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Jiang Z, Hu S, Ma J, Liu Y, Qiao Z, Yan Q, Gao Y, Yang S. Crystal structure of a chitinase (RmChiA) from the thermophilic fungus Rhizomucor miehei with a real active site tunnel. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140709. [PMID: 34358705 DOI: 10.1016/j.bbapap.2021.140709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 02/05/2023]
Abstract
A chitinase gene (RmChiA) encoding 445 amino acid (aa) residues from a fungus Rhizomucor miehei was cloned and overexpressed in Escherichia coli. Two kinds of RmChiA crystal forms, with space groups P32 2 1 and P1, were obtained by sitting-drop vapor diffusion and the structures were determined by X-ray diffraction. The overall structure of RmChiA monomer, which is the first structure of bacterial-type chitinases from nonpathogenic fungi, adopts a canonical triosephosphate isomerase (TIM) barrel fold with two protruding chitinase insertion domains. RmChiA exhibited a unique NxDxE catalytical motif and a real active site tunnel structure, which are firstly found in GH family 18 chitinases. The motif had high structural homolog with the typical DxDxE motif in other GH family 18 chitinases. The tunnel is formed by two unusual long loops, containing 15 aa and 45 aa respectively, linked by a disulfide bond across the substrate-binding cleft. Mutation experiments found that opening the roof of tunnel structure increased the hydrolysis efficiency of RmChiA, but the thermostability of the mutants decreased. Moreover, the tunnel structure endowed RmChiA with the exo-chitinase character.
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Affiliation(s)
- Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Songqing Hu
- College of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Junwen Ma
- Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yuchun Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Qiaojuan Yan
- Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yonggui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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2
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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3
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Cavada BS, Osterne VJS, Oliveira MV, Pinto-Junior VR, Silva MTL, Bari AU, Lima LD, Lossio CF, Nascimento KS. Reviewing Mimosoideae lectins: A group of under explored legume lectins. Int J Biol Macromol 2020; 154:159-165. [PMID: 32184140 DOI: 10.1016/j.ijbiomac.2020.03.113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/02/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023]
Abstract
Lectins are proteins capable of specific and reversible binding to mono- and/or oligosaccharides, and within this group, Legume lectins are the most studied. However, most of these studies focus on the Papilionoideae subfamily, with Caesalpinioideae and Mimosoideae lectins being significantly less explored in the literature. The Mimosoideae subfamily consists of at least 79 genera and 3275 species, but, to date, only about 14 lectins have been purified, a fact which shows the lack of studies for this group. Based on their purification protocols, as well as physicochemical and structural properties, Mimosoideae lectins are very heterogeneous. Despite the few studies, a wide variety of biological activities have been tested, including, for example, inflammatory, anticancer, antibacterial, and antifungal. In this context, the present review aims to summarize the available data regarding the purification, physicochemical and structural properties, as well as biological activities, of lectins extracted from plants of the Mimosoideae subfamily in order to bring more insight to researchers interested in further exploring the potential of these molecules.
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Affiliation(s)
- Benildo Sousa Cavada
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil.
| | | | - Messias Vital Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | | | - Alfa Umaro Bari
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Lara Dias Lima
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
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4
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Kumar S, Kumar A, Patel AK. TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity. PHYTOCHEMISTRY 2020; 170:112221. [PMID: 31790908 DOI: 10.1016/j.phytochem.2019.112221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
The ICChI is a 35-kDa, glycosylated protein isolated from the latex of the weed Ipomoea carnea. It displays chitinase and lysozyme activity, which could be important for the defense against pathogenic fungi, insects and bacteria. The ICChI enzyme was crystallized, and a diffraction data set was collected from a single crystal to 1.42 Å resolution. The crystals belong to the primitive tetragonal space group P43212, with unit-cell parameters a = b = 57.9, c = 172.0 Å, and α = β = γ = 90°. The structure was elucidated by molecular replacement method using a mixed model of three homologous structures from the N-terminal sequence of ICChI. The refined model consists of 272 amino acid residues and has a Rfactor of 18.93% and Rfree of 22.42%. The protein consists of a single globular domain with a (α/β)8 triosephosphate isomerase barrel fold. Three of the consensus sites for N-glycosylation viz., Asn45, Asn172, and Asn194 containing carbohydrate moieties N-Acetylglucosamine (NAG), mannose, fucose, and xylose. The putative catalytic residues are Asp125, Glu127, and Tyr184. The crystal structure may provide fundamental information of GH18 family chitinases.
