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Dodda SR, Hossain M, Mondal S, Das S, Khator (Jain) S, Aikat K, Mukhopadhyay SS. The S-S bridge mutation between the A2 and A4 loops (T416C-I432C) of Cel7A of Aspergillus fumigatus enhances catalytic activity and thermostability. Appl Environ Microbiol 2024; 90:e0232923. [PMID: 38440989 PMCID: PMC11022540 DOI: 10.1128/aem.02329-23] [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: 12/22/2023] [Accepted: 01/28/2024] [Indexed: 03/06/2024] Open
Abstract
Disulfide bonds are important for maintaining the structural conformation and stability of the protein. The introduction of the disulfide bond is a promising strategy to increase the thermostability of the protein. In this report, cysteine residues are introduced to form disulfide bonds in the Glycoside Hydrolase family GH 7 cellobiohydrolase (GH7 CBHs) or Cel7A of Aspergillus fumigatus. Disulfide by Design 2.0 (DbD2), an online tool is used for the detection of the mutation sites. Mutations are created (D276C-G279C; DSB1, D322C-G327C; DSB2, T416C-I432C; DSB3, G460C-S465C; DSB4) inside and outside of the peripheral loops but, not in the catalytic region. The introduction of cysteine in the A2 and A4 loop of DSB3 mutant showed higher thermostability (70% activity at 70°C), higher substrate affinity (Km = 0.081 mM) and higher catalytic activity (Kcat = 9.75 min-1; Kcat/Km = 120.37 mM min-1) compared to wild-type AfCel7A (50% activity at 70°C; Km = 0.128 mM; Kcat = 4.833 min-1; Kcat/Km = 37.75 mM min-1). The other three mutants with high B factor showed loss of thermostability and catalytic activity. Molecular dynamic simulations revealed that the mutation T416C-I432C makes the tunnel wider (DSB3: 13.6 Å; Wt: 5.3 Å) at the product exit site, giving flexibility in the entrance region or mobility of the substrate in the exit region. It may facilitate substrate entry into the catalytic tunnel and release the product faster than the wild type, whereas in other mutants, the tunnel is not prominent (DSB4), the exit is lost (DSB1), and the ligand binding site is absent (DSB2). This is the first report of the gain of function of both thermostability and enzyme activity of cellobiohydrolase Cel7A by disulfide bond engineering in the loop.IMPORTANCEBioethanol is one of the cleanest renewable energy and alternatives to fossil fuels. Cost efficient bioethanol production can be achieved through simultaneous saccharification and co-fermentation that needs active polysaccharide degrading enzymes. Cellulase enzyme complex is a crucial enzyme for second-generation bioethanol production from lignocellulosic biomass. Cellobiohydrolase (Cel7A) is an important member of this complex. In this work, we engineered (disulfide bond engineering) the Cel7A to increase its thermostability and catalytic activity which is required for its industrial application.
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Affiliation(s)
- Subba Reddy Dodda
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Musaddique Hossain
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Sudipa Mondal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Shalini Das
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Sneha Khator (Jain)
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Kaustav Aikat
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Sudit S. Mukhopadhyay
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
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2
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de Araújo EA, Cortez AA, Pellegrini VDOA, Vacilotto MM, Cruz AF, Batista PR, Polikarpov I. Molecular mechanism of cellulose depolymerization by the two-domain BlCel9A enzyme from the glycoside hydrolase family 9. Carbohydr Polym 2024; 329:121739. [PMID: 38286536 DOI: 10.1016/j.carbpol.2023.121739] [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: 07/21/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/31/2024]
Abstract
Carbohydrate-active enzymes from the glycoside hydrolase family 9 (GH9) play a key role in processing lignocellulosic biomass. Although the structural features of some GH9 enzymes are known, the molecular mechanisms that drive their interactions with cellulosic substrates remain unclear. To investigate the molecular mechanisms that the two-domain Bacillus licheniformis BlCel9A enzyme utilizes to depolymerize cellulosic substrates, we used a combination of biochemical assays, X-ray crystallography, small-angle X-ray scattering, and molecular dynamics simulations. The results reveal that BlCel9A breaks down cellulosic substrates, releasing cellobiose and glucose as the major products, but is highly inefficient in cleaving oligosaccharides shorter than cellotetraose. In addition, fungal lytic polysaccharide oxygenase (LPMO) TtLPMO9H enhances depolymerization of crystalline cellulose by BlCel9A, while exhibiting minimal impact on amorphous cellulose. The crystal structures of BlCel9A in both apo form and bound to cellotriose and cellohexaose were elucidated, unveiling the interactions of BlCel9A with the ligands and their contribution to substrate binding and products release. MD simulation analysis reveals that BlCel9A exhibits higher interdomain flexibility under acidic conditions, and SAXS experiments indicate that the enzyme flexibility is induced by pH and/or temperature. Our findings provide new insights into BlCel9A substrate specificity and binding, and synergy with the LPMOs.
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Affiliation(s)
- Evandro Ares de Araújo
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Giuseppe Maximo Scolfaro, 10000, Campinas, SP 13083-970, Brazil; Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Anelyse Abreu Cortez
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | | | - Milena Moreira Vacilotto
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Amanda Freitas Cruz
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Paulo Ricardo Batista
- Oswaldo Cruz Foundation, Scientific Computing Programme, Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Igor Polikarpov
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil.
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3
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Haataja T, Hansson H, Moriya S, Sandgren M, Ståhlberg J. The crystal structure of RsSymEG1 reveals a unique form of smaller GH7 endoglucanases alongside GH7 cellobiohydrolases in protist symbionts of termites. FEBS J 2024; 291:1168-1185. [PMID: 38073120 DOI: 10.1111/febs.17029] [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: 07/12/2023] [Revised: 10/31/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Glycoside hydrolase family 7 (GH7) cellulases are key enzymes responsible for carbon cycling on earth through their role in cellulose degradation and constitute highly important industrial enzymes as well. Although these enzymes are found in a wide variety of evolutionarily distant organisms across eukaryotes, they exhibit remarkably conserved features within two groups: exo-acting cellobiohydrolases and endoglucanases. However, recently reports have emerged of a separate clade of GH7 endoglucanases from protist symbionts of termites that are 60-80 amino acids shorter. In this work, we describe the first crystal structure of a short GH7 endoglucanase, RsSymEG1, from a symbiont of the lower termite Reticulitermes speratus. A more open flat surface and shorter loops around the non-reducing end of the cellulose-binding cleft indicate enhanced access to cellulose chains on the surface of cellulose microfibrils. Additionally, when comparing activities on polysaccharides to a typical fungal GH7 endoglucanase (Trichoderma longibrachiatum Cel7B), RsSymEG1 showed significantly faster initial hydrolytic activity. We also examine the prevalence and diversity of GH7 enzymes that the symbionts provide to the termite host, compare overall structures and substrate binding between cellobiohydrolase and long and short endoglucanase, and highlight the presence of similar short GH7s in other organisms.
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Affiliation(s)
- Topi Haataja
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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4
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Leadbeater DR, Bruce NC. Functional characterisation of a new halotolerant seawater active glycoside hydrolase family 6 cellobiohydrolase from a salt marsh. Sci Rep 2024; 14:3205. [PMID: 38332324 PMCID: PMC10853513 DOI: 10.1038/s41598-024-53886-4] [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: 10/18/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Realising a fully circular bioeconomy requires the valorisation of lignocellulosic biomass. Cellulose is the most attractive component of lignocellulose but depolymerisation is inefficient, expensive and resource intensive requiring substantial volumes of potable water. Seawater is an attractive prospective replacement, however seawater tolerant enzymes are required for the development of seawater-based biorefineries. Here, we report a halophilic cellobiohydrolase SMECel6A, identified and isolated from a salt marsh meta-exo-proteome dataset with high sequence divergence to previously characterised cellobiohydrolases. SMECel6A contains a glycoside hydrolase family 6 (GH6) domain and a carbohydrate binding module family 2 (CBM2) domain. Characterisation of recombinant SMECel6A revealed SMECel6A to be active upon crystalline and amorphous cellulose. Mono- and oligosaccharide product profiles revealed cellobiose as the major hydrolysis product confirming SMECel6A as a cellobiohydrolase. We show SMECel6A to be halophilic with optimal activity achieved in 0.5X seawater displaying 80.6 ± 6.93% activity in 1 × seawater. Structural predictions revealed similarity to a characterised halophilic cellobiohydrolase despite sharing only 57% sequence identity. Sequential thermocycling revealed SMECel6A had the ability to partially reversibly denature exclusively in seawater retaining significant activity. Our study confirms that salt marsh ecosystems harbour enzymes with attractive traits with biotechnological potential for implementation in ionic solution based bioprocessing systems.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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5
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Shao H. Cloning, expression, and molecular modification of glycoside hydrolase family 5 genes from Thermoascus aurantiacus. PLoS One 2023; 18:e0285680. [PMID: 37713448 PMCID: PMC10503741 DOI: 10.1371/journal.pone.0285680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 04/27/2023] [Indexed: 09/17/2023] Open
Abstract
In this paper, a novel bifunctional cellulase gene cel1 was cloned from Thermoascus aurantiacus by PCR and heterologously expressed in Pichia pastoris GS115. Bioinformatics and other related tools were used to compare the nucleotide homology of target genes, and analyze the signal peptide, transmembrane domain, hydrophilicity, secondary and tertiary structure of proteins. It was concluded that cel1 has similar endoglucanase nucleotide sequences and falls under the GH5 family. It was also found that cel1 has nucleotide sequences similar to glucosidase, which can infer that cel1 may have the properties of glucosidase, indicating that cel1 is multifunctional. At the same time, a part of the nucleotide sequence of the gene was removed to obtain a new gene cel2, and after highly efficient heterologous expression, its specific activity was found to be 2.1 times higher. Its enhancement is related to the exposure of the protein's hollow three-dimensional structure. This paper provides good material for exploring the relationship between the structure of bifunctional enzymes and their functions, which lays a solid foundation for further research and applications, and provides useful insight for gene mining of other novel enzymes.
