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You Y, Kong H, Li C, Gu Z, Ban X, Li Z. Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes. Biotechnol Adv 2024; 73:108365. [PMID: 38677391 DOI: 10.1016/j.biotechadv.2024.108365] [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: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Carbohydrate binding modules (CBMs) are independent non-catalytic domains widely found in carbohydrate-active enzymes (CAZymes), and they play an essential role in the substrate binding process of CAZymes by guiding the appended catalytic modules to the target substrates. Owing to their precise recognition and selective affinity for different substrates, CBMs have received increasing research attention over the past few decades. To date, CBMs from different origins have formed a large number of families that show a variety of substrate types, structural features, and ligand recognition mechanisms. Moreover, through the modification of specific sites of CBMs and the fusion of heterologous CBMs with catalytic domains, improved enzymatic properties and catalytic patterns of numerous CAZymes have been achieved. Based on cutting-edge technologies in computational biology, gene editing, and protein engineering, CBMs as auxiliary components have become portable and efficient tools for the evolution and application of CAZymes. With the aim to provide a theoretical reference for the functional research, rational design, and targeted utilization of novel CBMs in the future, we systematically reviewed the function-related characteristics and potentials of CAZyme-derived CBMs in this review, including substrate recognition and binding mechanisms, non-catalytic contributions to enzyme performances, module modifications, and innovative applications in various fields.
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Affiliation(s)
- Yuxian You
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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2
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Kundu S. Insights into the mechanism(s) of digestion of crystalline cellulose by plant class C GH9 endoglucanases. J Mol Model 2019; 25:240. [PMID: 31338614 PMCID: PMC7385011 DOI: 10.1007/s00894-019-4133-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 07/11/2019] [Indexed: 02/03/2023]
Abstract
Biofuels such as γ-valerolactone, bioethanol, and biodiesel are derived from potentially fermentable cellulose and vegetable oils. Plant class C GH9 endoglucanases are CBM49-encompassing hydrolases that cleave the β (1 → 4) glycosidic linkage of contiguous D-glucopyranose residues of crystalline cellulose. Here, I analyse 3D-homology models of characterised and putative class C enzymes to glean insights into the contribution of the GH9, linker, and CBM49 to the mechanism(s) of crystalline cellulose digestion. Crystalline cellulose may be accommodated in a surface groove which is imperfectly bounded by the GH9_CBM49, GH9_linker, and linker_CBM49 surfaces and thence digested in a solvent accessible subsurface cavity. The physical dimensions and distortions thereof, of the groove, are mediated in part by the bulky side chains of aromatic amino acids that comprise it and may also result in a strained geometry of the bound cellulose polymer. These data along with an almost complete absence of measurable cavities, along with poorly conserved, hydrophobic, and heterogeneous amino acid composition, increased atomic motion of the CBM49_linker junction, and docking experiements with ligands of lower degrees of polymerization suggests a modulatory rather than direct role for CBM49 in catalysis. Crystalline cellulose is the de facto substrate for CBM-containing plant and non-plant GH9 enzymes, a finding supported by exceptional sequence- and structural-homology. However, despite the implied similarity in general acid-base catalysis of crystalline cellulose, this study also highlights qualitative differences in substrate binding and glycosidic bond cleavage amongst class C members. Results presented may aid the development of novel plant-based GH9 endoglucanases that could extract and utilise potential fermentable carbohydrates from biomass. Crystalline cellulose digestion by plant class C GH9 endoglucanases - an in silico assessment of function. ![]()
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Army College of Medical Sciences, Brar Square, Delhi Cantt., New Delhi, 110010, India.