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Affiliation(s)
- Sunil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ashwani Kumar
- Raja Ramanna Centre for Advanced Technology, Indore, 452 013, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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5
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Wang YJ, Jiang WX, Zhang YS, Cao HY, Zhang Y, Chen XL, Li CY, Wang P, Zhang YZ, Song XY, Li PY. Structural Insight Into Chitin Degradation and Thermostability of a Novel Endochitinase From the Glycoside Hydrolase Family 18. Front Microbiol 2019; 10:2457. [PMID: 31736903 PMCID: PMC6831621 DOI: 10.3389/fmicb.2019.02457] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/14/2019] [Indexed: 01/25/2023] Open
Abstract
Bacterial endochitinases play important roles in environmental chitin degradation and have good applications. Although the structures of some endochitinases, most belonging to the glycoside hydrolase (GH) family 18 and thermostable, have been reported, the structural basis of these enzymes for chitin degradation still remain unclear due to the lack of functional confirmation, and the molecular mechanism for their thermostability is also unknown. Here, we characterized a GH18 endochitinase, Chi23, from marine bacterium Pseudoalteromonas aurantia DSM6057, and solved its structure. Chi23 is a thermostable enzyme that can non-processively hydrolyze crystalline and colloidal chitin. Chi23 contains only a catalytic domain that adopts a classical (β/α)8 TIM-barrel fold. Compared to other GH18 bacterial endochitinases, Chi23 lacks the chitin-binding domain and the β-hairpin subdomain, indicating that Chi23 has a novel structure. Based on structural analysis of Chi23 docked with (GlcNAc)5 and mutational analysis, the key catalytic residue (Glu117) and seven substrate-binding residues (Asn9, Gln157, Tyr189, Asn190, Asp229, Trp260, and Gln261) are revealed. Among these identified residues, Asn9, Asp229 and Gln261 are unique to Chi23, and their cumulative roles contribute to the activity of Chi23 against both crystalline and soluble chitin. Five substrate-binding residues (Tyr189, Asn190, Asp229, Trp260, and Gln261) are found to play important roles in maintaining the thermostability of Chi23. In particular, hydrogen bond networks involving Asp229 and Gln261 are formed to stabilize the protein structure of Chi23. Phylogenetic analysis indicated that Chi23 and its homologs represent a new group of GH18 endochitinases, which are widely distributed in bacteria. This study sheds light on the molecular mechanism of a GH18 endochitinase for chitin degradation.
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Affiliation(s)
- Yan-Jun Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Wen-Xin Jiang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yi-Shuo Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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6
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Bitencourt-Ferreira G, de Azevedo WF. Docking with GemDock. Methods Mol Biol 2019; 2053:169-188. [PMID: 31452105 DOI: 10.1007/978-1-4939-9752-7_11] [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] [Indexed: 06/10/2023]
Abstract
GEMDOCK is a protein-ligand docking software that makes use of an elegant biologically inspired computational methodology based on the differential evolution algorithm. As any docking program, GEMDOCK has two major features to predict the binding of a small-molecule ligand to the binding site of a protein target: the search algorithm and the scoring function to evaluate the generated poses. The GEMDOCK scoring function uses a piecewise potential energy function integrated into the differential evolutionary algorithm. GEMDOCK has been applied to a wide range of protein systems with docking accuracy similar to other docking programs such as Molegro Virtual Docker, AutoDock4, and AutoDock Vina. In this chapter, we explain how to carry out protein-ligand docking simulations with GEMDOCK. We focus this tutorial on the protein target cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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7
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Abstract
Since the early 1980s, we have witnessed considerable progress in the development and application of docking programs to assess protein-ligand interactions. Most of these applications had as a goal the identification of potential new binders to protein targets. Another remarkable progress is taking place in the determination of the structures of protein-ligand complexes, mostly using X-ray diffraction crystallography. Considering these developments, we have a favorable scenario for the creation of a computational tool that integrates into one workflow all steps involved in molecular docking simulations. We had these goals in mind when we developed the program SAnDReS. This program allows the integration of all computational features related to modern docking studies into one workflow. SAnDReS not only carries out docking simulations but also evaluates several docking protocols allowing the selection of the best approach for a given protein system. SAnDReS is a free and open-source (GNU General Public License) computational environment for running docking simulations. Here, we describe the combination of SAnDReS and AutoDock4 for protein-ligand docking simulations. AutoDock4 is a free program that has been applied to over a thousand receptor-ligand docking simulations. The dataset described in this chapter is available for downloading at https://github.com/azevedolab/sandres.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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8
