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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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Wayllace NM, Martín M, Busi MV, Gomez-Casati DF. Microbial glucoamylases: structural and functional properties and biotechnological uses. World J Microbiol Biotechnol 2023; 39:293. [PMID: 37653355 DOI: 10.1007/s11274-023-03731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Glucoamylases (GAs) are one of the principal groups of enzymes involved in starch hydrolysis and belong to the glycosylhydrolase family. They are classified as exo-amylases due to their ability to hydrolyze α-1,4 glycosidic bonds from the non-reducing end of starch, maltooligosaccharides, and related substrates, releasing β-D-glucose. Structurally, GAs possess a characteristic catalytic domain (CD) with an (α/α)6 fold and exhibit five conserved regions within this domain. The CD may or may not be linked to a non-catalytic domain with variable functions depending on its origin. GAs are versatile enzymes with diverse applications in food, biofuel, bioplastic and other chemical industries. Although fungal GAs are commonly employed for these purposes, they have limitations such as their low thermostability and an acidic pH requirement. Alternatively, GAs derived from prokaryotic organisms are a good option to save costs as they exhibit greater thermostability compared to fungal GAs. Moreover, a group of cold-adapted GAs from psychrophilic organisms demonstrates intriguing properties that make them suitable for application in various industries. This review provides a comprehensive overview of the structural and sequential properties as well as biotechnological applications of GAs in different industrial processes.
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Affiliation(s)
- Natael M Wayllace
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Mariana Martín
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - María V Busi
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
| | - Diego F Gomez-Casati
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
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Emoto Y, Katayama R, Hibino E, Ishihara S, Goda N, Tenno T, Kobashigawa Y, Morioka H, Hiroaki H. A Cost-Effective Immobilization Method for MBP Fusion Proteins on Microtiter Plates Using a Gelatinized Starch-Agarose Mixture and Its Application for Convenient Protein-Protein Interaction Analysis. Methods Protoc 2023; 6:mps6030044. [PMID: 37218904 DOI: 10.3390/mps6030044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The detection and quantification of protein-protein interactions (PPIs) is a crucial technique that often involves the use of recombinant proteins with fusion protein tags, such as maltose-binding protein (MBP) and glutathione-S-transferase (GST). In this study, we improved the cohesive and sticky properties of gelatinized starch by supplementing it with agarose, resulting in a harder gel that could coat the bottom of a microtiter plate. The resulting gelatinized starch/agarose mixture allowed for the efficient immobilization of MBP-tagged proteins on the coated plates, enabling the use of indirect ELISA-like PPI assays. By using the enzymatic activity of GST as an indicator, we succeeded in determining the dissociation constants between MBP-tagged and GST-tagged proteins on 96-well microtiter plates and a microplate reader without any expensive specialized equipment.
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Affiliation(s)
- Yuri Emoto
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Ryoya Katayama
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- Graduate Program of Transformative Chem-Bio Research, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Emi Hibino
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- WISE Program, Convolution of Informatics and Biomedical Sciences on Glocal Alliances, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Aichi, Japan
| | - Sho Ishihara
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Natsuko Goda
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- BeCellBar LLC., 1 Kamimura, Showa-ku, Nagoya 466-0802, Aichi, Japan
| | - Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University; 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Kumamoto, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University; 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Kumamoto, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- Graduate Program of Transformative Chem-Bio Research, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- WISE Program, Convolution of Informatics and Biomedical Sciences on Glocal Alliances, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Aichi, Japan
- BeCellBar LLC., 1 Kamimura, Showa-ku, Nagoya 466-0802, Aichi, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya 464-8601, Aichi, Japan
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Tong L, Huang H, Zheng J, Wang X, Bai Y, Wang X, Wang Y, Tu T, Yao B, Qin X, Luo H. Engineering a carbohydrate-binding module to increase the expression level of glucoamylase in Pichia pastoris. Microb Cell Fact 2022; 21:95. [PMID: 35643500 PMCID: PMC9148494 DOI: 10.1186/s12934-022-01833-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/13/2022] [Indexed: 12/04/2022] Open
Abstract
Background Glucoamylase is an important industrial enzyme for the saccharification of starch during sugar production, but the production cost of glucoamylase is a major limiting factor for the growth of the starch-based sugar market. Therefore, seeking strategies for high-level expression of glucoamylase in heterologous hosts are considered as the main way to reduce the enzyme cost. Results ReGa15A from Rasamsonia emersonii and TlGa15B-GA2 from Talaromyces leycettanus have similar properties. However, the secretion level of ReGa15A was significantly higher than TlGa15B-GA2 in Pichia pastoris. To explore the underlying mechanisms affecting the differential expression levels of glucoamylase in P. pastoris, the amino acid sequences and three-dimensional structures of them were compared and analyzed. First, the CBM region was identified by fragment replacement as the key region affecting the expression levels of ReGa15A and TlGa15B-GA2. Then, through the substitution and site-directed mutation of the motifs in the CBM region, three mutants with significantly increased expression levels were obtained. The eight-point mutant TlGA-M4 (S589D/Q599A/G600Y/V603Q/T607I/V608L/N609D/R613Q), the three-point mutant TlGA-M6 (Q599A/G600Y/V603Q) and the five-point mutant TlGA-M7 (S589D/T607I/V608L/N609D/R613Q) have the same specific activity with the wild-type, and the enzyme activity and secretion level have increased by 4–5 times, respectively. At the same time, the expression levels were 5.8-, 2.0- and 2.4-fold higher than that of wild type, respectively. Meanwhile, the expression of genes related to the unfolded protein responses (UPR) in the endoplasmic reticulum (ER) did not differ significantly between the mutants and wild type. In addition, the most highly expressed mutant, TlGA-M7 exhibits rapidly and effectively hydrolyze raw corn starch. Conclusions Our results constitute the first demonstration of improved expression and secretion of a glucoamylase in P. pastoris by introducing mutations within the non-catalytic CBM. This provides a novel and effective strategy for improving the expression of recombinant proteins in heterologous host expression systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01833-1.
