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Rykov SV, Selimzyanova AI, Nikolaeva AY, Lazarenko VA, Tsurin NV, Akentyev PI, Zverlov VV, Liebl W, Schwarz WH, Berezina OV. Unusual substrate specificity in GH family 12: structure-function analysis of glucanases Bgh12A and Xgh12B from Aspergillus cervinus, and Egh12 from Thielavia terrestris. Appl Microbiol Biotechnol 2022; 106:1493-1509. [PMID: 35129654 DOI: 10.1007/s00253-022-11811-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 01/17/2022] [Accepted: 01/26/2022] [Indexed: 11/28/2022]
Abstract
In this study, we compared the properties and structures of three fungal GH12 enzymes: the strict endoglucanase Bgh12A and the xyloglucanase Xgh12B from Aspergillus cervinus, and the endoglucanase Egh12 from Thielavia terrestris combining activity on linear β-glucan and branched xyloglucan. Egh12 from T. terrestris was produced in Pichia pastoris, purified, and characterized as a thermostable enzyme with maximal activity at 70 ºC and a half-life time of 138 min at 65 °C. We for the first time demonstrated that the GH12 endoglucanases Egh12 and Bgh12A, but not the strict xyloglucanase Xgh12B, hydrolyzed (1,3)-β-linkages in (1,3;1,4)-β-D-glucooligosaccharides and had transglycosylase activity on (1,3)-β-D-glucooligosaccharides. Phylogenetic analysis indicated that Egh12 from T. terrestris and Bgh12A from A. cervinus are more related than Bgh12A and Xgh12B isolated from one strain. The X-ray structure of Bgh12A was determined with 2.17 Å resolution and compared with 3D-homology models of Egh12 and Xgh12B. The enzymes have a β-jelly roll structure with a catalytic cleft running across the protein. Comparative analysis and a docking study demonstrated the importance of endoglucanase-specific loop 1 partly covering the catalytic cleft for correct placement of the linear substrates. Variability in substrate specificity between the GH12 endoglucanases is determined by non-conservative residues in structural loops framing the catalytic cleft. A residue responsible for the thermostability of Egh12 was predicted. The key structural elements and residues described in this study may serve as potential targets for modification aimed at the improvement of enzymatic properties. KEY POINTS: • Thermostable endoglucanase Egh12 from T. terrestris was produced in P. pastoris, purified, and characterized • The X-ray structure of GH12 endoglucanase Bgh12A from A. cervinus was resolved • GH12 endoglucanases, but not GH12 xyloglucanases, hydrolyze (1,3)-β-linkages in (1,3;1,4)-β-D-glucooligosaccharides.
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Affiliation(s)
- Sergey V Rykov
- National Research Center «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhniy pr. 1, 117545, Moscow, Russian Federation.,National Research Center «Kurchatov Institute», Kurchatov Sq. 1, 123182, Moscow, Russian Federation
| | - Alina I Selimzyanova
- National Research Center «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhniy pr. 1, 117545, Moscow, Russian Federation
| | - Alena Y Nikolaeva
- National Research Center «Kurchatov Institute» - Institute of Molecular Genetics, Kurchatov Sq. 2, 123182, Moscow, Russian Federation
| | - Vladimir A Lazarenko
- National Research Center «Kurchatov Institute» - Institute of Molecular Genetics, Kurchatov Sq. 2, 123182, Moscow, Russian Federation
| | - Nikita V Tsurin
- National Research Center «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhniy pr. 1, 117545, Moscow, Russian Federation
| | - Philipp I Akentyev
- National Research Center «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhniy pr. 1, 117545, Moscow, Russian Federation.,National Research Center «Kurchatov Institute», Kurchatov Sq. 1, 123182, Moscow, Russian Federation
| | - Vladimir V Zverlov
- National Research Center «Kurchatov Institute» - Institute of Molecular Genetics, Kurchatov Sq. 2, 123182, Moscow, Russian Federation. .,Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354, Freising, Germany.
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | | | - Oksana V Berezina
- National Research Center «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhniy pr. 1, 117545, Moscow, Russian Federation. .,National Research Center «Kurchatov Institute», Kurchatov Sq. 1, 123182, Moscow, Russian Federation.
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Ma J, Li Y, Han S, Jiang Z, Yan Q, Yang S. Structural and biochemical insights into the substrate-binding mechanism of a glycoside hydrolase family 12 β-1,3-1,4-glucanase from Chaetomium sp. J Struct Biol 2021; 213:107774. [PMID: 34329700 DOI: 10.1016/j.jsb.2021.107774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022]
Abstract
β-1,3-1,4-Glucanases are a type of hydrolytic enzymes capable of catalyzing the strict cleavage of β-1,4 glycosidic bonds adjacent to β-1,3 linkages in β-D-glucans and have exhibited great potential in food and feed industrials. In this study, a novel glycoside hydrolase (GH) family 12 β-1,3-1,4-glucanase (CtGlu12A) from the thermophilic fungus Chaetomium sp. CQ31 was identified and biochemically characterized. CtGlu12A was most active at pH 7.5 and 65 °C, respectively, and exhibited a high specific activity of 999.9 U mg-1 towards lichenin. It maintained more than 80% of its initial activity in a wide pH range of 5.0-11.0, and up to 60 °C after incubation at 55 °C for 60 min. Moreover, the crystal structures of CtGlu12A with gentiobiose and tetrasccharide were resolved. CtGlu12A had a β-jellyroll fold, and performed retaining mechanism with two glutamic acids severing as the catalytic residues. In the complex structure, cellobiose molecule showed two binding modes, occupying subsites -2 to -1 and subsites + 1 to + 2, respectively. The concave cleft made mixed β-1,3-1,4-glucan substrates maintain a bent conformation to fit into the active site. Overall, this study is not only helpful for the understanding of the substrate-binding model and catalytic mechanism of GH 12 β-1,3-1,4-glucanases, but also provides a basis for further enzymatic engineering of β-1,3-1,4-glucanases.