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Abstract
Homology modeling is a computational approach to generate three-dimensional structures of protein targets when experimental data about similar proteins are available. Although experimental methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy successfully solved the structures of nearly 150,000 macromolecules, there is still a gap in our structural knowledge. We can fulfill this gap with computational methodologies. Our goal in this chapter is to explain how to perform homology modeling of protein targets for drug development. We choose as a homology modeling tool the program MODELLER. To illustrate its use, we describe how to model the structure of human cyclin-dependent kinase 3 using MODELLER. We explain the modeling procedure of CDK3 apoenzyme and the structure of this enzyme in complex with roscovitine.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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9
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Liu T, Zhu W, Wang J, Zhou Y, Duan Y, Qu M, Yang Q. The deduced role of a chitinase containing two nonsynergistic catalytic domains. Acta Crystallogr D Struct Biol 2018; 74:30-40. [PMID: 29372897 PMCID: PMC5786006 DOI: 10.1107/s2059798317018289] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/21/2017] [Indexed: 01/27/2023] Open
Abstract
The glycoside hydrolase family 18 chitinases degrade or alter chitin. Multiple catalytic domains in a glycoside hydrolase family 18 chitinase function synergistically during chitin degradation. Here, an insect group III chitinase from the agricultural pest Ostrinia furnacalis (OfChtIII) is revealed to be an arthropod-conserved chitinase that contains two nonsynergistic GH18 domains according to its catalytic properties. Both GH18 domains are active towards single-chained chitin substrates, but are inactive towards insoluble chitin substrates. The crystal structures of each unbound GH18 domain, as well as of GH18 domains complexed with hexa-N-acetyl-chitohexaose or penta-N-acetyl-chitopentaose, suggest that the two GH18 domains possess endo-specific activities. Physiological data indicated that the developmental stage-dependent gene-expression pattern of OfChtIII was the same as that of the chitin synthase OfChsA but significantly different from that of the chitinase OfChtI, which is indispensable for cuticular chitin degradation. Additionally, immunological staining indicated that OfChtIII was co-localized with OfChsA. Thus, OfChtIII is most likely to be involved in the chitin-synthesis pathway.
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Affiliation(s)
- Tian Liu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Weixing Zhu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Jing Wang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yong Zhou
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yanwei Duan
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Mingbo Qu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Qing Yang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, People’s Republic of China
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10
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Liu T, Chen L, Zhou Y, Jiang X, Duan Y, Yang Q. Structure, Catalysis, and Inhibition of OfChi-h, the Lepidoptera-exclusive Insect Chitinase. J Biol Chem 2017; 292:2080-2088. [PMID: 28053084 DOI: 10.1074/jbc.m116.755330] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/28/2016] [Indexed: 12/31/2022] Open
Abstract
Chitinase-h (Chi-h) is of special interest among insect chitinases due to its exclusive distribution in lepidopteran insects and high sequence identity with bacterial and baculovirus homologs. Here OfChi-h, a Chi-h from Ostrinia furnacalis, was investigated. Crystal structures of both OfChi-h and its complex with chitoheptaose ((GlcN)7) reveal that OfChi-h possesses a long and asymmetric substrate binding cleft, which is a typical characteristics of a processive exo-chitinase. The structural comparison between OfChi-h and its bacterial homolog SmChiA uncovered two phenylalanine-to-tryptophan site variants in OfChi-h at subsites +2 and possibly -7. The F232W/F396W double mutant endowed SmChiA with higher hydrolytic activities toward insoluble substrates, such as insect cuticle, α-chitin, and chitin nanowhisker. An enzymatic assay demonstrated that OfChi-h outperformed OfChtI, an insect endo-chitinase, toward the insoluble substrates, but showed lower activity toward the soluble substrate ethylene glycol chitin. Furthermore, OfChi-h was found to be inhibited by N,N',N″-trimethylglucosamine-N,N',N″,N″'-tetraacetylchitotetraose (TMG-(GlcNAc)4), a substrate analog which can be degraded into TMG-(GlcNAc)1-2 Injection of TMG-(GlcNAc)4 into 5th-instar O. furnacalis larvae led to severe defects in pupation. This work provides insights into a molting-indispensable insect chitinase that is phylogenetically closer to bacterial chitinases than insect chitinases.