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Liu Y, Wang P, Tian J, Seidi F, Guo J, Zhu W, Xiao H, Song J. Carbohydrate-Binding Modules of Potential Resources: Occurrence in Nature, Function, and Application in Fiber Recognition and Treatment. Polymers (Basel) 2022; 14:polym14091806. [PMID: 35566977 PMCID: PMC9100146 DOI: 10.3390/polym14091806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 02/04/2023] Open
Abstract
Great interests have recently been aroused in the independent associative domain of glycoside hydrolases that utilize insoluble polysaccharides-carbohydrate-binding module (CBM), which responds to binding while the catalytic domain reacts with the substrate. In this mini-review, we first provide a brief introduction on CBM and its subtypes including the classifications, potential sources, structures, and functions. Afterward, the applications of CBMs in substrate recognition based on different types of CBMs have been reviewed. Additionally, the progress of CBMs in paper industry as a new type of environmentally friendly auxiliary agent for fiber treatment is summarized. At last, other applications of CBMs and the future outlook have prospected. Due to the specificity in substrate recognition and diversity in structures, CBM can be a prosperous and promising ‘tool’ for wood and fiber processing in the future.
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Affiliation(s)
- Yena Liu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Peipei Wang
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Jing Tian
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Farzad Seidi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Jiaqi Guo
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Wenyuan Zhu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB E3B 5A3, Canada;
| | - Junlong Song
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
- Correspondence: ; Tel.: +86-25-8542-8163; Fax: +86-25-8542-8689
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Characterization of SdGA, a cold-adapted glucoamylase from Saccharophagus degradans. ACTA ACUST UNITED AC 2021; 30:e00625. [PMID: 34041001 PMCID: PMC8141877 DOI: 10.1016/j.btre.2021.e00625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 11/24/2022]
Abstract
We investigated the structural and functional properties of SdGA, a glucoamylase (GA) from Saccharophagus degradans, a marine bacterium which degrades different complex polysaccharides at high rate. SdGA is composed mainly by a N-terminal GH15_N domain linked to a C-terminal catalytic domain (CD) found in the GH15 family of glycosylhydrolases with an overall structure similar to other bacterial GAs. The protein was expressed in Escherichia coli cells, purified and its biochemical properties were investigated. Although SdGA has a maximum activity at 39 °C and pH 6.0, it also shows high activity in a wide range, from low to mild temperatures, like cold-adapted enzymes. Furthermore, SdGA has a higher content of flexible residues and a larger CD due to various amino acid insertions compared to other thermostable GAs. We propose that this novel SdGA, is a cold-adapted enzyme that might be suitable for use in different industrial processes that require enzymes which act at low or medium temperatures.
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Kobashigawa Y, Namikawa M, Sekiguchi M, Inada Y, Yamauchi S, Kimoto Y, Okazaki K, Toyota Y, Sato T, Morioka H. Expression, Purification and Characterization of CAR/NCOA-1 Tethered Protein in E. coli Using Maltose-Binding Protein Fusion Tag and Gelatinized Corn Starch. Biol Pharm Bull 2021; 44:125-130. [PMID: 33390539 DOI: 10.1248/bpb.b20-00759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The constitutive active/androstane receptor (CAR) is a nuclear receptor that functions as a xenobiotic sensor, which regulates the expression of enzymes involved in drug metabolism and of efflux transporters. Evaluation of the binding properties between CAR and a drug was assumed to facilitate the prediction of drug-drug interaction, thereby contributing to drug discovery. The purpose of this study is to construct a system for the rapid evaluation of interactions between CAR and drugs. We prepared recombinant CAR protein using the Escherichia coli expression system. Since isolated CAR protein is known to be unstable, we designed a fusion protein with the CAR binding sequence of the nuclear receptor coactivator 1 (NCOA1), which was expressed as a fusion protein with maltose binding protein (MBP), and purified it by several chromatography steps. The thus-obtained CAR/NCOA1 tethered protein (CAR-NCOA1) was used to evaluate the interactions of CAR with agonists and inverse agonists by a thermal denaturation experiment using differential scanning fluorometry (DSF) in the presence and absence of drugs. An increase in the melting temperature was observed with the addition of the drugs, confirming the direct interaction between them and CAR. DSF is easy to set up and compatible with multiwell plate devices (such as 96-well plates). The use of DSF and the CAR-NCOA1 fusion protein together allows for the rapid evaluation of the interaction between a drug and CAR, and is thereby considered to be useful in drug discovery.