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Affiliation(s)
- Junwen Ma
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yanxiao Li
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing 100083, China
| | - Susu Han
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qiaojuan Yan
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, Beijing 100083, China
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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Dorival J, Philys S, Giuntini E, Brailly R, de Ruyck J, Czjzek M, Biondi E, Bompard C. Structural and enzymatic characterisation of the Type III effector NopAA (=GunA) from Sinorhizobium fredii USDA257 reveals a Xyloglucan hydrolase activity. Sci Rep 2020; 10:9932. [PMID: 32555346 PMCID: PMC7303141 DOI: 10.1038/s41598-020-67069-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 04/28/2020] [Indexed: 12/03/2022] Open
Abstract
Rhizobia are nitrogen-fixing soil bacteria that can infect legume plants to establish root nodules symbiosis. To do that, a complex exchange of molecular signals occurs between plants and bacteria. Among them, rhizobial Nops (Nodulation outer proteins), secreted by a type III secretion system (T3SS) determine the host-specificity for efficient symbiosis with plant roots. Little is known about the molecular function of secreted Nops (also called effectors (T3E)) and their role in the symbiosis process. We performed the structure-function characterization of NopAA, a T3E from Sinorhizobium fredii by using a combination of X-ray crystallography, biochemical and biophysical approaches. This work displays for the first time a complete structural and biochemical characterization of a symbiotic T3E. Our results showed that NopAA has a catalytic domain with xyloglucanase activity extended by a N-terminal unfolded secretion domain that allows its secretion. We proposed that these original structural properties combined with the specificity of NopAA toward xyloglucan, a key component of root cell wall which is also secreted by roots in the soil, can give NopAA a strategic position to participate in recognition between bacteria and plant roots and to intervene in nodulation process.
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Affiliation(s)
- Jonathan Dorival
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, Bretagne, France
| | - Sonia Philys
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Elisa Giuntini
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Romain Brailly
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Jérôme de Ruyck
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Mirjam Czjzek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, Bretagne, France
| | | | - Coralie Bompard
- CNRS, Univ. Lille, Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France.
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You S, Xie C, Ma R, Huang HQ, Herman RA, Su XY, Ge Y, Cai HY, Yao B, Wang J, Luo HY. Improvement in catalytic activity and thermostability of a GH10 xylanase and its synergistic degradation of biomass with cellulase. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:278. [PMID: 31827606 PMCID: PMC6892236 DOI: 10.1186/s13068-019-1620-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/25/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Xylanase is one of the most extensively used biocatalysts for biomass degradation. However, its low catalytic efficiency and poor thermostability limit its applications. Therefore, improving the properties of xylanases to enable synergistic degradation of lignocellulosic biomass with cellulase is of considerable significance in the field of bioenergy. RESULTS Using fragment replacement, we improved the catalytic performance and thermostability of a GH10 xylanase, XylE. Of the ten hybrid enzymes obtained, seven showed xylanase activity. Substitution of fragments, M3, M6, M9, and their combinations enhanced the catalytic efficiency (by 2.4- to fourfold) as well as the specific activity (by 1.2- to 3.3-fold) of XylE. The hybrids, XylE-M3, XylE-M3/M6, XylE-M3/M9, and XylE-M3/M6/M9, showed enhanced thermostability, as observed by the increase in the T 50 (3-4.7 °C) and T m (1.1-4.7 °C), and extended t 1/2 (by 1.8-2.3 h). In addition, the synergistic effect of the mutant xylanase and cellulase on the degradation of mulberry bark showed that treatment with both XylE-M3/M6 and cellulase exhibited the highest synergistic effect. In this case, the degree of synergy reached 1.3, and the reducing sugar production and dry matter reduction increased by 148% and 185%, respectively, compared to treatment with only cellulase. CONCLUSIONS This study provides a successful strategy to improve the catalytic properties and thermostability of enzymes. We identified several xylanase candidates for applications in bioenergy and biorefinery. Synergistic degradation experiments elucidated a possible mechanism of cellulase inhibition by xylan and xylo-oligomers.