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3
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The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans. Nat Commun 2019; 10:905. [PMID: 30796211 PMCID: PMC6385246 DOI: 10.1038/s41467-019-08812-y] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/03/2019] [Indexed: 12/11/2022] Open
Abstract
β-Mannans are plant cell wall polysaccharides that are commonly found in human diets. However, a mechanistic understanding into the key populations that degrade this glycan is absent, especially for the dominant Firmicutes phylum. Here, we show that the prominent butyrate-producing Firmicute Roseburia intestinalis expresses two loci conferring metabolism of β-mannans. We combine multi-“omic” analyses and detailed biochemical studies to comprehensively characterize loci-encoded proteins that are involved in β-mannan capturing, importation, de-branching and degradation into monosaccharides. In mixed cultures, R. intestinalis shares the available β-mannan with Bacteroides ovatus, demonstrating that the apparatus allows coexistence in a competitive environment. In murine experiments, β-mannan selectively promotes beneficial gut bacteria, exemplified by increased R. intestinalis, and reduction of mucus-degraders. Our findings highlight that R. intestinalis is a primary degrader of this dietary fiber and that this metabolic capacity could be exploited to selectively promote key members of the healthy microbiota using β-mannan-based therapeutic interventions. How dietary β-mannans are utilized by gut Gram-positive bacteria is unclear. Here, the authors uncover the enzymatic pathway for β-mannan metabolism in Roseburia intestinalis and show that these polysaccharides promote beneficial gut bacteria, highlighting a potential for β-mannan-based therapeutic interventions.
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4
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Zhao H, Taherzadeh G, Zhou Y, Yang Y. Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites. ACTA ACUST UNITED AC 2018; 94:e75. [PMID: 30106511 DOI: 10.1002/cpps.75] [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: 12/27/2022]
Abstract
Protein-carbohydrate interaction is essential for biological systems, and carbohydrate-binding proteins (CBPs) are important targets when designing antiviral and anticancer drugs. Due to the high cost and difficulty associated with experimental approaches, many computational methods have been developed as complementary approaches to predict CBPs or carbohydrate-binding sites. However, most of these computational methods are not publicly available. Here, we provide a comprehensive review of related studies and demonstrate our two recently developed bioinformatics methods. The method SPOT-CBP is a template-based method for detecting CBPs based on structure through structural homology search combined with a knowledge-based scoring function. This method can yield model complex structure in addition to accurate prediction of CBPs. Furthermore, it has been observed that similarly accurate predictions can be made using structures from homology modeling, which has significantly expanded its applicability. The other method, SPRINT-CBH, is a de novo approach that predicts binding residues directly from protein sequences by using sequence information and predicted structural properties. This approach does not need structurally similar templates and thus is not limited by the current database of known protein-carbohydrate complex structures. These two complementary methods are available at https://sparks-lab.org. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Huiying Zhao
- Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ghazaleh Taherzadeh
- School of Information and Communication Technology, Griffith University, Gold Coast, Queensland, Australia
| | - Yaoqi Zhou
- School of Information and Communication Technology, Griffith University, Gold Coast, Queensland, Australia.,Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Yuedong Yang
- School of Information and Communication Technology, Griffith University, Gold Coast, Queensland, Australia.,Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.,School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
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5
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Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, Rodríguez-Sanoja R. Advances in molecular engineering of carbohydrate-binding modules. Proteins 2017; 85:1602-1617. [PMID: 28547780 DOI: 10.1002/prot.25327] [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: 03/03/2017] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 11/06/2022]
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic domains that are generally appended to carbohydrate-active enzymes. CBMs have a broadly conserved structure that allows recognition of a notable variety of carbohydrates, in both their soluble and insoluble forms, as well as in their alpha and beta conformations and with different types of bonds or substitutions. This versatility suggests a high functional plasticity that is not yet clearly understood, in spite of the important number of studies relating protein structure and function. Several studies have explored the flexibility of these systems by changing or improving their specificity toward substrates of interest. In this review, we examine the molecular strategies used to identify CBMs with novel or improved characteristics. The impact of the spatial arrangement of the functional amino acids of CBMs is discussed in terms of unexpected new functions that are not related to the original biological roles of the enzymes. Proteins 2017; 85:1602-1617. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Silvia Armenta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Silvia Moreno-Mendieta
- CONACYT, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Zaira Sánchez-Cuapio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
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6
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Engineering a family 27 carbohydrate-binding module into an Aspergillus usamii β-mannanase to perfect its enzymatic properties. J Biosci Bioeng 2017; 123:294-299. [DOI: 10.1016/j.jbiosc.2016.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 11/21/2022]
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7
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Kundu S, Sharma R. In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases. FRONTIERS IN PLANT SCIENCE 2016; 7:1185. [PMID: 27570528 PMCID: PMC4981690 DOI: 10.3389/fpls.2016.01185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/22/2016] [Indexed: 05/08/2023]
Abstract
The glycoside hydrolase 9 superfamily, mainly comprising the endoglucanases, is represented in all three domains of life. The current division of GH9 enzymes, into three subclasses, namely A, B, and C, is centered on parameters derived from sequence information alone. However, this classification is ambiguous, and is limited by the paralogous ancestry of classes B and C endoglucanases, and paucity of biochemical and structural data. Here, we extend this classification schema to putative GH9 endoglucanases present in green plants, with an emphasis on identifying novel members of the class C subset. These enzymes cleave the β(1 → 4) linkage between non-terminal adjacent D-glucopyranose residues, in both, amorphous and crystalline regions of cellulose. We utilized non redundant plant GH9 enzymes with characterized molecular data, as the training set to construct Hidden Markov Models (HMMs) and train an Artificial Neural Network (ANN). The parameters that were used for predicting dominant enzyme function, were derived from this training set, and subsequently refined on 147 sequences with available expression data. Our knowledge-based approach, can ascribe differential endoglucanase activity (A, B, or C) to a query sequence with high confidence, and was used to construct a local repository of class C GH9 endoglucanases (GH9C = 241) from 32 sequenced green plants.