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Affiliation(s)
- Tian Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Lei Chen
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Yong Zhou
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Xi Jiang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Yanwei Duan
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Qing Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and .,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China
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11
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Fahrenkamp D, Li J, Ernst S, Schmitz-Van de Leur H, Chatain N, Küster A, Koschmieder S, Lüscher B, Rossetti G, Müller-Newen G. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization. Sci Rep 2016; 6:35454. [PMID: 27752093 PMCID: PMC5067585 DOI: 10.1038/srep35454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022] Open
Abstract
STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.
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Affiliation(s)
- Dirk Fahrenkamp
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jinyu Li
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany.,College of Chemistry, Fuzhou University, Fuzhou, China.,Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
| | - Sabrina Ernst
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | | | - Nicolas Chatain
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Andrea Küster
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany.,Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Jülich, Germany
| | - Gerhard Müller-Newen
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
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12
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Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism. J Chem Biol 2015; 8:95-105. [PMID: 26101551 DOI: 10.1007/s12154-015-0135-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/27/2015] [Indexed: 12/25/2022] Open
Abstract
Kinetin, a cytokinin which promotes seed germination by inhibiting the action of abscisic acid, is an important molecule known to trigger various molecular mechanisms by interacting with an array of proteins shown from experimental observations in various model organisms. We report here the prediction of most probable protein targets of kinetin from spinach proteome using in silico approaches. Inverse docking and ligand-based similarity search was performed using kinetin as molecule. The former method prioritized six spinach proteins, whereas the latter method provided a list of protein targets retrieved from several model organisms. The most probable protein targets were selected by comparing the rank list of docking and ligand similarity methods. Both of these methods prioritized chitinase as the most probable protein target (ΔG pred = 5.064 kcal/mol) supported by the experimental structure of yeast chitinase 1 complex with kinetin (PDB: 2UY5) and Gliocladium roseum chitinase complex with 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (caffeine; 3G6M) which bears a 3D similarity of 0.43 with kinetin. An in vitro study to evaluate the effect of kinetin on spinach seed germination indicated that a very low concentration of kinetin (0.5 mg/l) did not show a significant effect compared to control in inducing seed germination process. Further, higher levels of kinetin (>0.5 mg/l) constituted an antagonist effect on spinach seed germination. It is anticipated that kinetin may have a molecular interaction with prioritized protein targets synthesized during the seed germination process and reduces growth. Thus, it appears that kinetin may not be a suitable hormone for enhancing spinach seed germination in vitro.
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Kesari P, Patil DN, Kumar P, Tomar S, Sharma AK, Kumar P. Structural and functional evolution of chitinase-like proteins from plants. Proteomics 2015; 15:1693-705. [PMID: 25728311 DOI: 10.1002/pmic.201400421] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 02/06/2023]
Abstract
The plant genome contains a large number of sequences that encode catalytically inactive chitinases referred to as chitinase-like proteins (CLPs). Although CLPs share high sequence and structural homology with chitinases of glycosyl hydrolase 18 (TIM barrel domain) and 19 families, they may lack the binding/catalytic activity. Molecular genetic analysis revealed that gene duplication events followed by mutation in the existing chitinase gene have resulted in the loss of activity. The evidences show that adaptive functional diversification of the CLPs has been achieved through alterations in the flexible regions than in the rigid structural elements. The CLPs plays an important role in the defense response against pathogenic attack, biotic and abiotic stress. They are also involved in the growth and developmental processes of plants. Since the physiological roles of CLPs are similar to chitinase, such mutations have led to plurifunctional enzymes. The biochemical and structural characterization of the CLPs is essential for understanding their roles and to develop potential utility in biotechnological industries. This review sheds light on the structure-function evolution of CLPs from chitinases.