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Affiliation(s)
- Shuai You
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018 People’s Republic of China
| | - Chen Xie
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018 People’s Republic of China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Huo-qing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Richard Ansah Herman
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018 People’s Republic of China
| | - Xiao-yun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yan Ge
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018 People’s Republic of China
| | - Hui-yi Cai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jun Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212018 People’s Republic of China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018 People’s Republic of China
| | - Hui-ying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Rykov SV, Kornberger P, Herlet J, Tsurin NV, Zorov IN, Zverlov VV, Liebl W, Schwarz WH, Yarotsky SV, Berezina OV. Novel endo-(1,4)-β-glucanase Bgh12A and xyloglucanase Xgh12B from Aspergillus cervinus belong to GH12 subgroup I and II, respectively. Appl Microbiol Biotechnol 2019; 103:7553-7566. [PMID: 31332485 DOI: 10.1007/s00253-019-10006-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/24/2019] [Accepted: 06/30/2019] [Indexed: 12/15/2022]
Abstract
In spite of intensive exploitation of aspergilli for the industrial production of carbohydrases, little is known about hydrolytic enzymes of fungi from the section Cervini. Novel glycoside hydrolases Bgh12A and Xgh12B from Aspergillus cervinus represent examples of divergent activities within one enzyme family and belong to the GH12 phylogenetic subgroup I (endo-(1,4)-β-glucanases) and II (endo-xyloglucanases), respectively. The bgh12A and xgh12B genes were identified in the unsequenced genome of A. cervinus using primers designed for conservative regions of the corresponding subgroups and a genome walking approach. The recombinant enzymes were heterologously produced in Pichia pastoris, purified, and characterized. Bgh12A was an endo-(1,4)-β-glucanase (EC 3.2.1.4) hydrolyzing the unbranched soluble β-(1,4)-glucans and mixed linkage β-(1,3;1,4)-D-glucans. Bgh12A exhibited maximum activity on barley β-glucan (BBG), which amounted to 614 ± 30 U/mg of protein. The final products of BBG and lichenan hydrolysis were glucose, cellobiose, cellotriose, 4-O-β-laminaribiosyl-glucose, and a range of higher mixed-linkage gluco-oligosaccharides. In contrast, the activity of endo-xyloglucanase Xgh12B (EC 3.2.1.151) was restricted to xyloglucan, with 542 ± 39 U/mg protein. The enzyme cleaved the (1,4)-β-glycosidic bonds of the xyloglucan backbone at the unsubstituted glucose residues finally generating cellotetraose-based hepta-, octa, and nona-oligosaccharides. Bgh12A and Xgh12B had maximal activity at 55 °C, pH 5.0. At these conditions, the half-time of Xgh12B inactivation was 158 min, whereas the half-life of Bgh12A was 5 min. Recombinant P. pastoris strains produced up to 106 U/L of the target enzymes with at least 75% of recombinant protein in the total extracellular proteins. The Bgh12A and Xgh12B sequences show 43% identity. Strict differences in substrate specificity of Bgh12A and Xgh12B were in congruence with the presence of subgroup-specific structural loops and substrate-binding aromatic residues in the catalytic cleft of the enzymes. Individual composition of aromatic residues in the catalytic cleft defined variability in substrate selectivity within GH12 subgroups I and II.
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Affiliation(s)
- Sergey V Rykov
- State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center «Kurchatov Institute», 1-st Dorozhniy pr. 1, Moscow, Russian Federation, 117545
| | - Petra Kornberger
- Department of Microbiology, Technical University Munich, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Jonathan Herlet
- Department of Microbiology, Technical University Munich, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Nikita V Tsurin
- State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center «Kurchatov Institute», 1-st Dorozhniy pr. 1, Moscow, Russian Federation, 117545
| | - Ivan N Zorov
- Russian Academy of Sciences, Federal Research Centre "Fundamentals of Biotechnology", Leninsky prospect, 33, build. 2, Moscow, 119071, Russian Federation
| | - Vladimir V Zverlov
- Department of Microbiology, Technical University Munich, Emil-Ramann-Str. 4, 85354, Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, Russian Federation, 123182
| | - Wolfgang Liebl
- Department of Microbiology, Technical University Munich, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Wolfgang H Schwarz
- Department of Microbiology, Technical University Munich, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Sergey V Yarotsky
- State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center «Kurchatov Institute», 1-st Dorozhniy pr. 1, Moscow, Russian Federation, 117545
| | - Oksana V Berezina
- State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center «Kurchatov Institute», 1-st Dorozhniy pr. 1, Moscow, Russian Federation, 117545.
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Montoir D, Amoura M, Ababsa ZEA, Vishwanatha TM, Yen-Pon E, Robert V, Beltramo M, Piller V, Alami M, Aucagne V, Messaoudi S. Synthesis of aryl-thioglycopeptides through chemoselective Pd-mediated conjugation. Chem Sci 2018; 9:8753-8759. [PMID: 30627396 PMCID: PMC6295873 DOI: 10.1039/c8sc02370k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/18/2018] [Indexed: 12/17/2022] Open
Abstract
We describe herein a Pd-catalyzed methodology for the thioglycoconjugation of iodoaryl peptides and aminoacids. This operationally simple process occurs under semi-aqueous conditions and displays wide substrate scope. The strategy has been successfully applied to both the thioglycosylation of unprotected peptides and the generation of thioglyco-aminoacid building blocks, including those suitable for solid phase peptide synthesis. To demonstrate the broad potential of this technique for late stage functionalization, we successfully incorporated challenging unprotected β-S-GlcNAc- and α-S-GalNAc-derivatives into very long unprotected peptides. This study opens the way to new applications in chemical biology, considering the well-recognized advantages of S-glycosides over O-glycosides in terms of resistance towards both enzymatic and chemical degradation.