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Affiliation(s)
- Hongwei Shao
- School of Life Sciences, Qilu Normal University, Ji’nan, China
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6
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Yang J, Zhang X, Sun Q, Li R, Wang X, Zhao G, He X, Zheng F. Modulation of the catalytic activity and thermostability of a thermostable GH7 endoglucanase by engineering the key loop B3. Int J Biol Macromol 2023; 248:125945. [PMID: 37482151 DOI: 10.1016/j.ijbiomac.2023.125945] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
The loop B3 of glycoside hydrolase family 7 (GH7) endoglucanases is confined into long and short types. TtCel7 is a thermophilic GH7 endoglucanase from Thermothelomyces thermophilus ATCC 42464 with a long loop B3. TtCel7 was distinct for the excellent thermostability (>30 % residual activity after 1-h incubation at 90 °C). The catalytic efficiency was reduced by removing the disulfide bond in loop B3 (C220A) and truncated the loop B3 (B3cut). However, B3cut exhibited improved thermostability, the remaining enzyme activity increased by 39 %-171 % compared toTtCel7 when treated at 70-90 °C for 1-h. Based on the analysis of molecular dynamics simulation, both loops B1 and A3 of B3cut swing toward the catalytic center, which contributed to the reduced cleft-space and increased structure-rigidity. Conversely, the deletion of disulfide bond resulted in a reduction of structural rigidity in C220A. Through structure-directed enzyme modulation, this study has identified two structural elements that are related to the catalysis and thermostability of TtCel7. The loop B3 of TtCel7 possibly stretches the catalytic pocket, thereby increases the openness of the catalytic tunnel and enhancing flexibility for efficient catalysis. Additionally, the disulfide bond within loop B3 serves to enhance structural stability and maintain a heightened level of activity.
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Affiliation(s)
- Junzhao Yang
- College of Biological Sciences, Beijing Forestry University, Beijing 100083, China
| | - Xinrui Zhang
- College of Biological Sciences, Beijing Forestry University, Beijing 100083, China
| | - Qingyang Sun
- College of Biological Sciences, Beijing Forestry University, Beijing 100083, China
| | - Ruilin Li
- College of Biological Sciences, Beijing Forestry University, Beijing 100083, China
| | - Xiaoyu Wang
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guozhu Zhao
- College of Biological Sciences, Beijing Forestry University, Beijing 100083, China
| | - Xiangwei He
- College of Biological Sciences, Beijing Forestry University, Beijing 100083, China
| | - Fei Zheng
- College of Biological Sciences, Beijing Forestry University, Beijing 100083, China.
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7
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Chaudhari YB, Várnai A, Sørlie M, Horn SJ, Eijsink VGH. Engineering cellulases for conversion of lignocellulosic biomass. Protein Eng Des Sel 2023; 36:gzad002. [PMID: 36892404 PMCID: PMC10394125 DOI: 10.1093/protein/gzad002] [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: 10/28/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.
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Affiliation(s)
- Yogesh B Chaudhari
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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8
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Haataja T, Gado JE, Nutt A, Anderson NT, Nilsson M, Momeni MH, Isaksson R, Väljamäe P, Johansson G, Payne CM, Ståhlberg J. Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding: insights from crystal structures and MD simulation. FEBS J 2023; 290:379-399. [PMID: 35997626 PMCID: PMC10087753 DOI: 10.1111/febs.16602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/30/2022] [Accepted: 08/17/2022] [Indexed: 02/05/2023]
Abstract
Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) (EC3.2.1.176) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p-nitrophenyl-β-d-cellobioside (pNPC), p-nitrophenyl-β-d-lactoside (pNPL) and methylumbelliferyl-β-d-cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o-nitrophenyl-β-d-cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium. Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non-productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non-productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates (kcat ) than TrCel7A, but higher Michaelis-Menten (KM ) constants as well. Furthermore, oNPC turned out to be useful as an active-site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.
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Affiliation(s)
- Topi Haataja
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA.,Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Anu Nutt
- Department of Chemistry, Uppsala University, Sweden.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Nolan T Anderson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Mikael Nilsson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Majid Haddad Momeni
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roland Isaksson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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9
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Penneru SK, Saharay M, Krishnan M. CelS-Catalyzed Processive Cellulose Degradation and Cellobiose Extraction for the Production of Bioethanol. J Chem Inf Model 2022; 62:6628-6638. [PMID: 35649216 DOI: 10.1021/acs.jcim.2c00239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial cellulase enzymes are potent candidates for the efficient production of bioethanol, a promising alternative to fossil fuels, from cellulosic biomass. These enzymes catalyze the breakdown of cellulose in plant biomass into simple sugars and then to bioethanol. In the absence of the enzyme, the cellulosic biomass is recalcitrant to decomposition due to fermentation-resistant lignin and pectin coatings on the cellulose surface, which make them inaccessible for hydrolysis. Cellobiohydrolase CelS is a microbial enzyme that binds to cellulose fiber and efficiently cleaves it into a simple sugar (cellobiose) by a repeated processive chopping mechanism. The two contributing factors to the catalytic reaction rate and the yield of cellobiose are the efficient product expulsion from the product binding site of CelS and the movement of the substrate or cellulose chain into the active site. Despite progress in understanding product expulsion in other cellulases, much remains to be understood about the molecular mechanism of processive action of these enzymes. Here, nonequilibrium molecular dynamics simulations using suitable reaction coordinates are carried out to investigate the energetics and mechanism of the substrate dynamics and product expulsion in CelS. The calculated free energy barrier for the product expulsion is three times lower than that for the processive action indicating that product removal is relatively easier and faster than the sliding of the substrate to the catalytic active site. The water traffic near the active site in response to the product expulsion and the processive action is also explored.
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Affiliation(s)
- Sree Kavya Penneru
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996-1939, United States
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500046, Telangana, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
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10
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Uchiyama T, Uchihashi T, Ishida T, Nakamura A, Vermaas JV, Crowley MF, Samejima M, Beckham GT, Igarashi K. Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface. SCIENCE ADVANCES 2022; 8:eade5155. [PMID: 36563138 PMCID: PMC9788756 DOI: 10.1126/sciadv.ade5155] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/21/2022] [Indexed: 05/31/2023]
Abstract
Efficient depolymerization of crystalline cellulose requires cooperation between multiple cellulolytic enzymes. Through biochemical approaches, molecular dynamics (MD) simulation, and single-molecule observations using high-speed atomic force microscopy (HS-AFM), we quantify and track synergistic activity for cellobiohydrolases (CBHs) with a lytic polysaccharide monooxygenase (LPMO) from Phanerochaete chrysosporium. Increasing concentrations of LPMO (AA9D) increased the activity of a glycoside hydrolase family 6 CBH, Cel6A, whereas the activity of a family 7 CBH (Cel7D) was enhanced only at lower concentrations of AA9D. MD simulation suggests that the result of AA9D action to produce chain breaks in crystalline cellulose can oxidatively disturb the crystalline surface by disrupting hydrogen bonds. HS-AFM observations showed that AA9D increased the number of Cel7D molecules moving on the substrate surface and increased the processivity of Cel7D, thereby increasing the depolymerization performance, suggesting that AA9D not only generates chain ends but also amorphizes the crystalline surface, thereby increasing the activity of CBHs.