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Affiliation(s)
- Pooja Kesari
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Dipak Narhari Patil
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pramod Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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Van Holle S, Van Damme EJM. Distribution and evolution of the lectin family in soybean (Glycine max). Molecules 2015; 20:2868-91. [PMID: 25679048 PMCID: PMC6272470 DOI: 10.3390/molecules20022868] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/06/2015] [Indexed: 01/02/2023] Open
Abstract
Lectins are a diverse group of proteins that bind specific carbohydrates and are found throughout all kingdoms. In plants, lectins are involved in a range of important processes such as plant defense and stress signaling. Although the genome sequence of Glycine max (soybean) has been published, little is known about the abundance and expansion patterns of lectin genes in soybean. Using BLAST and hidden Markov models, a total of 359 putative lectin genes have been identified. Furthermore, these sequences could be classified in nine of the twelve plant lectin families identified today. Analysis of the domain organization demonstrated that most of the identified lectin genes encode chimerolectins, consisting of one or multiple lectin domains combined with other known protein domains. Both tandem and segmental duplication events have contributed to the expansion of the lectin gene family. These data provide a detailed understanding of the domain architecture and molecular evolution of the lectin gene family in soybean.
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Affiliation(s)
- Sofie Van Holle
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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Chen L, Liu T, Zhou Y, Chen Q, Shen X, Yang Q. Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:932-42. [PMID: 24699639 PMCID: PMC3975886 DOI: 10.1107/s1399004713033841] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/13/2013] [Indexed: 11/23/2022]
Abstract
Insects possess a greater number of chitinases than any other organisms. This work is the first report of unliganded and oligosaccharide-complexed crystal structures of the insect chitinase OfChtI from Ostrinia furnacalis, which is essential to moulting. The obtained crystal structures were solved at resolutions between 1.7 and 2.2 Å. A structural comparison with other chitinases revealed that OfChtI contains a long substrate-binding cleft similar to the bacterial chitinase SmChiB from Serratia marcescens. However, unlike the exo-acting SmChiB, which has a blocked and tunnel-like cleft, OfChtI possesses an open and groove-like cleft. The complexed structure of the catalytic domain of OfChtI (OfChtI-CAD) with (GlcNAc)2/3 indicates that the reducing sugar at subsite -1 is in an energetically unfavoured `boat' conformation, a state that possibly exists just before the completion of catalysis. Because OfChtI is known to act from nonreducing ends, (GlcNAc)3 would be a hydrolysis product of (GlcNAc)6, suggesting that OfChtI possesses an endo enzymatic activity. Furthermore, a hydrophobic plane composed of four surface-exposed aromatic residues is adjacent to the entrance to the substrate-binding cleft. Mutations of these residues greatly impair the chitin-binding activity, indicating that this hydrophobic plane endows OfChtI-CAD with the ability to anchor chitin. This work reveals the unique structural characteristics of an insect chitinase.
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Affiliation(s)
- Lei Chen
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Tian Liu
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
- State Key Laboratory for Biocontrol, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Yong Zhou
- School of Software, Dalian University of Technology, 321 Tuqiang Street, Dalian, Liaoning 116620, People’s Republic of China
| | - Qi Chen
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Xu Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People’s Republic of China
| | - Qing Yang
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
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16
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Silva HC, Bari AU, Rocha BAM, Nascimento KS, Ponte EL, Pires AF, Delatorre P, Teixeira EH, Debray H, Assreuy AMS, Nagano CS, Cavada BS. Purification and primary structure of a mannose/glucose-binding lectin from Parkia biglobosa Jacq. seeds with antinociceptive and anti-inflammatory properties. J Mol Recognit 2014; 26:470-8. [PMID: 23996489 DOI: 10.1002/jmr.2289] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/07/2013] [Accepted: 06/07/2013] [Indexed: 11/06/2022]
Abstract
Parkia biglobosa (subfamily Mimosoideae), a typical tree from African savannas, possess a seed lectin that was purified by combination of ammonium sulfate precipitation and affinity chromatography on a Sephadex G-100 column. The P. biglobosa lectin (PBL) strongly agglutinated rabbit erythrocytes, an effect that was inhibited by d-mannose and d-glucose-derived sugars, especially α-methyl-d-mannopyranoside and N-acetyl-d-glucosamine. The hemagglutinating activity of PBL was maintained after incubation at a wide range of temperature and pH and also was independent of divalent cations. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, PBL exhibited an electrophoretic profile consisting of a single band with apparent molecular mass of 45 kDa. An analysis using electrospray ionization-mass spectrometry indicated that purified lectin possesses a molecular average mass of 47 562 ± 4 Da, and the analysis by gel filtration showed that PBL is a dimer in solution. The complete amino acid sequence of PBL, as determined using tandem mass spectrometry, consists of 443 amino acid residues. PBL is composed of a single non-glycosylated polypeptide chain of three tandemly arranged jacalin-related domains. Sequence heterogeneity was found in six positions, indicating that the PBL preparations contain highly homologous isolectins. PBL showed important antinociceptive activity associated to the inhibition of inflammatory process.