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Affiliation(s)
- David Montoir
- BioCIS , Univ. Paris-Sud , CNRS , Univ. Paris-Saclay , Châtenay-Malabry , France . ; Tel: +33 0146835887
| | - Mehdi Amoura
- Centre de Biophysique Moléculaire , CNRS , Orléans , France . ; Tel: +33 0238255577
| | - Zine El Abidine Ababsa
- BioCIS , Univ. Paris-Sud , CNRS , Univ. Paris-Saclay , Châtenay-Malabry , France . ; Tel: +33 0146835887
| | - T M Vishwanatha
- Centre de Biophysique Moléculaire , CNRS , Orléans , France . ; Tel: +33 0238255577
| | - Expédite Yen-Pon
- BioCIS , Univ. Paris-Sud , CNRS , Univ. Paris-Saclay , Châtenay-Malabry , France . ; Tel: +33 0146835887
| | - Vincent Robert
- UMR Physiologie de la Reproduction et des Comportements , INRA , CNRS , Univ. Tours , IFCE , Nouzilly , France
| | - Massimiliano Beltramo
- UMR Physiologie de la Reproduction et des Comportements , INRA , CNRS , Univ. Tours , IFCE , Nouzilly , France
| | - Véronique Piller
- Centre de Biophysique Moléculaire , CNRS , Orléans , France . ; Tel: +33 0238255577
| | - Mouad Alami
- BioCIS , Univ. Paris-Sud , CNRS , Univ. Paris-Saclay , Châtenay-Malabry , France . ; Tel: +33 0146835887
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire , CNRS , Orléans , France . ; Tel: +33 0238255577
| | - Samir Messaoudi
- BioCIS , Univ. Paris-Sud , CNRS , Univ. Paris-Saclay , Châtenay-Malabry , France . ; Tel: +33 0146835887
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Tanaka H, Akutsu H, Yabuta I, Hara M, Sugimoto H, Ikegami T, Watanabe T, Fujiwara T. A novel chitin‐binding mode of the chitin‐binding domain of chitinase A1 from
Bacillus circulans
WL
‐12 revealed by solid‐state
NMR. FEBS Lett 2018; 592:3173-3182. [DOI: 10.1002/1873-3468.13226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Hiroki Tanaka
- Institute for Protein Research Osaka University Suita Japan
| | - Hideo Akutsu
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Izumi Yabuta
- Institute for Protein Research Osaka University Suita Japan
| | - Masashi Hara
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Hayuki Sugimoto
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Takahisa Ikegami
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Takeshi Watanabe
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
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Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:52. [PMID: 28413443 PMCID: PMC5327597 DOI: 10.1186/s13068-017-0732-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The high crystallinity of cellulosic biomass myofibrils as well as the complexity of their intermolecular structure is a significant impediment for biofuel production. Cloning of celB-, celC-encoded cellulases (cel12B and cel8C) and peh-encoded polygalacturonase (peh28) from Pectobacterium carotovorum subsp. carotovorum (Pcc) was carried out in our previous study using Escherichia coli as a host vector. The current study partially characterizes the enzymes' molecular structures as well as their catalytic performance on different substrates which can be used to improve their potential for lignocellulosic biomass conversion. RESULTS β-Jelly roll topology, (α/α)6 antiparallel helices and right-handed β-helices were the folds identified for cel12B, cel8C, and peh28, respectively, in their corresponding protein model structures. Purifications of 17.4-, 6.2-, and 6.0-fold, compared to crude extract, were achieved for cel12B and cel8C, and peh28, respectively, using specific membrane ultrafiltrations and size-exclusion chromatography. Avicel and carboxymethyl cellulose (CMC) were substrates for cel12B, whereas for cel8C catalytic activity was only shown on CMC. The enzymes displayed significant synergy on CMC but not on Avicel when tested for 3 h at 45 °C. No observed β-glucosidase activities were identified for cel8C and cel12B when tested on p-nitrophenyl-β-d-glucopyranoside. Activity stimulation of 130% was observed when a recombinant β-glucosidase from Pcc was added to cel8C and cel12B as tested for 3 h at 45 °C. Optimum temperature and pH of 45 °C and 5.4, respectively, were identified for all three enzymes using various substrates. Catalytic efficiencies (kcat/Km) were calculated for cel12B and cel8C on CMC as 0.141 and 2.45 ml/mg/s respectively, at 45 °C and pH 5.0 and for peh28 on polygalacturonic acid as 4.87 ml/mg/s, at 40 °C and pH 5.0. Glucose and cellobiose were the end-products identified for cel8C, cel12B, and β-glucosidase acting together on Avicel or CMC, while galacturonic acid and other minor co-products were identified for peh28 action on pectin. CONCLUSIONS This study provides some insight into which parameters should be optimized when application of cel8C, cel12B, and peh28 to biomass conversion is the goal.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Kim D. Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Keith E. Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4 Canada
| | - Ebtesam N. Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Patrick L. Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Jean M. Escudero
- Department of Basic Science, St. Louis College of Pharmacy, St. Louis, MO 63110-1088 USA
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9
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Identification of Glutaminyl Cyclase Genes Involved in Pyroglutamate Modification of Fungal Lignocellulolytic Enzymes. mBio 2017; 8:mBio.02231-16. [PMID: 28096492 PMCID: PMC5241404 DOI: 10.1128/mbio.02231-16] [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] [Indexed: 11/25/2022] Open
Abstract