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Affiliation(s)
- Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Mana Namikawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Mitsuhiro Sekiguchi
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University
| | - Yuki Inada
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Soichiro Yamauchi
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Yuu Kimoto
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University
| | - Kyo Okazaki
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Yuya Toyota
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Takashi Sato
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University
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Tokunaga Y, Nagata T, Kondo K, Katahira M, Watanabe T. NMR elucidation of nonproductive binding sites of lignin models with carbohydrate-binding module of cellobiohydrolase I. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:164. [PMID: 33042221 PMCID: PMC7541279 DOI: 10.1186/s13068-020-01805-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/27/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Highly efficient enzymatic saccharification of pretreated lignocellulose is a key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase that possesses carbohydrate-binding module 1 (TrCBM1) at the C-terminal domain. The nonproductive binding of TrCBM1 to lignin significantly decreases the enzymatic saccharification efficiency and increases the cost of biomass conversion because of the additionally required enzymes. Understanding the interaction mechanism between lignin and TrCBM1 is essential for realizing a cost-effective biofuel production; however, the binding sites in lignin have not been clearly elucidated. RESULTS Three types of 13C-labeled β-O-4 lignin oligomer models were synthesized and characterized. The 2D 1H-13C heteronuclear single-quantum correlation (HSQC) spectra of the 13C-labeled lignin models confirmed that the three types of the 13C labels were correctly incorporated in the (1) aromatic rings and β positions, (2) α positions, and (3) methoxy groups, respectively. The TrCBM1-binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic 13C-labeled β-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. These findings indicated that hydrophobic interactions and π-π stacking were dominating factors in nonproductive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C(I) and C(II). The C(I) ring showed remarkable perturbation compared with the C(II), which indicated that the binding of TrCBM1 was markedly affected by the configuration of the lignin models. The long-chain lignin models (degree of polymerization (DP) 4.16-4.70) clearly bound to TrCBM1. The interactions of TrCBM1 with the short-chain lignin models (DP 2.64-3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding. CONCLUSION The CSP analysis using 13C-labeled β-O-4 lignin oligomer models enabled the identification of the TrCBM1 binding sites in lignins at the atomic level. This specific interaction analysis will provide insights for new molecular designs of cellulase having a controlled affinity to cellulose and lignin for a cost-effective biorefinery process.
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Affiliation(s)
- Yuki Tokunaga
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Takashi Nagata
- Institute of Advanced Energy (IAE), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Keiko Kondo
- Institute of Advanced Energy (IAE), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Masato Katahira
- Institute of Advanced Energy (IAE), Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Takashi Watanabe
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Uji, Kyoto 611-0011 Japan
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Andersen S, Svensson B, Møller MS. Roles of the N-terminal domain and remote substrate binding subsites in activity of the debranching barley limit dextrinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140294. [DOI: 10.1016/j.bbapap.2019.140294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/15/2019] [Accepted: 10/10/2019] [Indexed: 11/28/2022]
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Janeček Š, Mareček F, MacGregor EA, Svensson B. Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv 2019; 37:107451. [PMID: 31536775 DOI: 10.1016/j.biotechadv.2019.107451] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 09/15/2019] [Indexed: 01/05/2023]
Abstract
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - E Ann MacGregor
- 2 Nicklaus Green, Livingston EH54 8RX, West Lothian, United Kingdom
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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Armenta S, Sánchez-Cuapio Z, Munguia ME, Pulido NO, Farrés A, Manoutcharian K, Hernandez-Santoyo A, Moreno-Mendieta S, Sánchez S, Rodríguez-Sanoja R. The role of conserved non-aromatic residues in the Lactobacillus amylovorus α-amylase CBM26-starch interaction. Int J Biol Macromol 2019; 121:829-838. [DOI: 10.1016/j.ijbiomac.2018.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 10/12/2018] [Accepted: 10/14/2018] [Indexed: 10/28/2022]
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12
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Kumar GS, Choy MS, Koveal DM, Lorinsky MK, Lyons SP, Kettenbach AN, Page R, Peti W. Identification of the substrate recruitment mechanism of the muscle glycogen protein phosphatase 1 holoenzyme. SCIENCE ADVANCES 2018; 4:eaau6044. [PMID: 30443599 PMCID: PMC6235537 DOI: 10.1126/sciadv.aau6044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/15/2018] [Indexed: 05/04/2023]
Abstract
Glycogen is the primary storage form of glucose. Glycogen synthesis and breakdown are tightly controlled by glycogen synthase (GYS) and phosphorylase, respectively. The enzyme responsible for dephosphorylating GYS and phosphorylase, which results in their activation (GYS) or inactivation (phosphorylase) to robustly stimulate glycogen synthesis, is protein phosphatase 1 (PP1). However, our understanding of how PP1 recruits these substrates is limited. Here, we show how PP1, together with its muscle glycogen-targeting (GM) regulatory subunit, recruits and selectively dephosphorylates its substrates. Our molecular data reveal that the GM carbohydrate binding module (GM CBM21), which is amino-terminal to the GM PP1 binding domain, has a dual function in directing PP1 substrate specificity: It either directly recruits substrates (i.e., GYS) or recruits them indirectly by localization (via glycogen for phosphorylase). Our data provide the molecular basis for PP1 regulation by GM and reveal how PP1-mediated dephosphorylation is driven by scaffolding-based substrate recruitment.