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Affiliation(s)
- Helton C Silva
- BioMol-Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, PO Box 6043, 60440-970, Fortaleza, CE, Brazil
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Structural investigation of a novel N-acetyl glucosamine binding chi-lectin which reveals evolutionary relationship with class III chitinases. PLoS One 2013; 8:e63779. [PMID: 23717482 PMCID: PMC3662789 DOI: 10.1371/journal.pone.0063779] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 04/06/2013] [Indexed: 01/03/2023] Open
Abstract
The glycosyl hydrolase 18 (GH18) family consists of active chitinases as well as chitinase like lectins/proteins (CLPs). The CLPs share significant sequence and structural similarities with active chitinases, however, do not display chitinase activity. Some of these proteins are reported to have specific functions and carbohydrate binding property. In the present study, we report a novel chitinase like lectin (TCLL) from Tamarindus indica. The crystal structures of native TCLL and its complex with N-acetyl glucosamine were determined. Similar to the other CLPs of the GH18 members, TCLL lacks chitinase activity due to mutations of key active site residues. Comparison of TCLL with chitinases and other chitin binding CLPs shows that TCLL has substitution of some chitin binding site residues and more open binding cleft due to major differences in the loop region. Interestingly, the biochemical studies suggest that TCLL is an N-acetyl glucosamine specific chi-lectin, which is further confirmed by the complex structure of TCLL with N-acetyl glucosamine complex. TCLL has two distinct N-acetyl glucosamine binding sites S1 and S2 that contain similar polar residues, although interaction pattern with N-acetyl glucosamine varies extensively among them. Moreover, TCLL structure depicts that how plants utilize existing structural scaffolds ingenuously to attain new functions. To date, this is the first structural investigation of a chi-lectin from plants that explore novel carbohydrate binding sites other than chitin binding groove observed in GH18 family members. Consequently, TCLL structure confers evidence for evolutionary link of lectins with chitinases.
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Kirby JM, Thiyagarajan N, Roberts AK, Shone CC, Acharya KR. Expression, purification, crystallization and preliminary crystallographic analysis of a putative Clostridium difficile surface protein Cwp19. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:762-7. [PMID: 21795789 PMCID: PMC3144791 DOI: 10.1107/s1744309111016770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 05/03/2011] [Indexed: 11/15/2022]
Abstract
Cwp19 is a putatively surface-located protein from Clostridium difficile. A recombinant N-terminal protein (residues 27-401) lacking the signal peptide and the C-terminal cell-wall-binding repeats (PFam04122) was crystallized using the sitting-drop vapour-diffusion method and diffracted to 2 Å resolution. The crystal appeared to belong to the primitive monoclinic space group P2(1), with unit-cell parameters a=109.1, b=61.2, c=109.2 Å, β=111.85°, and is estimated to contain two molecules of Cwp19 per asymmetric unit.