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Affiliation(s)
- Taku Uchiyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takayuki Uchihashi
- Department of Physics and Structural Biology Research Center, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Physics, Structural Biology Center, and Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8602, Japan
| | - Takuya Ishida
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
| | - Josh V. Vermaas
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael F. Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano 380-8533, Japan
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- VTT Technical Research Center of Finland Ltd., Tietotie 2, P.O. Box 1000, Espoo, FI-02044 VTT, Finland
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11
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Zajki-Zechmeister K, Eibinger M, Nidetzky B. Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose. ACS Catal 2022; 12:10984-10994. [PMID: 36082050 PMCID: PMC9442579 DOI: 10.1021/acscatal.2c02377] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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12
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Schaller KS, Molina GA, Kari J, Schiano-di-Cola C, Sørensen TH, Borch K, Peters GH, Westh P. Virtual Bioprospecting of Interfacial Enzymes: Relating Sequence and Kinetics. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kay S. Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - Corinna Schiano-di-Cola
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
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13
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Gado JE, Harrison BE, Sandgren M, Ståhlberg J, Beckham GT, Payne CM. Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases. J Biol Chem 2021; 297:100931. [PMID: 34216620 PMCID: PMC8329511 DOI: 10.1016/j.jbc.2021.100931] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 11/28/2022] Open
Abstract
Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These enzymes are often bimodular, including a catalytic domain and carbohydrate-binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able to discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our machine learning results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.
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Affiliation(s)
- Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, USA; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Brent E Harrison
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, USA.
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14
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Summers SR, Alamdari S, Kraft CJ, Brunecky R, Pfaendtner J, Kaar JL. Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus Cellulolyticus. Protein Eng Des Sel 2021; 34:6476618. [PMID: 34935952 DOI: 10.1093/protein/gzab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 09/22/2021] [Accepted: 11/13/2021] [Indexed: 11/14/2022] Open
Abstract
Cellulases are largely afflicted by inhibition from their reaction products, especially at high-substrate loading, which represents a major challenge for biomass processing. This challenge was overcome for endoglucanase 1 (E1) from Acidothermus cellulolyticus by identifying a large conformational change involving distal residues upon binding cellobiose. Having introduced alanine substitutions at each of these residues, we identified several mutations that reduced cellobiose inhibition of E1, including W212A, W213A, Q247A, W249A and F250A. One of the mutations (W212A) resulted in a 47-fold decrease in binding affinity of cellobiose as well as a 5-fold increase in the kcat. The mutation further increased E1 activity on Avicel and dilute-acid treated corn stover and enhanced its productivity at high-substrate loadings. These findings were corroborated by funnel metadynamics, which showed that the W212A substitution led to reduced affinity for cellobiose in the +1 and +2 binding sites due to rearrangement of key cellobiose-binding residues.
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Affiliation(s)
- Samantha R Summers
- Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA 98195-1750, USA
| | - Casey J Kraft
- Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Lab, 15013 Denver W Pkwy, Golden, CO 80401, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA 98195-1750, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80309, USA
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15
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New thermostable endoglucanase from Spirochaeta thermophila and its mutants with altered substrate preferences. Appl Microbiol Biotechnol 2021; 105:1133-1145. [PMID: 33427929 DOI: 10.1007/s00253-020-11077-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/30/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Endoglucanases are key elements in several industrial applications, such as cellulosic biomass hydrolysis, cellulose fiber modification for the production paper and composite materials, and in nanocellulose production. In all of these applications, the desired function of the endoglucanase is to create nicks in the amorphous regions of the cellulose. However, endoglucanase can be diverted from its activity on the fibers by other substrates-soluble oligosaccharides. This issue was addressed in the current study using enzyme engineering and an enzyme evolution approach. To this end, a hypothetical endoglucanase from a thermostable bacterium Spirochaeta thermophila was for the first time cloned and characterized. The wild-type enzyme was used as a starting point for mutagenesis and molecular evolution toward a preference for the higher molecular weight substrates. The best of the evolved enzymes was more active than the wild-type enzyme toward high molecular weight substrate at temperatures below 45 °C (3-fold more active at 30 °C) and showed little or no activity with low molecular weight substrates. These findings can be instrumental in bioeconomy sectors, such as second-generation biofuels and biomaterials from lignocellulosic biomass. KEY POINTS: • A new thermostable endoglucanase was characterized. • The substrate specificity of this endoglucanase was changed by means of genetic engineering. • A mutant with a preference for long molecular weight substrate was obtained and proposed to be beneficial for cellulose fiber modification.
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16
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Abstract
Some cellulases exhibit “processivity”: the ability to degrade crystalline cellulose through successive hydrolytic catalytic reactions without the release of the enzyme from the substrate surface. We previously observed the movement of fungal processive cellulases by high-speed atomic force microscopy, and here, we use the same technique to directly observe the processive movement of bacterial cellobiohydrolases settling a long-standing controversy. Although fungal and bacterial processive cellulases have completely different protein folds, they have evolved to acquire processivity through the same strategy of adding subsites to extend the substrate-binding site and forming a tunnel-like active site by increasing the number of loops covering the active site. This represents an example of protein-level convergent evolution to acquire the same functions from different ancestors. Cellulose is the most abundant biomass on Earth, and many microorganisms depend on it as a source of energy. It consists mainly of crystalline and amorphous regions, and natural degradation of the crystalline part is highly dependent on the degree of processivity of the degrading enzymes (i.e., the extent of continuous hydrolysis without detachment from the substrate cellulose). Here, we report high-speed atomic force microscopic (HS-AFM) observations of the movement of four types of cellulases derived from the cellulolytic bacteria Cellulomonas fimi on various insoluble cellulose substrates. The HS-AFM images clearly demonstrated that two of them (CfCel6B and CfCel48A) slide on crystalline cellulose. The direction of processive movement of CfCel6B is from the nonreducing to the reducing end of the substrate, which is opposite that of processive cellulase Cel7A of the fungus Trichoderma reesei (TrCel7A), whose movement was first observed by this technique, while CfCel48A moves in the same direction as TrCel7A. When CfCel6B and TrCel7A were mixed on the same substrate, “traffic accidents” were observed, in which the two cellulases blocked each other’s progress. The processivity of CfCel6B was similar to those of fungal family 7 cellulases but considerably higher than those of fungal family 6 cellulases. The results indicate that bacteria utilize family 6 cellulases as high-processivity enzymes for efficient degradation of crystalline cellulose, whereas family 7 enzymes have the same function in fungi. This is consistent with the idea of convergent evolution of processive cellulases in fungi and bacteria to achieve similar functionality using different protein foldings.
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17
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Machado AS, Valadares F, Silva TF, Milagres AMF, Segato F, Ferraz A. The Secretome of Phanerochaete chrysosporium and Trametes versicolor Grown in Microcrystalline Cellulose and Use of the Enzymes for Hydrolysis of Lignocellulosic Materials. Front Bioeng Biotechnol 2020; 8:826. [PMID: 32766234 PMCID: PMC7379840 DOI: 10.3389/fbioe.2020.00826] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/29/2020] [Indexed: 12/26/2022] Open
Abstract
The ability of white-rot fungi to degrade polysaccharides in lignified plant cell walls makes them a suitable reservoir for CAZyme prospects. However, to date, CAZymes from these species are barely studied, which limits their use in the set of choices for biomass conversion in modern biorefineries. The current work joined secretome studies of two representative white-rot fungi, Phanerochaete chrysosporium and Trametes versicolor, with expression analysis of cellobiohydrolase (CBH) genes, and use of the secretomes to evaluate enzymatic conversion of simple and complex sugarcane-derived substrates. Avicel was used to induce secretion of high levels of CBHs in the extracellular medium. A total of 56 and 58 proteins were identified in cultures of P. chrysosporium and T. versicolor, respectively, with 78-86% of these proteins corresponding to plant cell wall degrading enzymes (cellulolytic, hemicellulolytic, pectinolytic, esterase, and auxiliary activity). CBHI predominated among the plant cell wall degrading enzymes, corresponding to 47 and 34% of the detected proteins in P. chrysosporium and T. versicolor, respectively, which confirms that Avicel is an efficient CBH inducer in white-rot fungi. The induction by Avicel of genes encoding CBHs (cel) was supported by high expression levels of cel7D and cel7C in P. chrysosporium and T. versicolor, respectively. Both white-rot fungi secretomes enabled hydrolysis experiments at 10 FPU/g substrate, despite the varied proportions of CBHs and other enzymes present in each case. When low recalcitrance sugarcane pith was used as a substrate, P. chrysosporium and T. versicolor secretomes performed similarly to Cellic® CTec2. However, the white-rot fungi secretomes were less efficient than Cellic® CTec2 during hydrolysis of more recalcitrant substrates, such as acid or alkaline sulfite-pretreated sugarcane bagasse, likely because Cellic® CTec2 contains an excess of CBHs compared with the white-rot fungi secretomes. General comparison of the white-rot fungi secretomes highlighted T. versicolor enzymes for providing high glucan conversions, even at lower proportion of CBHs, probably because the other enzymes present in this secretome and CBHs lacking carbohydrate-binding modules compensate for problems associated with unproductive binding to lignin.