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Dr. Baba Saheb Ambedkar Medical College & HospitalNew Delhi, India
- Mathematical and Computational Biology, Information Technology Research Academy, Media Lab AsiaNew Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
- *Correspondence: Siddhartha Kundu
| | - Rita Sharma
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
- Rita Sharma
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8
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Yu S, Su T, Wu H, Liu S, Wang D, Zhao T, Jin Z, Du W, Zhu MJ, Chua SL, Yang L, Zhu D, Gu L, Ma LZ. PslG, a self-produced glycosyl hydrolase, triggers biofilm disassembly by disrupting exopolysaccharide matrix. Cell Res 2015; 25:1352-67. [PMID: 26611635 PMCID: PMC4670989 DOI: 10.1038/cr.2015.129] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 10/10/2015] [Accepted: 10/10/2015] [Indexed: 01/07/2023] Open
Abstract
Biofilms are surface-associated communities of microorganism embedded in extracellular matrix. Exopolysaccharide is a critical component in the extracellular matrix that maintains biofilm architecture and protects resident biofilm bacteria from antimicrobials and host immune attack. However, self-produced factors that target the matrix exopolysaccharides, are still poorly understood. Here, we show that PslG, a protein involved in the synthesis of a key biofilm matrix exopolysaccharide Psl in Pseudomonas aeruginosa, prevents biofilm formation and disassembles existing biofilms within minutes at nanomolar concentrations when supplied exogenously. The crystal structure of PslG indicates the typical features of an endoglycosidase. PslG mainly disrupts the Psl matrix to disperse bacteria from biofilms. PslG treatment markedly enhances biofilm sensitivity to antibiotics and macrophage cells, resulting in improved biofilm clearance in a mouse implant infection model. Furthermore, PslG shows biofilm inhibition and disassembly activity against a wide range of Pseudomonas species, indicating its great potential in combating biofilm-related complications.
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Affiliation(s)
- Shan Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tiantian Su
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Huijun Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shiheng Liu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianhu Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zengjun Jin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mei-Jun Zhu
- School of Food Science, Washington State University, Pullman, WA 99164-6120, USA
| | - Song Lin Chua
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Liang Yang
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Deyu Zhu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China,E-mail:
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,E-mail:
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9
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Jacobson F, Karkehabadi S, Hansson H, Goedegebuur F, Wallace L, Mitchinson C, Piens K, Stals I, Sandgren M. The crystal structure of the core domain of a cellulose induced protein (Cip1) from Hypocrea jecorina, at 1.5 Å resolution. PLoS One 2013; 8:e70562. [PMID: 24039705 PMCID: PMC3764139 DOI: 10.1371/journal.pone.0070562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 06/25/2013] [Indexed: 11/19/2022] Open
Abstract
In an effort to characterise the whole transcriptome of the fungus Hypocrea jecorina, cDNA clones of this fungus were identified that encode for previously unknown proteins that are likely to function in biomass degradation. One of these newly identified proteins, found to be co-regulated with the major H. jecorina cellulases, is a protein that was denoted Cellulose induced protein 1 (Cip1). This protein consists of a glycoside hydrolase family 1 carbohydrate binding module connected via a linker region to a domain with yet unknown function. After cloning and expression of Cip1 in H. jecorina, the protein was purified and biochemically characterised with the aim of determining a potential enzymatic activity for the novel protein. No hydrolytic activity against any of the tested plant cell wall components was found. The proteolytic core domain of Cip1 was then crystallised, and the three-dimensional structure of this was determined to 1.5 Å resolution utilising sulphur single-wavelength anomalous dispersion phasing (sulphor-SAD). A calcium ion binding site was identified in a sequence conserved region of Cip1 and is also seen in other proteins with the same general fold as Cip1, such as many carbohydrate binding modules. The presence of this ion was found to have a structural role. The Cip1 structure was analysed and a structural homology search was performed to identify structurally related proteins. The two published structures with highest overall structural similarity to Cip1 found were two poly-lyases: CsGL, a glucuronan lyase from H. jecorina and vAL-1, an alginate lyase from the Chlorella virus. This indicates that Cip1 may be a lyase. However, initial trials did not detect significant lyase activity for Cip1. Cip1 is the first structure to be solved of the 23 currently known Cip1 sequential homologs (with a sequence identity cut-off of 25%), including both bacterial and fungal members.