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Affiliation(s)
- Ganesan Senthil Kumar
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Meng S. Choy
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Dorothy M. Koveal
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Michael K. Lorinsky
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Scott P. Lyons
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Rebecca Page
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Corresponding author.
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13
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Suyama Y, Muraki N, Kusunoki M, Miyake H. Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger. Acta Crystallogr F Struct Biol Commun 2017; 73:550-554. [PMID: 28994402 PMCID: PMC5633921 DOI: 10.1107/s2053230x17012894] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/09/2017] [Indexed: 11/10/2022] Open
Abstract
Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 Å resolution. The SBD consisted of seven β-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each β-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the Cα atom of Cys509 between the X-ray- and NMR-determined structures was 13.3 Å. In addition, the B factors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible.
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Affiliation(s)
- Yousuke Suyama
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Norifumi Muraki
- Faculty of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Masami Kusunoki
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-3-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Hideo Miyake
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
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14
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Xie C, Gong W, Zhu Z, Yan L, Hu Z, Peng Y. Comparative transcriptomics of Pleurotus eryngii reveals blue-light regulation of carbohydrate-active enzymes (CAZymes) expression at primordium differentiated into fruiting body stage. Genomics 2017; 110:201-209. [PMID: 28970048 DOI: 10.1016/j.ygeno.2017.09.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/10/2017] [Accepted: 09/27/2017] [Indexed: 02/03/2023]
Abstract
Blue light is an important environmental factor which could induce mushroom primordium differentiation and fruiting body development. However, the mechanisms of Pleurotus eryngii primordium differentiation and development induced by blue light are still unclear. The CAZymes (carbohydrate-active enzymes) play important roles in degradation of renewable lignocelluloses to provide carbohydrates for fungal growth, development and reproduction. In the present research, the expression profiles of genes were measured by comparison between the Pleurotus eryngii at primordium differentiated into fruiting body stage after blue light stimulation and dark using high-throughput sequencing approach. After assembly and compared to the Pleurotus eryngii reference genome, 11,343 unigenes were identified. 539 differentially expressed genes including white collar 2 type of transcription factor gene, A mating type protein gene, MAP kinase gene, oxidative phosphorylation associated genes, CAZymes genes and other metabolism related genes were identified during primordium differentiated into fruiting body stage after blue light stimulation. KEGG results showed that carbon metabolism, glycolysis/gluconeogenesis and biosynthesis of amino acids pathways were affected during blue light inducing primordia formation. Most importantly, 319 differentially expressed CAZymes participated in carbon metabolism were identified. The expression patterns of six representative CAZymes and laccase genes were further confirmed by qRT-PCR. Enzyme activity results indicated that the activities of CAZymes and laccase were affected in primordium differentiated into fruiting body under blue light stimulation. In conclusion, the comprehensive transcriptome and CAZymes of Pleurotus eryngii at primordium differentiated into fruiting body stage after blue light stimulation were obtained. The biological insights gained from this integrative system represent a valuable resource for future genomic studies on this commercially important mushroom.
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Affiliation(s)
- Chunliang Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Wenbing Gong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Zuohua Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Li Yan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Zhenxiu Hu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China.
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15
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Fungal Hybrid B heme peroxidases - unique fusions of a heme peroxidase domain with a carbohydrate-binding domain. Sci Rep 2017; 7:9393. [PMID: 28839281 PMCID: PMC5571214 DOI: 10.1038/s41598-017-09581-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/26/2017] [Indexed: 01/03/2023] Open
Abstract
Heme peroxidases, essential peroxide converting oxidoreductases are divided into four independently evolved superfamilies. Within the largest one – the peroxidase-catalase superfamily - two hybrid lineages were described recently. Whereas Hybrid A heme peroxidases represent intermediate enzymes between ascorbate peroxidases and cytochrome c peroxidases, Hybrid B heme peroxidases are unique fusion proteins comprised of a conserved N-terminal heme peroxidase domain and a C-terminal domain of various sugar binding motifs. So far these peculiar peroxidases are only found in the kingdom of Fungi. Here we present a phylogenetic reconstruction of the whole superfamily with focus on Hybrid B peroxidases. We analyse the domain assembly and putative structure and function of the newly discovered oligosaccharide binding domains. Two distinct carbohydrate binding modules (CBM21 and CBM34) are shown to occur in phytopathogenic ascomycetous orthologs of Hybrid B heme peroxidases only. Based on multiple sequence alignment and homology modeling the structure-function relationships are discussed with respect to physiological function. A concerted action of peroxide cleavage with specific cell-wall carbohydrate binding can support phytopathogens survival within the plant host.