The breakdown of plant biomass to simple sugars is essential for the production of second-generation biofuels and high-value bioproducts. Currently, enzymes produced from filamentous fungi are used for deconstructing plant cell wall polysaccharides into fermentable sugars for biorefinery applications. A post-translational N-terminal pyroglutamate modification observed in some of these enzymes occurs when N-terminal glutamine or glutamate is cyclized to form a five-membered ring. This modification has been shown to confer resistance to thermal denaturation for CBH-1 and EG-1 cellulases. In mammalian cells, the formation of pyroglutamate is catalyzed by glutaminyl cyclases. Using the model filamentous fungus Neurospora crassa, we identified two genes (qc-1 and qc-2) that encode proteins homologous to mammalian glutaminyl cyclases. We show that qc-1 and qc-2 are essential for catalyzing the formation of an N-terminal pyroglutamate on CBH-1 and GH5-1. CBH-1 and GH5-1 produced in a Δqc-1 Δqc-2 mutant, and thus lacking the N-terminal pyroglutamate modification, showed greater sensitivity to thermal denaturation, and for GH5-1, susceptibility to proteolytic cleavage. QC-1 and QC-2 are endoplasmic reticulum (ER)-localized proteins. The pyroglutamate modification is predicted to occur in a number of additional fungal proteins that have diverse functions. The identification of glutaminyl cyclases in fungi may have implications for production of lignocellulolytic enzymes, heterologous expression, and biotechnological applications revolving around protein stability. Pyroglutamate modification is the post-translational conversion of N-terminal glutamine or glutamate into a cyclized amino acid derivative. This modification is well studied in animal systems but poorly explored in fungal systems. In Neurospora crassa, we show that this modification takes place in the ER and is catalyzed by two well-conserved enzymes, ubiquitously conserved throughout the fungal kingdom. We demonstrate that the modification is important for the structural stability and aminopeptidase resistance of CBH-1 and GH5-1, two important cellulase enzymes utilized in industrial plant cell wall deconstruction. Many additional fungal proteins predicted in the genome of N. crassa and other filamentous fungi are predicted to carry an N-terminal pyroglutamate modification. Pyroglutamate addition may also be a useful way to stabilize secreted proteins and peptides, which can be easily produced in fungal production systems.
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10
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Zhang X, Wang S, Wu X, Liu S, Li D, Xu H, Gao P, Chen G, Wang L. Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12. Sci Rep 2015; 5:18357. [PMID: 26670009 PMCID: PMC4680936 DOI: 10.1038/srep18357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/16/2015] [Indexed: 01/22/2023] Open
Abstract
The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties. The results also revealed that the binding constant of a certain residue remained unchanged when altering its location, while the catalytic efficiency changed dramatically. Increased binding affinity at a relatively distant subsite, such as the mutant of W7Y at the -4 subsite, resulted in a marked increase in the intermediate product of cellotetraose and enhanced the reactivity of endoglucanase by 144%; while tighter binding near the catalytic center, i.e. W22Y at the -2 subsite, enabled the enzyme to bind and hydrolyze smaller oligosaccharides. Clarification of the specific roles of the aromatics at different subsites may pave the way for a more rational design of GHs.
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Affiliation(s)
- Xiaomei Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shuai Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Xiuyun Wu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shijia Liu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Dandan Li
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Hao Xu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China
| | - Peiji Gao
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Guanjun Chen
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
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11
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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12
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V. Sambasivarao S, M. Granum D, Wang H, Mark Maupin C. Identifying the Enzymatic Mode of Action for Cellulase Enzymes by Means of Docking Calculations and a Machine Learning Algorithm. AIMS MOLECULAR SCIENCE 2014. [DOI: 10.3934/molsci.2014.1.59] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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13
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Vizoná Liberato M, Cardoso Generoso W, Malagó W, Henrique-Silva F, Polikarpov I. Crystallization and preliminary X-ray diffraction analysis of endoglucanase III from Trichoderma harzianum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:306-9. [PMID: 22442229 PMCID: PMC3310537 DOI: 10.1107/s1744309112000838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/09/2012] [Indexed: 11/06/2023]
Abstract
Endoglucanases are enzymes that hydrolyze cellulose and are important components of the cellulolytic complex. In contrast to other members of the complex, they cleave internal β-1,4-glycosidic bonds in the cellulose polymer, allowing cellulose to be used as an energy source. Since biomass is an important renewable source of energy, the structural and functional characterization of these enzymes is of interest. In this study, endoglucanase III from Trichoderma harzianum was produced in Pichia pastoris and purified. Crystals belonging to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 47.54, b = 55.57, c = 157.3 Å, were obtained by the sitting-drop vapour-diffusion method and an X-ray diffraction data set was collected to 2.07 Å resolution.