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Affiliation(s)
| | | | | | | | | | - André Ferraz
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
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18
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Sørlie M, Horn SJ, Vaaje-Kolstad G, Eijsink VG. Using chitosan to understand chitinases and the role of processivity in the degradation of recalcitrant polysaccharides. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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19
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Røjel N, Kari J, Sørensen TH, Badino SF, Morth JP, Schaller K, Cavaleiro AM, Borch K, Westh P. Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues. J Biol Chem 2020; 295:1454-1463. [PMID: 31848226 PMCID: PMC7008363 DOI: 10.1074/jbc.ra119.011420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases effectively degrade cellulose and are of biotechnological interest because they can convert lignocellulosic biomass to fermentable sugars. Here, we implemented a fluorescence-based method for real-time measurements of complexation and decomplexation of the processive cellulase Cel7A and its insoluble substrate, cellulose. The method enabled detailed kinetic and thermodynamic analyses of ligand binding in a heterogeneous system. We studied WT Cel7A and several variants in which one or two of four highly conserved Trp residues in the binding tunnel had been replaced with Ala. WT Cel7A had on/off-rate constants of 1 × 105 m-1 s-1 and 5 × 10-3 s-1, respectively, reflecting the slow dynamics of a solid, polymeric ligand. Especially the off-rate constant was many orders of magnitude lower than typical values for small, soluble ligands. Binding rate and strength both were typically lower for the Trp variants, but effects of the substitutions were moderate and sometimes negligible. Hence, we propose that lowering the activation barrier for complexation is not a major driving force for the high conservation of the Trp residues. Using so-called Φ-factor analysis, we analyzed the kinetic and thermodynamic results for the variants. The results of this analysis suggested a transition state for complexation and decomplexation in which the reducing end of the ligand is close to the tunnel entrance (near Trp-40), whereas the rest of the binding tunnel is empty. We propose that this structure defines the highest free-energy barrier of the overall catalytic cycle and hence governs the turnover rate of this industrially important enzyme.
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Affiliation(s)
- Nanna Røjel
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Silke F Badino
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kay Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, DK-2800 Kgs. Lyngby Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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20
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Molecular recognition in the product site of cellobiohydrolase Cel7A regulates processive step length. Biochem J 2020; 477:99-110. [PMID: 31816027 DOI: 10.1042/bcj20190770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 11/17/2022]
Abstract
Cellobiohydrolase Cel7A is an industrial important enzyme that breaks down cellulose by a complex processive mechanism. The enzyme threads the reducing end of a cellulose strand into its tunnel-shaped catalytic domain and progresses along the strand while sequentially releasing the disaccharide cellobiose. While some molecular details of this intricate process have emerged, general structure-function relationships for Cel7A remain poorly elucidated. One interesting aspect is the occurrence of particularly strong ligand interactions in the product binding site. In this work, we analyze these interactions in Cel7A from Trichoderma reesei with special emphasis on the Arg251 and Arg394 residues. We made extensive biochemical characterization of enzymes that were mutated in these two positions and showed that the arginine residues contributed strongly to product binding. Specifically, ∼50% of the total standard free energy of product binding could be ascribed to four hydrogen bonds to Arg251 and Arg394, which had previously been identified in crystal structures. Mutation of either Arg251 or Arg394 lowered production inhibition of Cel7A, but at the same time altered the enzyme product profile and resulted in ∼50% reduction in both processivity and hydrolytic activity. The position of the two arginine residues closely matches the two-fold screw axis symmetry of the substrate, and this energetically favors the productive enzyme-substrate complex. Our results indicate that the strong and specific ligand interactions of Arg251 and Arg394 provide a simple proofreading system that controls the step length during consecutive hydrolysis and minimizes dead time associated with transient, non-productive complexes.
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21
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Hamre AG, Sørlie M. Kinetic relationships with processivity in Serratia marcescens family 18 glycoside hydrolases. Biochem Biophys Res Commun 2020; 521:120-124. [PMID: 31629467 DOI: 10.1016/j.bbrc.2019.10.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
Abstract
In nature, recalcitrant polysaccharides such as chitin and cellulose are degraded by glycoside hydrolases (GH) that act synergistically through different modes of action including attack from reducing-end and nonreducing-end (exo-mode) and random (endo-mode) on single polysaccharide chains. Both modes can be combined with a processive mechanism where the GH remain bound to the polysaccharide to perform multiple catalytic steps before dissociation into the solution. In this work, we have determined association rate constants and their activation paramaters for three co-evolved GHs from Serratia marcescens (SmChiA, SmChiB, and SmChiC) with an oligomeric substrate. Interestingly, we observe a positive correlation between the association rate constants and processive ability for the GHs. Previously, a positive correlation has been observed between substrate binding affinity and processive ability. SmChiA with highest processive ability of the three GHs bind with a kon of 11.5 ± 0.2 μM-1s-1, which is five-fold and 130-fold faster than SmChiB (less processive) and SmChiC (nonprocessive), respectively.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway.
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22
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Schiano‐di‐Cola C, Kołaczkowski B, Sørensen TH, Christensen SJ, Cavaleiro AM, Windahl MS, Borch K, Morth JP, Westh P. Structural and biochemical characterization of a family 7 highly thermostable endoglucanase from the fungusRasamsonia emersonii. FEBS J 2019; 287:2577-2596. [DOI: 10.1111/febs.15151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 01/21/2023]
Affiliation(s)
| | | | - Trine Holst Sørensen
- Department of Science and Environment Roskilde University Denmark
- Novozymes A/S Lyngby Denmark
| | | | | | - Michael Skovbo Windahl
- Department of Science and Environment Roskilde University Denmark
- Novozymes A/S Lyngby Denmark
| | | | - Jens Preben Morth
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
| | - Peter Westh
- Department of Science and Environment Roskilde University Denmark
- Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby Denmark
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23
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Abstract
Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.
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24
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Vu VV, Hangasky JA, Detomasi TC, Henry SJW, Ngo ST, Span EA, Marletta MA. Substrate selectivity in starch polysaccharide monooxygenases. J Biol Chem 2019; 294:12157-12166. [PMID: 31235519 DOI: 10.1074/jbc.ra119.009509] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/21/2019] [Indexed: 11/06/2022] Open
Abstract
Degradation of polysaccharides is central to numerous biological and industrial processes. Starch-active polysaccharide monooxygenases (AA13 PMOs) oxidatively degrade starch and can potentially be used with industrial amylases to convert starch into a fermentable carbohydrate. The oxidative activities of the starch-active PMOs from the fungi Neurospora crassa and Myceliophthora thermophila, NcAA13 and MtAA13, respectively, on three different starch substrates are reported here. Using high-performance anion-exchange chromatography coupled with pulsed amperometry detection, we observed that both enzymes have significantly higher oxidative activity on amylose than on amylopectin and cornstarch. Analysis of the product distribution revealed that NcAA13 and MtAA13 more frequently oxidize glycosidic linkages separated by multiples of a helical turn consisting of six glucose units on the same amylose helix. Docking studies identified important residues that are involved in amylose binding and suggest that the shallow groove that spans the active-site surface of AA13 PMOs favors the binding of helical amylose substrates over nonhelical substrates. Truncations of NcAA13 that removed its native carbohydrate-binding module resulted in diminished binding to amylose, but truncated NcAA13 still favored amylose oxidation over other starch substrates. These findings establish that AA13 PMOs preferentially bind and oxidize the helical starch substrate amylose. Moreover, the product distributions of these two enzymes suggest a unique interaction with starch substrates.
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Affiliation(s)
- Van V Vu
- Nguyen Tat Thanh Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam.
| | - John A Hangasky
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Tyler C Detomasi
- Department of Chemistry, University of California, Berkeley, California 94720
| | - Skylar J W Henry
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
| | - Elise A Span
- Biophysics Graduate Group, University of California, Berkeley, California 94720
| | - Michael A Marletta
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720; Department of Chemistry, University of California, Berkeley, California 94720; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720.