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16
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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: 61] [Impact Index Per Article: 8.7] [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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17
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Janeček Š, Majzlová K, Svensson B, MacGregor EA. The starch-binding domain family CBM41-Anin silicoanalysis of evolutionary relationships. Proteins 2017; 85:1480-1492. [DOI: 10.1002/prot.25309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/05/2017] [Accepted: 04/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Štefan Janeček
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
- Department of Biology; Faculty of Natural Sciences, University of SS. Cyril and Methodius; Trnava Slovakia
| | - Katarína Majzlová
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
| | - Birte Svensson
- Department of Biotechnology and Biomedicine; Technical University of Denmark; Kgs. Lyngby Denmark
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18
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Shobha MS, Gowda LR, Tharanathan RN. A novel catalysis by porcine pepsin in debranching guar galactomannan. Carbohydr Polym 2013; 102:615-21. [PMID: 24507326 DOI: 10.1016/j.carbpol.2013.11.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 11/16/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pepsin (porcine stomach mucosa, E.C. 3.4.23.1), an acid protease catalyzes the hydrolysis (debranching) of guar galactomannan (GG), a co-polymer of mannose and galactose residues thereby showing its non-specific catalysis towards glycosidic substrates. RESULTS AND CONCLUSIONS Use of non-specific inhibitors, chemical modification agents and peptide mapping of native and GG--bound pepsin upon proteolytic digestion with Staphylococcus aureus V8 protease revealed the involvement of Asp(138) residue in the catalysis, which was confirmed by computational modelling studies. GENERAL SIGNIFICANCE Here we show a novel mode of catalysis (other than proteolysis) by porcine pepsin with a different active site residue.
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Affiliation(s)
- Mysore S Shobha
- Department of Biochemistry and Nutrition, Central Food Technological Research Institute, Council of Scientific and Industrial Research, Mysore 570 020, India
| | - Lalitha R Gowda
- Department of Protein Chemistry and Technology, Central Food Technological Research Institute, Council of Scientific and Industrial Research, Mysore 570 020, India
| | - Rudrapatam N Tharanathan
- Department of Biochemistry and Nutrition, Central Food Technological Research Institute, Council of Scientific and Industrial Research, Mysore 570 020, India.
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19
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Chu CH, Li KM, Lin SW, Chang MDT, Jiang TY, Sun YJ. Crystal structures of starch binding domain from Rhizopus oryzae
glucoamylase in complex with isomaltooligosaccharide: Insights into polysaccharide binding mechanism of CBM21 family. Proteins 2013; 82:1079-85. [DOI: 10.1002/prot.24446] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/10/2013] [Accepted: 09/26/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Chen-Hsi Chu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science; National Tsing Hua University; Hsin Chu 30013 Taiwan Republic of China
| | - Kun-Mou Li
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science; National Tsing Hua University; Hsin Chu 30013 Taiwan Republic of China
| | - Shih-Wei Lin
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science; National Tsing Hua University; Hsin Chu 30013 Taiwan Republic of China
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology and Department of Medical Science; National Tsing Hua University; Hsinchu 300 Taiwan Republic of China
| | - Ting-Ying Jiang
- Institute of Molecular and Cellular Biology and Department of Medical Science; National Tsing Hua University; Hsinchu 300 Taiwan Republic of China
| | - Yuh-Ju Sun
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science; National Tsing Hua University; Hsin Chu 30013 Taiwan Republic of China
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20
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Tseng TS, Cheng CS, Hsu STD, Shih MF, He PL, Lyu PC. Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster. PLoS One 2013; 8:e54187. [PMID: 23349821 PMCID: PMC3551606 DOI: 10.1371/journal.pone.0054187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/07/2012] [Indexed: 11/19/2022] Open
Abstract
Drosophila melanogaster crammer is a novel cathepsin inhibitor involved in long-term memory formation. A molten globule-to-ordered structure transition is required for cathepsin inhibition. This study reports the use of alanine scanning to probe the critical residues in the two hydrophobic cores and the salt bridges of crammer in the context of disorder-to-order transition and cathepsin inhibition. Alanine substitution of the aromatic residues W9, Y12, F16, Y20, Y32, and W53 within the hydrophobic cores, and charged residues E8, R28, R29, and E67 in the salt bridges considerably decrease the ability of crammer to inhibit Drosophila cathepsin B (CTSB). Far-UV circular dichroism (CD), intrinsic fluorescence, and nuclear magnetic resonance (NMR) spectroscopies show that removing most of the aromatic and charged side-chains substantially reduces thermostability, alters pH-dependent helix formation, and disrupts the molten globule-to-ordered structure transition. Molecular modeling indicates that W53 in the hydrophobic Core 2 is essential for the interaction between crammer and the prosegment binding loop (PBL) of CTSB; the salt bridge between R28 and E67 is critical for the appropriate alignment of the α-helix 4 toward the CTSB active cleft. The results of this study show detailed residue-specific dissection of folding transition and functional contributions of the hydrophobic cores and salt bridges in crammer, which have hitherto not been characterized for cathepsin inhibition by propeptide-like cysteine protease inhibitors. Because of the involvements of cathepsin inhibitors in neurodegenerative diseases, these structural insights can serve as a template for further development of therapeutic inhibitors against human cathepsins.
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Affiliation(s)
- Tien-Sheng Tseng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Min-Fang Shih
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Pei-Lin He
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
- * E-mail:
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21
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Stephen P, Cheng KC, Lyu PC. Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites. PLoS One 2012; 7:e50488. [PMID: 23226294 PMCID: PMC3511584 DOI: 10.1371/journal.pone.0050488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 10/22/2012] [Indexed: 11/20/2022] Open
Abstract
Glucoamylases, containing starch-binding domains (SBD), have a wide range of scientific and industrial applications. Random mutagenesis and DNA shuffling of the gene encoding a starch-binding domain have resulted in only minor improvements in the affinities of the corresponding protein to their ligands, whereas circular permutation of the RoCBM21 substantially improved its binding affinity and selectivity towards longer-chain carbohydrates. For the study reported herein, we used a standard soluble ligand (amylose EX-I) to characterize the functional and structural aspects of circularly permuted RoCBM21 (CP90). Site-directed mutagenesis and the analysis of crystal structure reveal the dimerisation and an altered binding path, which may be responsible for improved affinity and altered selectivity of this newly created starch-binding domain. The functional and structural characterization of CP90 suggests that it has significant potential in industrial applications.