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Affiliation(s)
- Marcelo Vizoná Liberato
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Wesley Cardoso Generoso
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, km. 235, 13565-905 São Carlos-SP, Brazil
| | - Wilson Malagó
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, km. 235, 13565-905 São Carlos-SP, Brazil
| | - Flávio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, km. 235, 13565-905 São Carlos-SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
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14
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Sattelle BM, Almond A. Assigning kinetic 3D-signatures to glycocodes. Phys Chem Chem Phys 2012; 14:5843-8. [DOI: 10.1039/c2cp40071e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Li DC, Li AN, Papageorgiou AC. Cellulases from thermophilic fungi: recent insights and biotechnological potential. Enzyme Res 2011; 2011:308730. [PMID: 22145076 PMCID: PMC3226318 DOI: 10.4061/2011/308730] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 09/05/2011] [Accepted: 09/07/2011] [Indexed: 11/24/2022] Open
Abstract
Thermophilic fungal cellulases are promising enzymes in protein engineering efforts aimed at optimizing industrial processes, such as biomass degradation and biofuel production. The cloning and expression in recent years of new cellulase genes from thermophilic fungi have led to a better understanding of cellulose degradation in these species. Moreover, crystal structures of thermophilic fungal cellulases are now available, providing insights into their function and stability. The present paper is focused on recent progress in cloning, expression, regulation, and structure of thermophilic fungal cellulases and the current research efforts to improve their properties for better use in biotechnological applications.
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Affiliation(s)
- Duo-Chuan Li
- Department of Environmental Biology, Shandong Agricultural University, Taian, Shandong 271018, China
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16
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Cheng YS, Ko TP, Wu TH, Ma Y, Huang CH, Lai HL, Wang AHJ, Liu JR, Guo RT. Crystal structure and substrate-binding mode of cellulase 12A from Thermotoga maritima. Proteins 2011; 79:1193-204. [PMID: 21268113 DOI: 10.1002/prot.22953] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/10/2010] [Accepted: 11/17/2010] [Indexed: 11/12/2022]
Abstract
Cellulases have been used in many applications to treat various carbohydrate-containing materials. Thermotoga maritima cellulase 12A (TmCel12A) belongs to the GH12 family of glycoside hydrolases. It is a β-1,4-endoglucanase that degrades cellulose molecules into smaller fragments, facilitating further utilization of the carbohydrate. Because of its hyperthermophilic nature, the enzyme is especially suitable for industrial applications. Here the crystal structure of TmCel12A was determined by using an active-site mutant E134C and its mercury-containing derivatives. It adopts a β-jellyroll protein fold typical of the GH12-family enzymes, with two curved β-sheets A and B and a central active-site cleft. Structural comparison with other GH12 enzymes shows significant differences, as found in two longer and highly twisted β-strands B8 and B9 and several loops. A unique Loop A3-B3 that contains Arg60 and Tyr61 stabilizes the substrate by hydrogen bonding and stacking, as observed in the complex crystals with cellotetraose and cellobiose. The high-resolution structures allow clear elucidation of the network of interactions between the enzyme and its substrate. The sugar residues bound to the enzyme appear to be more ordered in the -2 and -1 subsites than in the +1, +2 and -3 subsites. In the E134C crystals the bound -1 sugar at the cleavage site consistently show the α-anomeric configuration, implicating an intermediate-like structure.
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Affiliation(s)
- Ya-Shan Cheng
- Institute of Biotechnology, National Taiwan University, Taiwan
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17
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18
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Several transition states from 4C1 to skew conformations of β-d-glucopyranose. Carbohydr Res 2009; 344:2266-9. [DOI: 10.1016/j.carres.2009.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2009] [Revised: 07/18/2009] [Accepted: 08/18/2009] [Indexed: 11/23/2022]
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19
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Powlowski J, Mahajan S, Schapira M, Master ER. Substrate recognition and hydrolysis by a fungal xyloglucan-specific family 12 hydrolase. Carbohydr Res 2009; 344:1175-9. [PMID: 19433323 DOI: 10.1016/j.carres.2009.04.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/16/2009] [Accepted: 04/19/2009] [Indexed: 11/30/2022]
Abstract
Biochemical studies to elucidate the structural basis for xyloglucan specificity among GH12 xyloglucanases are lacking. Accordingly, the substrate specificity of a GH12 xyloglucanase from Aspergillus niger (AnXEG12A) was investigated using pea xyloglucan and 12 xylogluco-oligosaccharides, and data were compared to a structural model of the enzyme. The specific activity of AnXEG12A with pea xyloglucan was 113 micromol min(-1)mg(-1), and apparent k(cat) and K(m) values were 49 s(-1) and 0.54 mg mL(-1), respectively. These values are similar to previously published results using xyloglucan from tamarind seed, and suggest that substrate fucosylation does not affect the specific activity of this enzyme. AnXEG12A preferred xylogluco-oligosaccharides containing more than six glucose units, and with xylose substitution at the -3 and +1 subsites. The specific activities of AnXEG12A on 100 microM XXXGXXXG and 100 microM XLLGXLLG were 60+/-4 and 72+/-9 micromol min(-1)mg(-1), respectively. AnXEG12A did not hydrolyze XXXXXXXG, consistent with other data that demonstrate the requirement for an unbranched glucose residue for hydrolysis by this enzyme.
