. [PMID: 27111557 PMCID: PMC4844120 DOI: 10.1371/journal.pone.0154190] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
Chitinases are enzymes that catalyze the hydrolysis of chitin. Human chitotriosidase (CHIT1) is one of the two active human chitinases, involved in the innate immune response and highly expressed in a variety of diseases. CHIT1 is composed of a catalytic domain linked by a hinge to its chitin binding domain (ChBD). This latter domain belongs to the carbohydrate-binding module family 14 (CBM14 family) and facilitates binding to chitin. So far, the available crystal structures of the human chitinase CHIT1 and the Acidic Mammalian Chitinase (AMCase) comprise only their catalytic domain. Here, we report a crystallization strategy combining cross-seeding and micro-seeding cycles which allowed us to obtain the first crystal structure of the full length CHIT1 (CHIT1-FL) at 1.95 Å resolution. The CHIT1 chitin binding domain (ChBDCHIT1) structure shows a distorted β-sandwich 3D fold, typical of CBM14 family members. Accordingly, ChBDCHIT1 presents six conserved cysteine residues forming three disulfide bridges and several exposed aromatic residues that probably are involved in chitin binding, including the highly conserved Trp465 in a surface- exposed conformation. Furthermore, ChBDCHIT1 presents a positively charged surface which may be involved in electrostatic interactions. Our data highlight the strong structural conservation of CBM14 family members and uncover the structural similarity between the human ChBDCHIT1, tachycitin and house mite dust allergens. Overall, our new CHIT1-FL structure, determined with an adapted crystallization approach, is one of the few complete bi-modular chitinase structures available and reveals the structural features of a human CBM14 domain.
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Affiliation(s)
- Firas Fadel
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
- * E-mail: (FF); (AP)
| | - Yuguang Zhao
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, United Kingdom
| | - Alexandra Cousido-Siah
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
| | - Francesc X. Ruiz
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
| | - André Mitschler
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
| | - Alberto Podjarny
- Department of Integrative Biology, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104, INSERM U 964, Université de Strasbourg, Illkirch, France
- * E-mail: (FF); (AP)
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11
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Stavros P, Malecki PH, Theodoridou M, Rypniewski W, Vorgias CE, Nounesis G. The stability of the TIM-barrel domain of a psychrophilic chitinase. Biochem Biophys Rep 2015; 3:108-116. [PMID: 29124173 PMCID: PMC5668695 DOI: 10.1016/j.bbrep.2015.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 11/22/2022] Open
Abstract
Chitinase 60 from the psychrophilic bacterium Moritella marina (MmChi60) is a four-domain protein whose structure revealed flexible hinge regions between the domains, yielding conformations in solution that range from fully extended to compact. The catalytic domain is a shallow-grooved TIM-barrel. Heat-induced denaturation experiments of the wild-type and mutants resulting from the deletions of the two-Ig-like domains and the chitin binding domain reveal calorimetric profiles that are consistent with non-collaborative thermal unfolding of the individual domains, a property that must be associated to the “hinge-regions”. The calorimetric measurements of the (β/α)8 catalytic domain reveal that the thermal unfolding is a slow-relaxation transition exhibiting a stable, partially structured intermediate state. Circular dichroism provides evidence that the intermediate exhibits features of a molten globule i.e., loss of tertiary structure while maintaining the secondary structural elements of the native. GdnHCl-induced denaturation studies of the TIM-barrel demonstrate an extraordinarily high resistance to the denaturant. Slow-relaxation kinetics characterize the unfolding with equilibration times exceeding six days, a property that is for the first time observed for a psychrophilic TIM barrel. On the other hand, the thermodynamic stability is ΔG=6.75±1.3 kcal/mol, considerably lower than for structural-insertions-containing barrels. The mutant E153Q used for the crystallographic studies of MmChi60 complexes with NAG ligands has a much lower stability than the wild-type. We use heat-induced and chemical denaturation to study MmChi60. The impact of “hinge” regions upon the DSC calorimetric profiles is explored. CD is used to characterize the thermal unfolding intermediate of the catalytic domain. The thermodynamic stability of the TIM-barrel is measured via chemical denaturation. High-resistance to denaturants is evidenced for the psychrophilic (β/α)8 domain.
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Affiliation(s)
- Philemon Stavros
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
- Physics Department, National and Kapodistrian University of Athens, 157 01 Zografou, Greece
| | - Piotr H. Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maria Theodoridou
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Constantinos E. Vorgias
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 157 01 Zografou, Greece
| | - George Nounesis
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
- Corresponding author.
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12
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Zhang Y, Zhao Z, Liu H. Deriving Chemically Essential Interactions Based on Active Site Alignments and Quantum Chemical Calculations: A Case Study on Glycoside Hydrolases. ACS Catal 2015. [DOI: 10.1021/cs501709d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yinliang Zhang
- School
of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230027, China
| | - Zheng Zhao
- Hefei
Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Haiyan Liu
- School
of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230027, China
- Hefei National Laboratory for Physical Sciences at the Microscales, Hefei, Anhui 230027, China
- Hefei
Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
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