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Affiliation(s)
- Preyesh Stephen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Kuo-Chang Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
- * E-mail:
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22
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Møller MS, Abou Hachem M, Svensson B, Henriksen A. Structure of the starch-debranching enzyme barley limit dextrinase reveals homology of the N-terminal domain to CBM21. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1008-12. [PMID: 22949184 PMCID: PMC3433187 DOI: 10.1107/s1744309112031004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/07/2012] [Indexed: 11/10/2022]
Abstract
Barley limit dextrinase (HvLD) is a debranching enzyme from glycoside hydrolase family 13 subfamily 13 (GH13_13) that hydrolyses α-1,6-glucosidic linkages in limit dextrins derived from amylopectin. The structure of HvLD was solved and refined to 1.9 Å resolution. The structure has a glycerol molecule in the active site and is virtually identical to the structures of HvLD in complex with the competitive inhibitors α-cyclodextrin and β-cyclodextrin solved to 2.5 and 2.1 Å resolution, respectively. However, three loops in the N-terminal domain that are shown here to resemble carbohydrate-binding module family 21 were traceable and were included in the present HvLD structure but were too flexible to be traced and included in the structures of the two HvLD-inhibitor complexes.
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Affiliation(s)
- Marie Sofie Møller
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, 2800 Kgs. Lyngby, Denmark
- Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, 2500 Valby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, 2800 Kgs. Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, 2800 Kgs. Lyngby, Denmark
| | - Anette Henriksen
- Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, 2500 Valby, Denmark
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23
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Jiang TY, Ci YP, Chou WI, Lee YC, Sun YJ, Chou WY, Li KM, Chang MDT. Two unique ligand-binding clamps of Rhizopus oryzae starch binding domain for helical structure disruption of amylose. PLoS One 2012; 7:e41131. [PMID: 22815939 PMCID: PMC3398936 DOI: 10.1371/journal.pone.0041131] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/17/2012] [Indexed: 11/30/2022] Open
Abstract
The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD) has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21) members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs.
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Affiliation(s)
- Ting-Ying Jiang
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Yuan-Pei Ci
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Wei-I Chou
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Simpson Biotech Company, Ltd., Taoyuan County, Taiwan, Republic of China
| | - Yuan-Chuan Lee
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Wei-Yao Chou
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Kun-Mou Li
- Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology and Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- * E-mail:
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24
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A molten globule-to-ordered structure transition of Drosophila melanogaster crammer is required for its ability to inhibit cathepsin. Biochem J 2012; 442:563-72. [PMID: 22150223 PMCID: PMC3286859 DOI: 10.1042/bj20111360] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drosophila melanogaster crammer is a novel cathepsin inhibitor that is involved in LTM (long-term memory) formation. The mechanism by which the inhibitory activity is regulated remains unclear. In the present paper we have shown that the oligomeric state of crammer is pH dependent. At neutral pH, crammer is predominantly dimeric in vitro as a result of disulfide bond formation, and is monomeric at acidic pH. Our inhibition assay shows that monomeric crammer, not disulfide-bonded dimer, is a strong competitive inhibitor of cathepsin L. Crammer is a monomeric molten globule in acidic solution, a condition that is similar to the environment in the lysosome where crammer is probably located. Upon binding to cathepsin L, however, crammer undergoes a molten globule-to-ordered structural transition. Using high-resolution NMR spectroscopy, we have shown that a cysteine-to-serine point mutation at position 72 (C72S) renders crammer monomeric at pH 6.0 and that the structure of the C72S variant highly resembles that of wild-type crammer in complex with cathepsin L at pH 4.0. We have determined the first solution structure of propeptide-like protease inhibitor in its active form and examined in detail using a variety of spectroscopic methods the folding properties of crammer in order to delineate its biomolecular recognition of cathepsin.
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Stephen P, Tseng KL, Liu YN, Lyu PC. Circular permutation of the starch-binding domain: inversion of ligand selectivity with increased affinity. Chem Commun (Camb) 2012; 48:2612-4. [PMID: 22294161 DOI: 10.1039/c2cc17376j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Proteins containing starch-binding domains (SBDs) are used in a variety of scientific and technological applications. A circularly permutated SBD (CP90) with improved affinity and selectivity toward longer-chain carbohydrates was synthesized, suggesting that a new starch-binding protein may be developed for specific scientific and industrial applications.