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Affiliation(s)
- Frida Jacobson
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Saeid Karkehabadi
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Louise Wallace
- DuPont, Industrial Biosciences, Palo Alto, California, United States of America
| | - Colin Mitchinson
- DuPont, Industrial Biosciences, Palo Alto, California, United States of America
| | - Kathleen Piens
- Department of Biochemistry, Physiology and Microbiology, Ghent University, Ghent, Belgium
| | - Ingeborg Stals
- Faculty of Applied Bioscience Engineering, University College Ghent and Ghent University, Ghent, Belgium
| | - Mats Sandgren
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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10
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Molecular insights into substrate specificity and thermal stability of a bacterial GH5-CBM27 endo-1,4-β-d-mannanase. J Struct Biol 2012; 177:469-76. [DOI: 10.1016/j.jsb.2011.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 11/04/2011] [Accepted: 11/18/2011] [Indexed: 11/23/2022]
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11
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Sunna A. Modular organisation and functional analysis of dissected modular β-mannanase CsMan26 from Caldicellulosiruptor Rt8B.4. Appl Microbiol Biotechnol 2009; 86:189-200. [DOI: 10.1007/s00253-009-2242-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 09/03/2009] [Accepted: 09/03/2009] [Indexed: 10/20/2022]
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12
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Filonova L, Kallas AM, Greffe L, Johansson G, Teeri TT, Daniel G. Analysis of the Surfaces of Wood Tissues and Pulp Fibers Using Carbohydrate-Binding Modules Specific for Crystalline Cellulose and Mannan. Biomacromolecules 2006; 8:91-7. [PMID: 17206793 DOI: 10.1021/bm060632z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbohydrate binding modules (CBMs) are noncatalytic substrate binding domains of many enzymes involved in carbohydrate metabolism. Here we used fluorescent labeled recombinant CBMs specific for crystalline cellulose (CBM1(HjCel7A)) and mannans (CBM27(TmMan5) and CBM35(CjMan5C)) to analyze the complex surfaces of wood tissues and pulp fibers. The crystalline cellulose CBM1(HjCel7A) was found as a reliable marker of both bacterially produced and plant G-layer cellulose, and labeling of spruce pulp fibers with CBM1(HjCel7A) revealed a signal that increased with degree of fiber damage. The mannan-specific CBM27(TmMan5) and CBM35(CjMan5C) CBMs were found to be more specific reagents than a monoclonal antibody specific for (1-->4)-beta-mannan/galacto-(1-->4)-beta-mannan for mapping carbohydrates on native substrates. We have developed a quantitative fluorometric method for analysis of crystalline cellulose accumulation on fiber surfaces and shown a quantitative difference in crystalline cellulose binding sites in differently processed pulp fibers. Our results indicated that CBMs provide useful, novel tools for monitoring changes in carbohydrate content of nonuniform substrate surfaces, for example, during wood or pulping processes and possibly fiber biosynthesis.