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Affiliation(s)
- Justin Powlowski
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, Canada H4B 1R6
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20
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Suzuki R, Fujimoto Z, Ito S, Kawahara SI, Kaneko S, Taira K, Hasegawa T, Kuno A. Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86. J Biochem 2009; 146:61-70. [PMID: 19279191 DOI: 10.1093/jb/mvp047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.
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Affiliation(s)
- Ryuichiro Suzuki
- Department of Material and Biological Chemistry, Yamagata University, Japan
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21
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Rudsander UJ, Sandstrom C, Piens K, Master ER, Wilson DB, Brumer III H, Kenne L, Teeri TT. Comparative NMR Analysis of Cellooligosaccharide Hydrolysis by GH9 Bacterial and Plant Endo-1,4-β-glucanases. Biochemistry 2008; 47:5235-41. [DOI: 10.1021/bi702193e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ulla J. Rudsander
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
| | - Corine Sandstrom
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
| | - Kathleen Piens
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
| | - Emma R. Master
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
| | - David B. Wilson
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
| | - Harry Brumer III
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
| | - Lennart Kenne
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
| | - Tuula T. Teeri
- KTH Biotechnology, Swedish Center for Biomimetic Fiber Engineering, AlbaNova, SE-10691 Stockholm, Sweden, Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden, and Department of Molecular Biology and Genetics, Cornell University, 458 Biotechnology Building, Ithaca, New York 14853-2703
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22
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Biarnés X, Ardèvol A, Planas A, Rovira C, Laio A, Parrinello M. The Conformational Free Energy Landscape of β-d-Glucopyranose. Implications for Substrate Preactivation in β-Glucoside Hydrolases. J Am Chem Soc 2007; 129:10686-93. [PMID: 17696342 DOI: 10.1021/ja068411o] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using ab initio metadynamics we have computed the conformational free energy landscape of beta-D-glucopyranose as a function of the puckering coordinates. We show that the correspondence between the free energy and the Stoddard's pseudorotational itinerary for the system is rather poor. The number of free energy minima (9) is smaller than the number of ideal structures (13). Moreover, only six minima correspond to a canonical conformation. The structural features, the electronic properties, and the relative stability of the predicted conformers permit the rationalization of the occurrence of distorted sugar conformations in all the available X-ray structures of beta-glucoside hydrolase Michaelis complexes. We show that these enzymes recognize the most stable distorted conformers of the isolated substrate and at the same time the ones better prepared for catalysis in terms of bond elongation/shrinking and charge distribution. This suggests that the factors governing the distortions present in these complexes are largely dictated by the intrinsic properties of a single glucose unit.
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Affiliation(s)
- Xevi Biarnés
- Centre especial de Recerca en Química Teorica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
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23
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Gloster TM, Ibatullin FM, Macauley K, Eklöf JM, Roberts S, Turkenburg JP, Bjørnvad ME, Jørgensen PL, Danielsen S, Johansen KS, Borchert TV, Wilson KS, Brumer H, Davies GJ. Characterization and Three-dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families GH5 and GH12. J Biol Chem 2007; 282:19177-89. [PMID: 17376777 DOI: 10.1074/jbc.m700224200] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The plant cell wall is a complex material in which the cellulose microfibrils are embedded within a mesh of other polysaccharides, some of which are loosely termed "hemicellulose." One such hemicellulose is xyloglucan, which displays a beta-1,4-linked d-glucose backbone substituted with xylose, galactose, and occasionally fucose moieties. Both xyloglucan and the enzymes responsible for its modification and degradation are finding increasing prominence, reflecting both the drive for enzymatic biomass conversion, their role in detergent applications, and the utility of modified xyloglucans for cellulose fiber modification. Here we present the enzymatic characterization and three-dimensional structures in ligand-free and xyloglucan-oligosaccharide complexed forms of two distinct xyloglucanases from glycoside hydrolase families GH5 and GH12. The enzymes, Paenibacillus pabuli XG5 and Bacillus licheniformis XG12, both display open active center grooves grafted upon their respective (beta/alpha)(8) and beta-jelly roll folds, in which the side chain decorations of xyloglucan may be accommodated. For the beta-jelly roll enzyme topology of GH12, binding of xylosyl and pendant galactosyl moieties is tolerated, but the enzyme is similarly competent in the degradation of unbranched glucans. In the case of the (beta/alpha)(8) GH5 enzyme, kinetically productive interactions are made with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides. The differential strategies for the accommodation of the side chains of xyloglucan presumably facilitate the action of these microbial hydrolases in milieus where diverse and differently substituted substrates may be encountered.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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24
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Desmet T, Cantaert T, Gualfetti P, Nerinckx W, Gross L, Mitchinson C, Piens K. An investigation of the substrate specificity of the xyloglucanase Cel74A from Hypocrea jecorina. FEBS J 2007; 274:356-63. [PMID: 17229143 DOI: 10.1111/j.1742-4658.2006.05582.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The substrate specificity of the xyloglucanase Cel74A from Hypocrea jecorina (Trichoderma reesei) was examined using several polysaccharides and oligosaccharides. Our results revealed that xyloglucan chains are hydrolyzed at substituted Glc residues, in contrast to the action of all known xyloglucan endoglucanases (EC 3.2.1.151). The building block of xyloglucan, XXXG (where X is a substituted Glc residue, and G is an unsubstituted Glc residue), was rapidly degraded to XX and XG (k(cat) = 7.2 s(-1) and Km = 120 microM at 37 degrees C and pH 5), which has only been observed before with the oligoxyloglucan-reducing-end-specific cellobiohydrolase from Geotrichum (EC 3.2.1.150). However, the cellobiohydrolase can only release XG from XXXGXXXG, whereas Cel74A hydrolyzed this substrate at both chain ends, resulting in XGXX. Differences in the length of a specific loop at subsite + 2 are discussed as being the basis for the divergent specificity of these xyloglucanases.