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Affiliation(s)
- Preyesh Stephen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan ROC
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26
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Janeček Š, Svensson B, MacGregor EA. Structural and evolutionary aspects of two families of non-catalytic domains present in starch and glycogen binding proteins from microbes, plants and animals. Enzyme Microb Technol 2011; 49:429-40. [DOI: 10.1016/j.enzmictec.2011.07.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 07/04/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
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Bieri M, Kwan AH, Mobli M, King GF, Mackay JP, Gooley PR. Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination. FEBS J 2011; 278:704-15. [PMID: 21214861 DOI: 10.1111/j.1742-4658.2011.08005.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A strength of NMR spectroscopy is its ability to monitor, on an atomic level, molecular changes and interactions. In this review, which is intended for non-spectroscopist, we describe major uses of NMR in protein science beyond solution structure determination. After first touching on how NMR can be used to quickly determine whether a mutation induces structural perturbations in a protein, we describe the unparalleled ability of NMR to monitor binding interactions over a wide range of affinities, molecular masses and solution conditions. We discuss the use of NMR to measure the dynamics of proteins at the atomic level and over a wide range of timescales. Finally, we outline new and expanding areas such as macromolecular structure determination in multicomponent systems, as well as in the solid state and in vivo.
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Affiliation(s)
- Michael Bieri
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
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28
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Glucoamylases: structural and biotechnological aspects. Appl Microbiol Biotechnol 2010; 89:1267-73. [DOI: 10.1007/s00253-010-3034-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 11/26/2022]
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29
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Chou WY, Chou WI, Pai TW, Lin SC, Jiang TY, Tang CY, Chang MDT. Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules. Bioinformatics 2010; 26:1022-8. [DOI: 10.1093/bioinformatics/btq084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Chen T, Lee TR, Liang WG, Chang WSW, Lyu PC. Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor. Proteins 2009; 77:209-19. [PMID: 19422058 DOI: 10.1002/prot.22432] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Human serine proteinase inhibitor Kazal-type 2 (SPINK2) functions as a trypsin/acrosin inhibitor and is synthesized mainly in the testis and seminal vesicle where its activity is engaged in fertility. The SPINK2 protein contains a typical Kazal domain composed by six cysteine residues forming three disulfide bridges. The expression of SPINK2 is closely related to cancer such as lymphomas, in that a high transcript level of SPINK2 in patients with primary cutaneous follicle center cell lymphomas have better prognosis with lower mortality. To clarify the role of SPINK2 in cancer, we performed quantitative real-time PCR and showed that the expression level of SPINK2 is significantly elevated in most leukemia cell lines except B-lymphoblast TK-6 cells. The molecular function and structural features of SPINK2 were also investigated by employing the recombinant active and mutant inactive SPINK2 proteins to determine its key P2-P2' (Pro(23)-Arg(24)-His(25)-Phe(26)) active site. The inhibition assay results demonstrated that Arg(24) at the P1 site is crucial for the specificity of SPINK2 on target enzyme. Although His(25) at the P1' and Phe(26) at the P2' residues are also involved in trypsin-SPINK2 interaction, Pro(23) at the P2 site may not be directly participated in interacting with trypsin. In addition, we determined the 3D solution structure of SPINK2 and used this structure to predict the SPINK2-proteinase complex structure and binding properties. These studies not only provide critical information about the structural properties and biophysical features of the SPINK2 proteinase inhibitor, but also suggest its important role in tumor progression and response to treatment.
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Affiliation(s)
- Ting Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
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31
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Kumar P, Satyanarayana T. Microbial glucoamylases: characteristics and applications. Crit Rev Biotechnol 2009; 29:225-55. [DOI: 10.1080/07388550903136076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Christiansen C, Abou Hachem M, Janecek S, Viksø-Nielsen A, Blennow A, Svensson B. The carbohydrate-binding module family 20--diversity, structure, and function. FEBS J 2009; 276:5006-29. [PMID: 19682075 DOI: 10.1111/j.1742-4658.2009.07221.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Starch-active enzymes often possess starch-binding domains (SBDs) mediating attachment to starch granules and other high molecular weight substrates. SBDs are divided into nine carbohydrate-binding module (CBM) families, and CBM20 is the earliest-assigned and best characterized family. High diversity characterizes CBM20s, which occur in starch-active glycoside hydrolase families 13, 14, 15, and 77, and enzymes involved in starch or glycogen metabolism, exemplified by the starch-phosphorylating enzyme glucan, water dikinase 3 from Arabidopsis thaliana and the mammalian glycogen phosphatases, laforins. The clear evolutionary relatedness of CBM20s to CBM21s, CBM48s and CBM53s suggests a common clan hosting most of the known SBDs. This review surveys the diversity within the CBM20 family, and makes an evolutionary comparison with CBM21s, CBM48s and CBM53s, discussing intrafamily and interfamily relationships. Data on binding to and enzymatic activity towards soluble ligands and starch granules are summarized for wild-type, mutant and chimeric fusion proteins involving CBM20s. Noticeably, whereas CBM20s in amylolytic enzymes confer moderate binding affinities, with dissociation constants in the low micromolar range for the starch mimic beta-cyclodextrin, recent findings indicate that CBM20s in regulatory enzymes have weaker, low millimolar affinities, presumably facilitating dynamic regulation. Structures of CBM20s, including the first example of a full-length glucoamylase featuring both the catalytic domain and the SBD, are summarized, and distinct architectural and functional features of the two SBDs and roles of pivotal amino acids in binding are described. Finally, some applications of SBDs as affinity or immobilization tags and, recently, in biofuel and in planta bioengineering are presented.