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25
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Nakabayashi M, Kamachi S, Malle D, Yanamoto T, Kishishita S, Fujii T, Inoue H, Ishikawa K. Construction of thermostable cellobiohydrolase I from the fungus Talaromyces cellulolyticus by protein engineering. Protein Eng Des Sel 2019; 32:33-40. [DOI: 10.1093/protein/gzz001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/09/2018] [Accepted: 01/07/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Fungus-derived GH-7 family cellobiohydrolase I (CBHI, EC 3.2.1.91) is one of the most important industrial enzymes for cellulosic biomass saccharification. Talaromyces cellulolyticus is well known as a mesophilic fungus producing a high amount of CBHI. Thermostability enhances the economic value of enzymes by making them more robust. However, CBHI has proven difficult to engineer, a fact that stems in part from its low expression in heterozygous hosts and its complex structure. Here, we report the successful improvement of the thermostability of CBHI from T. cellulolyticus using our homologous expression system and protein engineering method. We examined the key structures that seem to contribute to its thermostability using the 3D structural information of CBHI. Some parts of the structure of the Talaromyces emersonii CBHI were grafted into T. cellulolyticus CBHI and thermostable mutant CBHIs were constructed. The thermostability was primarily because of the improvement in the loop structures, and the positive effects of the mutations for thermostability were additive. By combing the mutations, the constructed thermophilic CBHI exhibits high hydrolytic activity toward crystalline cellulose with an optimum temperature at over 70°C. In addition, the strategy can be applied to the construction of the other thermostable CBHIs.
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Affiliation(s)
- Makoto Nakabayashi
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Saori Kamachi
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Dominggus Malle
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Faculty of Agriculture, Pattimura University, Jl. Ir. M. Putuhena, Kampus Poka, Ambon, Maluku, Indonesia
| | - Toshiaki Yanamoto
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Seiichiro Kishishita
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Tatsuya Fujii
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroyuki Inoue
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Kazuhiko Ishikawa
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka, Japan
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Schiano-di-Cola C, Røjel N, Jensen K, Kari J, Sørensen TH, Borch K, Westh P. Systematic deletions in the cellobiohydrolase (CBH) Cel7A from the fungus Trichoderma reesei reveal flexible loops critical for CBH activity. J Biol Chem 2018; 294:1807-1815. [PMID: 30538133 DOI: 10.1074/jbc.ra118.006699] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/08/2018] [Indexed: 11/06/2022] Open
Abstract
Glycoside hydrolase family 7 (GH7) cellulases are some of the most efficient degraders of cellulose, making them particularly relevant for industries seeking to produce renewable fuels from lignocellulosic biomass. The secretome of the cellulolytic model fungus Trichoderma reesei contains two GH7s, termed TrCel7A and TrCel7B. Despite having high structural and sequence similarities, the two enzymes are functionally quite different. TrCel7A is an exolytic, processive cellobiohydrolase (CBH), with high activity on crystalline cellulose, whereas TrCel7B is an endoglucanase (EG) with a preference for more amorphous cellulose. At the structural level, these functional differences are usually ascribed to the flexible loops that cover the substrate-binding areas. TrCel7A has an extensive tunnel created by eight peripheral loops, and the absence of four of these loops in TrCel7B makes its catalytic domain a more open cleft. To investigate the structure-function relationships of these loops, here we produced and kinetically characterized several variants in which four loops unique to TrCel7A were individually deleted to resemble the arrangement in the TrCel7B structure. Analysis of a range of kinetic parameters consistently indicated that the B2 loop, covering the substrate-binding subsites -3 and -4 in TrCel7A, was a key determinant for the difference in CBH- or EG-like behavior between TrCel7A and TrCel7B. Conversely, the B3 and B4 loops, located closer to the catalytic site in TrCel7A, were less important for these activities. We surmise that these results could be useful both in further mechanistic investigations and for guiding engineering efforts of this industrially important enzyme family.
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Affiliation(s)
- Corinna Schiano-di-Cola
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Nanna Røjel
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Jeppe Kari
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Trine Holst Sørensen
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Peter Westh
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, DK-2800 Kgs. Lyngby, Denmark
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28
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Rabinovich ML, Melnik MS, Herner ML, Voznyi YV, Vasilchenko LG. Predominant Nonproductive Substrate Binding by Fungal Cellobiohydrolase I and Implications for Activity Improvement. Biotechnol J 2018; 14:e1700712. [PMID: 29781240 DOI: 10.1002/biot.201700712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/08/2018] [Indexed: 12/20/2022]
Abstract
Enzymatic conversion of the most abundant renewable source of organic compounds, cellulose to fermentable sugars is attractive for production of green fuels and chemicals. The major component of industrial enzyme systems, cellobiohydrolase I from Hypocrea jecorina (Trichoderma reesei) (HjCel7A) processively splits disaccharide units from the reducing ends of tightly packed cellulose chains. HjCel7A consists of a catalytic domain (CD) and a carbohydrate-binding module (CBM) separated by a linker peptide. A tunnel-shaped substrate-binding site in the CD includes nine subsites for β-d-glucose units, seven of which (-7 to -1) precede the catalytic center. Low catalytic activity of Cel7A is the bottleneck and the primary target for improvement. Here it is shown for the first time that, in spite of much lower apparent kcat of HjCel7A at the hydrolysis of β-1,4-glucosidic linkages in the fluorogenic cellotetra- and -pentaose compared to the structurally related endoglucanase I (HjCel7B), the specificity constants (catalytic efficiency) kcat /Km for both enzymes are almost equal in these reactions. The observed activity difference appears from strong nonproductive substrate binding by HjCel7A, particularly significant for MU-β-cellotetraose (MUG4 ). Interaction of substrates with the subsites -6 and -5 proximal to the nonconserved Gln101 residue in HjCel7A decreases Km,ap by >1500 times. HjCel7A can be nonproductively bound onto cellulose surface with Kd ≈2-9 nM via CBM and CD that captures six terminal glucose units of cellulose chain. Decomposition of this nonproductive complex can determine the rate of cellulose conversion. MUG4 is a promising substrate to select active cellobiohydrolase I variants with reduced nonproductive substrate binding.
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Affiliation(s)
- Mikhail L Rabinovich
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Maria S Melnik
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Mikhail L Herner
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Yakov V Voznyi
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Lilia G Vasilchenko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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Abstract
Homology modeling is a very powerful tool in the absence of atomic structures for understanding the general fold of the enzyme, conserved residues, catalytic tunnel/pocket as well as substrate and product binding sites. This information is useful for structure-assisted enzyme design approach for the development of robust enzymes especially for industrial applications.
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Kobayashi H, Nagahama T, Arai W, Sasagawa Y, Umeda M, Hayashi T, Nikaido I, Watanabe H, Oguri K, Kitazato H, Fujioka K, Kido Y, Takami H. Polysaccharide hydrolase of the hadal zone amphipods Hirondellea gigas. Biosci Biotechnol Biochem 2018; 82:1123-1133. [PMID: 29623763 DOI: 10.1080/09168451.2018.1459178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Hirondellea species are common inhabitants in the hadal region deeper than 7,000 m. We found that Hirondellea gigas thrived in the Challenger Deep possessed polysaccharide hydrolases as digestive enzymes. To obtain various enzymes of other H. gigas, we captured amphipods from the Japan Trench, and Izu-Ogasawara (Bonin) Trench. A phylogenetic analysis based on the cytochrome oxidase I gene showed close relationships among amphipods, despite the geographic distance between the localities. However, several differences in enzymatic properties were observed in these H. gigas specimens. We also carried out RNA sequencing of H. gigas from the Izu-Ogasawara Trench. The cellulase gene of H. gigas was highly homologous to cellobiohydrolase of Glucosyl Hydrolase family 7 (GH7). On the other hand, enzymatic properties of H. gigas's cellulase were different from those of typical GH7 cellobiohydrolase. Thus, these results indicate that hadal-zone amphipod can be good candidates as the new enzyme resource.