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Affiliation(s)
- Lada Filonova
- Department of Wood Science, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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13
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Ficko-Blean E, Boraston AB. The Interaction of a Carbohydrate-binding Module from a Clostridium perfringens N-Acetyl-β-hexosaminidase with Its Carbohydrate Receptor. J Biol Chem 2006; 281:37748-57. [PMID: 16990278 DOI: 10.1074/jbc.m606126200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clostridium perfringens is a notable colonizer of the human gastrointestinal tract. This bacterium is quite remarkable for a human pathogen by the number of glycoside hydrolases found in its genome. The modularity of these enzymes is striking as is the frequent occurrence of modules having amino acid sequence identity with family 32 carbohydrate-binding modules (CBMs), often referred to as F5/8 domains. Here we report the properties of family 32 CBMs from a C. perfringens N-acetyl-beta-hexosaminidase. Macroarray, UV difference, and isothermal titration calorimetry binding studies indicate a preference for the disaccharide LacNAc (beta-d-galactosyl-1,4-beta-d-N-acetylglucosamine). The molecular details of the interaction of this CBM with galactose, LacNAc, and the type II blood group H-trisaccharide are revealed by x-ray crystallographic studies at resolutions of 1.49, 2.4, and 2.3 A, respectively.
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Affiliation(s)
- Elizabeth Ficko-Blean
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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14
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Veluraja K, Margulis CJ. Conformational Dynamics of Sialyl Lewisxin Aqueous Solution and Its Interaction with SelectinE. A Study by Molecular Dynamics. J Biomol Struct Dyn 2005; 23:101-11. [PMID: 15918681 DOI: 10.1080/07391102.2005.10507051] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Three dimensional structures of sialyl Lewis(x) (SLe(x)) in aqueous solution and bound to selectinE are described based on an exhaustive conformational analysis and several long molecular dynamics simulations using different glycosidic regions as starting conformations. It appears from this study that when the oligosaccharide is free in solution the NeuNAcalpha(2-3)Gal segment favors glycosidic conformation in three different regions in the (Phi,Psi) plane with propensity of populations in the ratio 1:8:1. Each one of these structures is characteristically stabilized by specific hydrogen bonding interaction between NeuNAc and Gal. On the other hand, the Gal-GlcNAc-Fuc segment can exist in four different conformational states. Based on the topology of SLe(x) we are able to predict that out of all the allowed conformations in solution only two of these structures possess a geometry that would fit without steric clashes into the binding location of selectinE. In both of these binding modes, segment Gal-GlcNAc-Fuc adopts a unique conformation. The only difference between the two SLe(x) conformers that can successfully bind to selectinE is given by two possible regions in glycosidic space in the fragment NeuNAcalpha(2-3)Gal. A large conformational departure from the crystallographic data is observed for two lysine residues at the binding site of selectinE. These two residues play an important role when SLe(x) binds selectinE in aqueous solution. These findings help reconcile the X-ray data, in which these residues appear to be 1 nm away from SLe(x), with recent liquid NMR data reporting couplings between these protein residues and the sugar.
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15
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Tunnicliffe RB, Bolam DN, Pell G, Gilbert HJ, Williamson MP. Structure of a mannan-specific family 35 carbohydrate-binding module: evidence for significant conformational changes upon ligand binding. J Mol Biol 2005; 347:287-96. [PMID: 15740741 DOI: 10.1016/j.jmb.2005.01.038] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Revised: 01/12/2005] [Accepted: 01/17/2005] [Indexed: 10/25/2022]
Abstract
Enzymes that digest plant cell wall polysaccharides generally contain non-catalytic, carbohydrate-binding modules (CBMs) that function by attaching the enzyme to the substrate, potentiating catalytic activity. Here, we present the first structure of a family 35 CBM, derived from the Cellvibrio japonicus beta-1,4-mannanase Man5C. The NMR structure has been determined for both the free protein and the protein bound to mannopentaose. The data show that the protein displays a typical beta-jelly-roll fold. Ligand binding is not located on the concave surface of the protein, as occurs in many CBMs that display the jelly-roll fold, but is formed by the loops that link the two beta-sheets of the protein, similar to family 6 CBMs. In contrast to the majority of CBMs, which are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. The curvature of the binding site and the narrow binding cleft are likely to be the main determinants of binding specificity. The predicted solvent exposure of O6 at several subsites provides an explanation for the observed accommodation of decorated mannans. Two of the key aromatic residues in Man5C-CBM35 that interact with mannopentaose are conserved in mannanase-derived CBM35s, which will guide specificity predictions based on the primary sequence of proteins in this CBM family.
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Affiliation(s)
- Richard B Tunnicliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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