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Affiliation(s)
- Jonathan M. Kirby
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
- Research Department, Health Protection Agency, Porton Down, Salisbury SP4 0JG, England
| | - Nethaji Thiyagarajan
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - April K. Roberts
- Research Department, Health Protection Agency, Porton Down, Salisbury SP4 0JG, England
| | - Clifford C. Shone
- Research Department, Health Protection Agency, Porton Down, Salisbury SP4 0JG, England
| | - K. Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
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Hsieh YC, Wu YJ, Chiang TY, Kuo CY, Shrestha KL, Chao CF, Huang YC, Chuankhayan P, Wu WG, Li YK, Chen CJ. Crystal structures of Bacillus cereus NCTU2 chitinase complexes with chitooligomers reveal novel substrate binding for catalysis: a chitinase without chitin binding and insertion domains. J Biol Chem 2010; 285:31603-15. [PMID: 20685646 DOI: 10.1074/jbc.m110.149310] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chitinases hydrolyze chitin, an insoluble linear polymer of N-acetyl-d-glucosamine (NAG)(n), into nutrient sources. Bacillus cereus NCTU2 chitinase (ChiNCTU2) predominantly produces chitobioses and belongs to glycoside hydrolase family 18. The crystal structure of wild-type ChiNCTU2 comprises only a catalytic domain, unlike other chitinases that are equipped with additional chitin binding and insertion domains to bind substrates into the active site. Lacking chitin binding and chitin insertion domains, ChiNCTU2 utilizes two dynamic loops (Gly-67-Thr-69 and Ile-106-Val-112) to interact with (NAG)(n), generating novel substrate binding and distortion for catalysis. Gln-109 is crucial for direct binding with substrates, leading to conformational changes of two loops with a maximum shift of ∼4.6 Å along the binding cleft. The structures of E145Q, E145Q/Y227F, and E145G/Y227F mutants complexed with (NAG)(n) reveal (NAG)(2), (NAG)(2), and (NAG)(4) in the active site, respectively, implying various stages of reaction: before hydrolysis, E145G/Y227F with (NAG)(4); in an intermediate state, E145Q/Y227F with a boat-form NAG at the -1 subsite, -1-(NAG); after hydrolysis, E145Q with a chair form -1-(NAG). Several residues were confirmed to play catalytic roles: Glu-145 in cleavage of the glycosidic bond between -1-(NAG) and +1-(NAG); Tyr-227 in the conformational change of -1-(NAG); Asp-143 and Gln-225 in stabilizing the conformation of -1-(NAG). Additionally, Glu-190 acts in the process of product release, and Tyr-193 coordinates with water for catalysis. Residues Asp-143, E145Q, Glu-190, and Tyr-193 exhibit multiple conformations for functions. The inhibitors zinc ions and cyclo-(l-His-l-Pro) are located at various positions and confirm the catalytic-site topology. Together with kinetics analyses of related mutants, the structures of ChiNCTU2 and its mutant complexes with (NAG)(n) provide new insights into its substrate binding and the mechanistic action.
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Affiliation(s)
- Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
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Ihrmark K, Asmail N, Ubhayasekera W, Melin P, Stenlid J, Karlsson M. Comparative molecular evolution of trichoderma chitinases in response to mycoparasitic interactions. Evol Bioinform Online 2010; 6:1-26. [PMID: 20454524 PMCID: PMC2865166 DOI: 10.4137/ebo.s4198] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Certain species of the fungal genus Trichoderma are potent mycoparasites and are used for biological control of fungal diseases on agricultural crops. In Trichoderma, whole-genome sequencing reveal between 20 and 36 different genes encoding chitinases, hydrolytic enzymes that are involved in the mycoparasitic attack. Sequences of Trichoderma chitinase genes chi18-5, chi18-13, chi18-15 and chi18-17, which all exhibit specific expression during mycoparasitism-related conditions, were determined from up to 13 different taxa and studied with regard to their evolutionary patterns. Two of them, chi18-13 and chi18-17, are members of the B1/B2 chitinase subgroup that have expanded significantly in paralog number in mycoparasitic Hypocrea atroviridis and H. virens. Chi18-13 contains two codons that evolve under positive selection and seven groups of co-evolving sites. Chi18-15 displays a unique codon-usage and contains five codons that evolve under positive selection and three groups of co-evolving sites. Regions of high amino acid variability are preferentially localized to substrate- or product side of the catalytic clefts. Differences in amino acid diversity/conservation patterns between different Trichoderma clades are observed. These observations show that Trichoderma chitinases chi18-13 and chi18-15 evolve in a manner consistent with rapid co-evolutionary interactions and identifies putative target regions involved in determining substrate-specificity.