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Affiliation(s)
- Hideki Kobayashi
- a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan
| | - Takahiko Nagahama
- b Department of Foods and Human Nutrition , Notre Dame Seishin University , Okayama , Japan
| | - Wataru Arai
- a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan
| | - Yohei Sasagawa
- c Bioinformatics Research Unit, Advanced Center for Computing and Communication , RIKEN , Saitama , Japan
| | - Mana Umeda
- c Bioinformatics Research Unit, Advanced Center for Computing and Communication , RIKEN , Saitama , Japan
| | - Tetsutaro Hayashi
- c Bioinformatics Research Unit, Advanced Center for Computing and Communication , RIKEN , Saitama , Japan
| | - Itoshi Nikaido
- c Bioinformatics Research Unit, Advanced Center for Computing and Communication , RIKEN , Saitama , Japan
| | - Hiromi Watanabe
- a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan
| | - Kazumasa Oguri
- a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan
| | - Hiroshi Kitazato
- a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan
| | - Kantaro Fujioka
- d Faculty of Engineering , Kanagawa University , Yokohama Chity , Japan
| | - Yukari Kido
- a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan
| | - Hideto Takami
- a Japan Agency for Marine-Earth Science and Technology (JAMSTEC) , Yokosuka , Japan
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Abstract
Glycoside Hydrolase Family 7 cellobiohydrolases (GH7 CBHs) catalyze cellulose depolymerization in cellulolytic eukaryotes, making them key discovery and engineering targets. However, there remains a lack of robust structure–activity relationships for these industrially important cellulases. Here, we compare CBHs from Trichoderma reesei (TrCel7A) and Penicillium funiculosum (PfCel7A), which exhibit a multi-modular architecture consisting of catalytic domain (CD), carbohydrate-binding module, and linker. We show that PfCel7A exhibits 60% greater performance on biomass than TrCel7A. To understand the contribution of each domain to this improvement, we measure enzymatic activity for a library of CBH chimeras with swapped subdomains, demonstrating that the enhancement is mainly caused by PfCel7A CD. We solve the crystal structure of PfCel7A CD and use this information to create a second library of TrCel7A CD mutants, identifying a TrCel7A double mutant with near-equivalent activity to wild-type PfCel7A. Overall, these results reveal CBH regions that enable targeted activity improvements. Cellobiohydrolases (CBHs) are critical for natural and industrial biomass degradation but their structure–activity relationships are not fully understood. Here, the authors present the biochemical and structural characterization of two CBHs, identifying protein regions that confer enhanced CBH activity.
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Kadowaki MAS, Higasi P, de Godoy MO, Prade RA, Polikarpov I. Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila. FEBS J 2018; 285:559-579. [PMID: 29222836 DOI: 10.1111/febs.14356] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/20/2017] [Accepted: 12/05/2017] [Indexed: 12/27/2022]
Abstract
Cellobiohydrolases hydrolyze cellulose, a linear polymer with glucose monomers linked exclusively by β-1,4 glycosidic linkages. The widespread hydrogen bonding network tethers individual cellulose polymers forming crystalline cellulose, which prevent the access of hydrolytic enzymes and water molecules. The most abundant enzyme secreted by Myceliophthora thermophila M77 in response to the presence of biomass is the cellobiohydrolase MtCel7A, which is composed by a GH7-catalytic domain (CD), a linker, and a CBM1-type carbohydrate-binding module. GH7 cellobiohydrolases have been studied before, and structural models have been proposed. However, currently available GH7 crystal structures only define separate catalytic domains and/or cellulose-binding modules and do not include the full-length structures that are involved in shaping the catalytic mode of operation. In this study, we determined the 3D structure of catalytic domain using X-ray crystallography and retrieved the full-length enzyme envelope via small-angle X-ray scattering (SAXS) technique. The SAXS data reveal a tadpole-like molecular shape with a rigid linker connecting the CD and CBM. Our biochemical studies show that MtCel7A has higher catalytic efficiency and thermostability as well as lower processivity when compared to the well-studied TrCel7A from Trichoderma reesei. Based on a comparison of the crystallographic structures of CDs and their molecular dynamic simulations, we demonstrate that MtCel7A has considerably higher flexibility than TrCel7A. In particular, loops that cover the active site are more flexible and undergo higher conformational fluctuations, which might account for decreased processivity and enhanced enzymatic efficiency. Our statistical coupling analysis suggests co-evolution of amino acid clusters comprising the catalytic site of MtCel7A, which correlate with the steps in the catalytic cycle of the enzyme. DATABASE The atomic coordinates and structural factors of MtCel7A have been deposited in the Protein Data Bank with accession number 5W11.
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Affiliation(s)
| | - Paula Higasi
- São Carlos Institute of Physics, University of São Paulo, Brazil
| | | | - Rolf A Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, Brazil
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Borisova AS, Eneyskaya EV, Jana S, Badino SF, Kari J, Amore A, Karlsson M, Hansson H, Sandgren M, Himmel ME, Westh P, Payne CM, Kulminskaya AA, Ståhlberg J. Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:5. [PMID: 29344086 PMCID: PMC5766984 DOI: 10.1186/s13068-017-1006-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/23/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate. RESULTS The TatCel7A, ThaCel7A, and TreCel7A enzymes were characterized for comparison of function. The catalytic domain of TatCel7A was crystallized, and two structures were determined: without ligand and with thio-cellotriose in the active site. Initial hydrolysis of bacterial cellulose was faster with TatCel7A than either ThaCel7A or TreCel7A. In synergistic saccharification of pretreated corn stover, both TatCel7A and ThaCel7A were more efficient than TreCel7A, although TatCel7A was more sensitive to thermal inactivation. Structural analyses and molecular dynamics (MD) simulations were performed to elucidate important structure/function correlations. Moreover, reverse conservation analysis (RCA) of sequence diversity revealed divergent regions of interest located outside the cellulose-binding tunnel of Trichoderma spp. GH7 CBHs. CONCLUSIONS We hypothesize that the combination of loop motifs is the main determinant for the observed differences in Cel7A activity on cellulosic substrates. Fine-tuning of the loop flexibility appears to be an important evolutionary target in Trichoderma spp., a conclusion supported by the RCA data. Our results indicate that, for industrial use, it would be beneficial to combine loop motifs from TatCel7A with the thermostability features of TreCel7A. Furthermore, one region implicated in thermal unfolding is suggested as a primary target for protein engineering.
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Affiliation(s)
- Anna S. Borisova
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
| | - Elena V. Eneyskaya
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, KY 40506-0046 USA
| | - Silke F. Badino
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Antonella Amore
- National Renewable Energy Laboratory, Biosciences Center, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Michael E. Himmel
- National Renewable Energy Laboratory, Biosciences Center, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Peter Westh
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, KY 40506-0046 USA
- Present Address: Division of Chemical, Bioengineering, Environmental, and Transport Systems, National Science Foundation, Alexandria, VA USA
| | - Anna A. Kulminskaya
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
- Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
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Matard-Mann M, Bernard T, Leroux C, Barbeyron T, Larocque R, Préchoux A, Jeudy A, Jam M, Nyvall Collén P, Michel G, Czjzek M. Structural insights into marine carbohydrate degradation by family GH16 κ-carrageenases. J Biol Chem 2017; 292:19919-19934. [PMID: 29030427 PMCID: PMC5712629 DOI: 10.1074/jbc.m117.808279] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Indexed: 11/06/2022] Open
Abstract
Carrageenans are sulfated α-1,3-β-1,4-galactans found in the cell wall of some red algae that are practically valuable for their gelation and biomimetic properties but also serve as a potential carbon source for marine bacteria. Carbohydrate degradation has been studied extensively for terrestrial plant/bacterial systems, but sulfation is not present in these cases, meaning the marine enzymes used to degrade carrageenans must possess unique features to recognize these modifications. To gain insights into these features, we have focused on κ-carrageenases from two distant bacterial phyla, which belong to glycoside hydrolase family 16 and cleave the β-1,4 linkage of κ-carrageenan. We have solved the crystal structure of the catalytic module of ZgCgkA from Zobellia galactanivorans at 1.66 Å resolution and compared it with the only other structure available, that of PcCgkA from Pseudoalteromonas carrageenovora 9T (ATCC 43555T). We also describe the first substrate complex in the inactivated mutant form of PcCgkA at 1.7 Å resolution. The structural and biochemical comparison of these enzymes suggests key determinants that underlie the functional properties of this subfamily. In particular, we identified several arginine residues that interact with the polyanionic substrate, and confirmed the functional relevance of these amino acids using a targeted mutagenesis strategy. These results give new insight into the diversity of the κ-carrageenase subfamily. The phylogenetic analyses show the presence of several distinct clades of enzymes that relate to differences in modes of action or subtle differences within the same substrate specificity, matching the hybrid character of the κ-carrageenan polymer.