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Affiliation(s)
- Camilla Christiansen
- VKR Research Centre Pro-Active Plants, Department of Plant Biology and Biotechnology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg, Denmark
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CBM21 starch-binding domain: A new purification tag for recombinant protein engineering. Protein Expr Purif 2009; 65:261-6. [DOI: 10.1016/j.pep.2009.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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An enzyme family reunion — similarities, differences and eccentricities in actions on α-glucans. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0164-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0162-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Crystal structures of the starch-binding domain from Rhizopus oryzae glucoamylase reveal a polysaccharide-binding path. Biochem J 2008; 416:27-36. [DOI: 10.1042/bj20080580] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GA (glucoamylase) hydrolyses starch and polysaccharides to β-D-glucose. RoGA (Rhizopus oryzae GA) consists of two functional domains, an N-terminal SBD (starch-binding domain) and a C-terminal catalytic domain, which are connected by an O-glycosylated linker. In the present study, the crystal structures of the SBD from RoGA (RoGACBM21) and the complexes with β-cyclodextrin (SBD–βCD) and maltoheptaose (SBD–G7) were determined. Two carbohydrate binding sites, I (Trp47) and II (Tyr32), were resolved and their binding was co-operative. Besides the hydrophobic interaction, two unique polyN loops comprising consecutive asparagine residues also participate in the sugar binding. A conformational change in Tyr32 was observed between unliganded and liganded SBDs. To elucidate the mechanism of polysaccharide binding, a number of mutants were constructed and characterized by a quantitative binding isotherm and Scatchard analysis. A possible binding path for long-chain polysaccharides in RoGACBM21 was proposed.
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Liu WT, Lin SC, Chou WI, Liu TH, Pan RL, Tzou DL, Hua TE, Chang MDT. Identification and characterization of a novel fibril forming peptide in fungal starch binding domain. Biochem Biophys Res Commun 2008; 377:966-70. [PMID: 18952064 DOI: 10.1016/j.bbrc.2008.10.085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022]
Abstract
Scanty information is available regarding the chemical basis for structural alterations of the carbohydrate-binding modules (CBMs). The N-terminal starch binding domain (SBD) of Rhizopus oryzae glucoamylase (GA) forms fibrils under thermal stress, presenting an unusual conformational change from immunoglobulin-like to beta-sheet-rich structure. Site-directed mutagenesis revealed that the C-terminal Lys of SBD played a crucial role in the fibril formation. The synthetic peptide (DNNNSANYQVSTSK) representing the C-terminal 14 amino acid residues of SBD was further demonstrated to act as a fibril-forming segment, in which terminal charges and an internal NNNxxNYQ motif were key fibril-forming determinants. The formation of fibril structure in a fungal SBD, caused by its chemical and biophysical requirements, was demonstrated for the first time.
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Affiliation(s)
- Wei-Ting Liu
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, No. 101, Section 2, Kuang Fu Road, Hsinchu 300, Taiwan, ROC
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38
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Koay A, Rimmer KA, Mertens HDT, Gooley PR, Stapleton D. Oligosaccharide recognition and binding to the carbohydrate binding module of AMP-activated protein kinase. FEBS Lett 2007; 581:5055-9. [PMID: 17919599 DOI: 10.1016/j.febslet.2007.09.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 09/04/2007] [Accepted: 09/20/2007] [Indexed: 11/16/2022]
Abstract
The AMP-activated protein kinase (AMPK) contains a carbohydrate-binding module (beta1-CBM) that is conserved from yeast to mammals. Beta1-CBM has been shown to localize AMPK to glycogen in intact cells and in vitro. Here we use Nuclear Magnetic Resonance spectroscopy to investigate oligosaccharide binding to 15N labelled beta1-CBM. We find that beta1-CBM shows greatest affinity to carbohydrates of greater than five glucose units joined via alpha,1-->4 glycosidic linkages with a single, but not multiple, glucose units in an alpha,1-->6 branch. The near identical chemical shift profile for all oligosaccharides whether cyclic or linear suggest a similar binding conformation and confirms the presence of a single carbohydrate-binding site.
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Affiliation(s)
- Ann Koay
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
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Role of the linker region in the expression of Rhizopus oryzae glucoamylase. BMC BIOCHEMISTRY 2007; 8:9. [PMID: 17593302 PMCID: PMC1933424 DOI: 10.1186/1471-2091-8-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 06/25/2007] [Indexed: 11/10/2022]
Abstract
Background Rhizopus oryzae glucoamylase (RoGA) consists of three domains: an amino (N)-terminal raw starch-binding domain (SBD), a glycosylated linker domain, and a carboxy (C)-terminal catalytic domain. The 36-amino-acid linker region (residues 132–167) connects the two functional domains, but its structural and functional roles are unclear. Results To characterize the linker sequences of RoGA and its involvement in protein expression, a number of RoGA variants containing deletions and mutations were constructed and expressed in Saccharomyces cerevisiae. Deletion analyses demonstrate that the linker region, especially within residues 161 to 167, is required for protein expression. In addition, site-directed mutagenesis and deglycosylation studies reveal that the linker region of RoGA contains both N- and O-linked carbohydrate moieties, and the N-linked oligosaccharides play a major role in the formation of active enzyme. Although the linker segment itself appears to have no ordered secondary structural conformation, the flexible region indeed contributes to the stabilization of functional N- and C-terminal domains. Conclusion Our data provide direct evidence that the length, composition, and glycosylation of the interdomain linker play a central role in the structure and function of RoGA.
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