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Affiliation(s)
- Katarina Ihrmark
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, S-75007, Uppsala, Sweden
| | - Nashwan Asmail
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, S-75007, Uppsala, Sweden
| | - Wimal Ubhayasekera
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Center, Box 590, S-75124, Uppsala, Sweden
- MAX-lab, Lund University, Box 118, S-221 00 Lund, Sweden and Institute of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark.
| | - Petter Melin
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, S-75007, Uppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, S-75007, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, S-75007, Uppsala, Sweden
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Li H, Greene LH. Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding. PLoS One 2010; 5:e8654. [PMID: 20084296 PMCID: PMC2805709 DOI: 10.1371/journal.pone.0008654] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 12/05/2009] [Indexed: 01/01/2023] Open
Abstract
Background Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. They break down chitin, which is the second most abundant carbohydrate in nature after cellulose. Hence, they are important for maintaining a balance between carbon and nitrogen trapped as insoluble chitin in biomass. Chitinases are classified into two families, 18 and 19 glycoside hydrolases. In addition to a catalytic domain, which is a triosephosphate isomerase barrel, many family 18 chitinases contain another module, i.e., chitinase insertion domain. While numerous studies focus on the biological role of the catalytic domain in chitinase activity, the function of the chitinase insertion domain is not completely understood. Bioinformatics offers an important avenue in which to facilitate understanding the role of residues within the chitinase insertion domain in chitinase function. Results Twenty-seven chitinase insertion domain sequences, which include four experimentally determined structures and span five kingdoms, were aligned and analyzed using a modified sequence entropy parameter. Thirty-two positions with conserved residues were identified. The role of these conserved residues was explored by conducting a structural analysis of a number of holo-enzymes. Hydrogen bonding and van der Waals calculations revealed a distinct subset of four conserved residues constituting two sequence motifs that interact with oligosaccharides. The other conserved residues may be key to the structure, folding, and stability of this domain. Conclusions Sequence and structural studies of the chitinase insertion domains conducted within the framework of evolution identified four conserved residues which clearly interact with the substrates. Furthermore, evolutionary studies propose a link between the appearance of the chitinase insertion domain and the function of family 18 chitinases in the subfamily A.
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Affiliation(s)
- Hai Li
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - Lesley H. Greene
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
- * E-mail:
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Patel AK, Singh VK, Yadav RP, Moir AJG, Jagannadham MV. ICChI, a glycosylated chitinase from the latex of Ipomoea carnea. PHYTOCHEMISTRY 2009; 70:1210-1216. [PMID: 19683318 DOI: 10.1016/j.phytochem.2009.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/03/2009] [Accepted: 07/06/2009] [Indexed: 05/28/2023]
Abstract
A multi-functional enzyme ICChI with chitinase/lysozyme/exochitinase activity from the latex of Ipomoea carnea subsp. fistulosa was purified to homogeneity using ammonium sulphate precipitation, hydrophobic interaction and size exclusion chromatography. The enzyme is glycosylated (14-15%), has a molecular mass of 34.94 kDa (MALDI-TOF) and an isoelectric point of pH 5.3. The enzyme is stable in pH range 5.0-9.0, 80 degrees C and the optimal activity is observed at pH 6.0 and 60 degrees C. Using p-nitrophenyl-N-acetyl-beta-D-glucosaminide, the kinetic parameters K(m), V(max), K(cat) and specificity constant of the enzyme were calculated as 0.5mM, 2.5 x 10(-8)mol min(-1)microg enzyme(-1), 29.0 s(-1) and 58.0mM(-1)s(-1) respectively. The extinction coefficient was estimated as 20.56 M(-1)cm(-1). The protein contains eight tryptophan, 20 tyrosine and six cysteine residues forming three disulfide bridges. The polyclonal antibodies raised and immunodiffusion suggests that the antigenic determinants of ICChI are unique. The first fifteen N-terminal residues G-E-I-A-I-Y-W-G-Q-N-G-G-E-G-S exhibited considerable similarity to other known chitinases. Owing to these unique properties the reported enzyme would find applications in agricultural, pharmaceutical, biomedical and biotechnological fields.
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Affiliation(s)
- Ashok Kumar Patel
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
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Purification of a PHA-Like Chitin-binding Protein from Acacia farnesiana Seeds: A Time-dependent Oligomerization Protein. Appl Biochem Biotechnol 2008; 150:97-111. [DOI: 10.1007/s12010-008-8144-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 01/02/2008] [Indexed: 10/22/2022]
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