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Affiliation(s)
- Maria Matard-Mann
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
- Amadéite SAS, "Pôle Biotechnologique" du Haut du Bois, 56580 Bréhan, France
| | - Thomas Bernard
- the Architecture et Fonction des Macromolécules Biologiques, Unité Mixed de Recherche 6098, CNRS, Universités Aix-Marseille I and II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Cédric Leroux
- the Sorbonne Universités, UPMC Université Paris 06, CNRS, FR 2424, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France, and
| | - Tristan Barbeyron
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Robert Larocque
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Aurélie Préchoux
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Alexandra Jeudy
- the Sorbonne Universités, UPMC Université Paris 06, CNRS, FR 2424, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France, and
| | - Murielle Jam
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Pi Nyvall Collén
- Amadéite SAS, "Pôle Biotechnologique" du Haut du Bois, 56580 Bréhan, France
| | - Gurvan Michel
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Mirjam Czjzek
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France,
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Goedegebuur F, Dankmeyer L, Gualfetti P, Karkehabadi S, Hansson H, Jana S, Huynh V, Kelemen BR, Kruithof P, Larenas EA, Teunissen PJM, Ståhlberg J, Payne CM, Mitchinson C, Sandgren M. Improving the thermal stability of cellobiohydrolase Cel7A from Hypocrea jecorina by directed evolution. J Biol Chem 2017; 292:17418-17430. [PMID: 28860192 DOI: 10.1074/jbc.m117.803270] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/24/2017] [Indexed: 11/06/2022] Open
Abstract
Secreted mixtures of Hypocrea jecorina cellulases are able to efficiently degrade cellulosic biomass to fermentable sugars at large, commercially relevant scales. H. jecorina Cel7A, cellobiohydrolase I, from glycoside hydrolase family 7, is the workhorse enzyme of the process. However, the thermal stability of Cel7A limits its use to processes where temperatures are no higher than 50 °C. Enhanced thermal stability is desirable to enable the use of higher processing temperatures and to improve the economic feasibility of industrial biomass conversion. Here, we enhanced the thermal stability of Cel7A through directed evolution. Sites with increased thermal stability properties were combined, and a Cel7A variant (FCA398) was obtained, which exhibited a 10.4 °C increase in Tm and a 44-fold greater half-life compared with the wild-type enzyme. This Cel7A variant contains 18 mutated sites and is active under application conditions up to at least 75 °C. The X-ray crystal structure of the catalytic domain was determined at 2.1 Å resolution and showed that the effects of the mutations are local and do not introduce major backbone conformational changes. Molecular dynamics simulations revealed that the catalytic domain of wild-type Cel7A and the FCA398 variant exhibit similar behavior at 300 K, whereas at elevated temperature (475 and 525 K), the FCA398 variant fluctuates less and maintains more native contacts over time. Combining the structural and dynamic investigations, rationales were developed for the stabilizing effect at many of the mutated sites.
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Affiliation(s)
- Frits Goedegebuur
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands,
| | - Lydia Dankmeyer
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | - Saeid Karkehabadi
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Suvamay Jana
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Vicky Huynh
- DuPont Industrial Biosciences, Palo Alto, California 94304
| | | | - Paulien Kruithof
- From DuPont Industrial Biosciences, Archimedesweg 30, Leiden 2333CN, The Netherlands
| | | | | | - Jerry Ståhlberg
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
| | - Christina M Payne
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | | | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, Uppsala SE-75007, Sweden, and
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Ogunmolu FE, Jagadeesha NBK, Kumar R, Kumar P, Gupta D, Yazdani SS. Comparative insights into the saccharification potentials of a relatively unexplored but robust Penicillium funiculosum glycoside hydrolase 7 cellobiohydrolase. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:71. [PMID: 28344646 PMCID: PMC5360062 DOI: 10.1186/s13068-017-0752-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/09/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND GH7 cellobiohydrolases (CBH1) are vital for the breakdown of cellulose. We had previously observed the enzyme as the most dominant protein in the active cellulose-hydrolyzing secretome of the hypercellulolytic ascomycete-Penicillium funiculosum (NCIM1228). To understand its contributions to cellulosic biomass saccharification in comparison with GH7 cellobiohydrolase from the industrial workhorse-Trichoderma reesei, we natively purified and functionally characterized the only GH7 cellobiohydrolase identified and present in the genome of the fungus. RESULTS There were marginal differences observed in the stability of both enzymes, with P. funiculosum (PfCBH1) showing an optimal thermal midpoint (Tm) of 68 °C at pH 4.4 as against an optimal Tm of 65 °C at pH 4.7 for T. reesei (TrCBH1). Nevertheless, PfCBH1 had an approximate threefold lower binding affinity (Km), an 18-fold higher turnover rate (kcat), a sixfold higher catalytic efficiency as well as a 26-fold higher enzyme-inhibitor complex equilibrium dissociation constant (Ki) than TrCBH1 on p-nitrophenyl-β-d-lactopyranoside (pNPL). Although both enzymes hydrolyzed cellooligomers (G2-G6) and microcrystalline cellulose, releasing cellobiose and glucose as the major products, the propensity was more with PfCBH1. We equally observed this trend during the hydrolysis of pretreated wheat straws in tandem with other core cellulases under the same conditions. Molecular dynamic simulations conducted on a homology model built using the TrCBH1 structure (PDB ID: 8CEL) as a template enabled us to directly examine the effects of substrate and products on the protein dynamics. While the catalytic triads-EXDXXE motifs-were conserved between the two enzymes, subtle variations in regions enclosing the catalytic path were observed, and relations to functionality highlighted. CONCLUSION To the best of our knowledge, this is the first report about a comprehensive and comparative description of CBH1 from hypercellulolytic ascomycete-P. funiculosum NCIM1228, against the backdrop of the same enzyme from the industrial workhorse-T. reesei. Our study reveals PfCBH1 as a viable alternative for CBH1 from T. reesei in industrial cellulase cocktails.
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Affiliation(s)
- Funso Emmanuel Ogunmolu
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Navya Bhatt Kammachi Jagadeesha
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Rakesh Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pawan Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Unhelkar MH, Duong VT, Enendu KN, Kelly JE, Tahir S, Butts CT, Martin RW. Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis. Biochim Biophys Acta Gen Subj 2017; 1861:636-643. [PMID: 28040565 PMCID: PMC6679993 DOI: 10.1016/j.bbagen.2016.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/06/2016] [Accepted: 12/09/2016] [Indexed: 12/28/2022]
Abstract
BACKGROUND Carnivorous plants possess diverse sets of enzymes with novel functionalities applicable to biotechnology, proteomics, and bioanalytical research. Chitinases constitute an important class of such enzymes, with future applications including human-safe antifungal agents and pesticides. Here, we compare chitinases from the genome of the carnivorous plant Drosera capensis to those from related carnivorous plants and model organisms. METHODS Using comparative modeling, in silico maturation, and molecular dynamics simulation, we produce models of the mature enzymes in aqueous solution. We utilize network analytic techniques to identify similarities and differences in chitinase topology. RESULTS Here, we report molecular models and functional predictions from protein structure networks for eleven new chitinases from D. capensis, including a novel class IV chitinase with two active domains. This architecture has previously been observed in microorganisms but not in plants. We use a combination of comparative and de novo structure prediction followed by molecular dynamics simulation to produce models of the mature forms of these proteins in aqueous solution. Protein structure network analysis of these and other plant chitinases reveal characteristic features of the two major chitinase families. GENERAL SIGNIFICANCE This work demonstrates how computational techniques can facilitate quickly moving from raw sequence data to refined structural models and comparative analysis, and to select promising candidates for subsequent biochemical characterization. This capability is increasingly important given the large and growing body of data from high-throughput genome sequencing, which makes experimental characterization of every target impractical.
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Affiliation(s)
- Megha H Unhelkar
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Vy T Duong
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Kaosoluchi N Enendu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - John E Kelly
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Seemal Tahir
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Carter T Butts
- Department of Sociology, University of California, Irvine, Irvine, CA 92697, USA; Department of Electrical Engineering and Computer Science, University of California, Irvine, Irvine, CA 92697, USA; Department of Statistics, University of California, Irvine, CA 92697, USA.
| | - Rachel W Martin
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.
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Kari J, Kont R, Borch K, Buskov S, Olsen JP, Cruyz-Bagger N, Väljamäe P, Westh P. Anomeric Selectivity and Product Profile of a Processive Cellulase. Biochemistry 2016; 56:167-178. [PMID: 28026938 DOI: 10.1021/acs.biochem.6b00636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellobiohydrolases (CBHs) make up an important group of enzymes for both natural carbon cycling and industrial deconstruction of lignocellulosic biomass. The consecutive hydrolysis of one cellulose strand relies on an intricate pattern of enzyme-substrate interactions in the long, tunnel-shaped binding site of the CBH. In this work, we have investigated the initial complexation mode with cellulose of the most thoroughly studied CBH, Cel7A from Hypocrea jecorina (HjCel7A). We found that HjCel7A predominantly produces glucose when it initiates a processive run on insoluble microcrystalline cellulose, confirming the validity of an even and odd product ratio as an estimate of processivity. Moreover, the glucose released from cellulose was predominantly α-glucose. A link between the initial binding mode of the enzyme and the reducing end configuration was investigated by inhibition studies with the two anomers of cellobiose. A clear preference for β-cellobiose in product binding site +2 was observed for HjCel7A, but not the homologous endoglucanase, HjCe7B. Possible relationships between this anomeric preference in the product site and the prevalence of odd-numbered initial-cut products are discussed, and a correlation between processivity and anomer selectivity is proposed.