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Affiliation(s)
- Tom Desmet
- Department of Biochemistry, Physiology and Microbiology, Faculty of Sciences, Ghent University, Belgium.
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25
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Kim YW, Lovering AL, Chen H, Kantner T, McIntosh LP, Strynadka NCJ, Withers SG. Expanding the Thioglycoligase Strategy to the Synthesis of α-Linked Thioglycosides Allows Structural Investigation of the Parent Enzyme/Substrate Complex. J Am Chem Soc 2006; 128:2202-3. [PMID: 16478160 DOI: 10.1021/ja057904a] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the first time, the thioglycoligase strategy has been successfully applied to alpha-glycosidases. The alpha-thioglycoligases derived from the family 31 glycosidases, alpha-xylosidase from E. coli (YicI) and alpha-glucosidase from Sulfolobus solfataricus, catalyze thioglycoligase reactions using alpha-glycosyl fluorides and deoxythioglycosides as donors and acceptors, respectively, in yields up to 86%. In addition, we describe the Michaelis complex of YicI using one of the thioglycosides as a nonhydrolyzable substrate analogue and discuss the structural insights this yields into the specificity and mechanism of family 31 alpha-glycosidases and the molecular basis of an associated genetic disease.
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Affiliation(s)
- Young-Wan Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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Crennell SJ, Cook D, Minns A, Svergun D, Andersen RL, Nordberg Karlsson E. Dimerisation and an Increase in Active Site Aromatic Groups as Adaptations to High Temperatures: X-ray Solution Scattering and Substrate-bound Crystal Structures of Rhodothermus marinus Endoglucanase Cel12A. J Mol Biol 2006; 356:57-71. [PMID: 16343530 DOI: 10.1016/j.jmb.2005.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 10/25/2005] [Accepted: 11/02/2005] [Indexed: 10/25/2022]
Abstract
Cellulose, a polysaccharide consisting of beta-1,4-linked glucose, is the major component of plant cell walls and consequently one of the most abundant biopolymers on earth. Carbohydrate polymers such as cellulose are molecules with vast diversity in structure and function, and a multiplicity of hydrolases operating in concert are required for depolymerisation. The bacterium Rhodothermus marinus, isolated from shallow water marine hot springs, produces a number of carbohydrate-degrading enzymes including a family 12 cellulase Cel12A. The structure of R.marinus Cel12A in the ligand-free form (at 1.54 angstroms) and structures of RmCel12A after crystals were soaked in cellopentaose for two different lengths of time, have been determined. The shorter soaked complex revealed the conformation of unhydrolysed cellotetraose, while cellopentaose had been degraded more completely during the longer soak. Comparison of these structures with those of mesophilic family 12 cellulases in complex with inhibitors and substrate revealed that RmCel12A has a more extensive aromatic network in the active site cleft which ejects products after hydrolysis. The substrate structure confirms that during hydrolysis by family 12 cellulases glucose does not pass through a (2,5)B conformation. Small-angle X-ray scattering analysis of RmCel12A showed that the enzyme forms a loosely associated antiparallel dimer in solution, which may target the enzyme to the antiparallel polymer strands in cellulose.
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Affiliation(s)
- Susan J Crennell
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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Sandgren M, Ståhlberg J, Mitchinson C. Structural and biochemical studies of GH family 12 cellulases: improved thermal stability, and ligand complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2004; 89:246-91. [PMID: 15950056 DOI: 10.1016/j.pbiomolbio.2004.11.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this review we will describe how we have gathered structural and biochemical information from several homologous cellulases from one class of glycoside hydrolases (GH family 12), and used this information within the framework of a protein-engineering program for the design of new variants of these enzymes. These variants have been characterized to identify some of the positions and the types of mutations in the enzymes that are responsible for some of the biochemical differences in thermal stability and activity between the homologous enzymes. In this process we have solved the three-dimensional structure of four of these homologous GH 12 cellulases: Three fungal enzymes, Humicola grisea Cel12A, Hypocrea jecorina Cel12A and Hypocrea schweinitzii Cel12A, and one bacterial, Streptomyces sp. 11AG8 Cel12A. We have also determined the three-dimensional structures of the two most stable H. jecorina Cel12A variants. In addition, four ligand-complex structures of the wild-type H. grisea Cel12A enzyme have been solved and have made it possible to characterize some of the interactions between substrate and enzyme. The structural and biochemical studies of these related GH 12 enzymes, and their variants, have provided insight on how specific residues contribute to protein thermal stability and enzyme activity. This knowledge can serve as a structural toolbox for the design of Cel12A enzymes with specific properties and features suited to existing or new applications.
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Affiliation(s)
- Mats Sandgren
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden.
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