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Affiliation(s)
- Jeppe Kari
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | - Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Kim Borch
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Steen Buskov
- Novozymes A/S , Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Johan Pelck Olsen
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
| | | | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu , Tartu, Estonia
| | - Peter Westh
- Research Unit for Functional Biomaterials, Roskilde University , Roskilde, Denmark
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39
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Crystal structures of wild‐type
Trichoderma reesei
Cel7A catalytic domain in open and closed states. FEBS Lett 2016; 590:4429-4438. [DOI: 10.1002/1873-3468.12464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 11/07/2022]
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40
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Kont R, Kari J, Borch K, Westh P, Väljamäe P. Inter-domain Synergism Is Required for Efficient Feeding of Cellulose Chain into Active Site of Cellobiohydrolase Cel7A. J Biol Chem 2016; 291:26013-26023. [PMID: 27780868 DOI: 10.1074/jbc.m116.756007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/21/2016] [Indexed: 01/27/2023] Open
Abstract
Structural polysaccharides like cellulose and chitin are abundant and their enzymatic degradation to soluble sugars is an important route in green chemistry. Processive glycoside hydrolases (GHs), like cellobiohydrolase Cel7A of Trichoderma reesei (TrCel7A) are key components of efficient enzyme systems. TrCel7A consists of a catalytic domain (CD) and a smaller carbohydrate-binding module (CBM) connected through the glycosylated linker peptide. A tunnel-shaped active site rests in the CD and contains 10 glucose unit binding sites. The active site of TrCel7A is lined with four Trp residues with two of them, Trp-40 and Trp-38, in the substrate binding sites near the tunnel entrance. Although addressed in numerous studies the elucidation of the role of CBM and active site aromatics has been obscured by a complex multistep mechanism of processive GHs. Here we studied the role of the CBM-linker and Trp-38 of TrCel7A with respect to binding affinity, on- and off-rates, processivity, and synergism with endoglucanase. The CBM-linker increased the on-rate and substrate affinity of the enzyme. The Trp-38 to Ala substitution resulted in increased off-rates and decreased processivity. The effect of the Trp-38 to Ala substitution on on-rates was strongly dependent on the presence of the CBM-linker. This compensation between CBM-linker and Trp-38 indicates synergism between CBM-linker and CD in feeding the cellulose chain into the active site. The inter-domain synergism was pre-requisite for the efficient degradation of cellulose in the presence of endoglucanase.
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Affiliation(s)
- Riin Kont
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Jeppe Kari
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Kim Borch
- Novozymes A/S, Bagsværd DK-2880, Denmark
| | - Peter Westh
- the Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark, and
| | - Priit Väljamäe
- From the Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia,
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41
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Sørensen TH, Windahl MS, McBrayer B, Kari J, Olsen JP, Borch K, Westh P. Loop variants of the thermophileRasamsonia emersoniiCel7A with improved activity against cellulose. Biotechnol Bioeng 2016; 114:53-62. [DOI: 10.1002/bit.26050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Trine Holst Sørensen
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | | | | | - Jeppe Kari
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | - Johan Pelck Olsen
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
| | | | - Peter Westh
- NSM, Research Unit for Functional Biomaterials, Roskilde University, Universitetsvej 1; Building 28, DK-4000 Roskilde Denmark
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42
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Biochemical and Structural Characterizations of Two Dictyostelium Cellobiohydrolases from the Amoebozoa Kingdom Reveal a High Level of Conservation between Distant Phylogenetic Trees of Life. Appl Environ Microbiol 2016; 82:3395-409. [PMID: 27037126 DOI: 10.1128/aem.00163-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/25/2016] [Indexed: 12/26/2022] Open
Abstract
UNLABELLED Glycoside hydrolase family 7 (GH7) cellobiohydrolases (CBHs) are enzymes commonly employed in plant cell wall degradation across eukaryotic kingdoms of life, as they provide significant hydrolytic potential in cellulose turnover. To date, many fungal GH7 CBHs have been examined, yet many questions regarding structure-activity relationships in these important natural and commercial enzymes remain. Here, we present the crystal structures and a biochemical analysis of two GH7 CBHs from social amoeba: Dictyostelium discoideum Cel7A (DdiCel7A) and Dictyostelium purpureum Cel7A (DpuCel7A). DdiCel7A and DpuCel7A natively consist of a catalytic domain and do not exhibit a carbohydrate-binding module (CBM). The structures of DdiCel7A and DpuCel7A, resolved to 2.1 Å and 2.7 Å, respectively, are homologous to those of other GH7 CBHs with an enclosed active-site tunnel. Two primary differences between the Dictyostelium CBHs and the archetypal model GH7 CBH, Trichoderma reesei Cel7A (TreCel7A), occur near the hydrolytic active site and the product-binding sites. To compare the activities of these enzymes with the activity of TreCel7A, the family 1 TreCel7A CBM and linker were added to the C terminus of each of the Dictyostelium enzymes, creating DdiCel7ACBM and DpuCel7ACBM, which were recombinantly expressed in T. reesei DdiCel7ACBM and DpuCel7ACBM hydrolyzed Avicel, pretreated corn stover, and phosphoric acid-swollen cellulose as efficiently as TreCel7A when hydrolysis was compared at their temperature optima. The Ki of cellobiose was significantly higher for DdiCel7ACBM and DpuCel7ACBM than for TreCel7A: 205, 130, and 29 μM, respectively. Taken together, the present study highlights the remarkable degree of conservation of the activity of these key natural and industrial enzymes across quite distant phylogenetic trees of life. IMPORTANCE GH7 CBHs are among the most important cellulolytic enzymes both in nature and for emerging industrial applications for cellulose breakdown. Understanding the diversity of these key industrial enzymes is critical to engineering them for higher levels of activity and greater stability. The present work demonstrates that two GH7 CBHs from social amoeba are surprisingly quite similar in structure and activity to the canonical GH7 CBH from the model biomass-degrading fungus T. reesei when tested under equivalent conditions (with added CBM-linker domains) on an industrially relevant substrate.
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Wang Y, Zhang S, Song X, Yao L. Cellulose chain binding free energy drives the processive move of cellulases on the cellulose surface. Biotechnol Bioeng 2016; 113:1873-80. [DOI: 10.1002/bit.25970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/17/2016] [Accepted: 02/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Shujun Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Xiangfei Song
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology; Chinese Academy of Sciences; Qingdao China
- Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao 266061 China
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44
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Jana S, Hamre AG, Wildberger P, Holen MM, Eijsink VGH, Beckham GT, Sørlie M, Payne CM. Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases. J Phys Chem B 2016; 120:1236-49. [PMID: 26824449 DOI: 10.1021/acs.jpcb.5b12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.
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Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Patricia Wildberger
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Matilde Mengkrog Holen
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
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45
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Nguyen-Thi N, Doucet N. Combining chitinase C and N-acetylhexosaminidase from Streptomyces coelicolor A3(2) provides an efficient way to synthesize N-acetylglucosamine from crystalline chitin. J Biotechnol 2016; 220:25-32. [DOI: 10.1016/j.jbiotec.2015.12.038] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 11/25/2015] [Accepted: 12/30/2015] [Indexed: 11/24/2022]
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46
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Olsen JP, Alasepp K, Kari J, Cruys-Bagger N, Borch K, Westh P. Mechanism of product inhibition for cellobiohydrolase Cel7A during hydrolysis of insoluble cellulose. Biotechnol Bioeng 2016; 113:1178-86. [DOI: 10.1002/bit.25900] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/23/2015] [Accepted: 11/29/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Johan P. Olsen
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Kadri Alasepp
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Jeppe Kari
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
| | - Nicolaj Cruys-Bagger
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
- Novozymes A/S; Bagsvaerd Denmark
| | | | - Peter Westh
- Research Unit for Functional Biomaterials; Roskilde University; NSM, 1 Universitetsvej, Build. 28 DK-4000 Roskilde Denmark
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47
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Hamre AG, Jana S, Reppert NK, Payne CM, Sørlie M. Processivity, Substrate Positioning, and Binding: The Role of Polar Residues in a Family 18 Glycoside Hydrolase. Biochemistry 2015; 54:7292-306. [PMID: 26503416 DOI: 10.1021/acs.biochem.5b00830] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzymatic degradation of recalcitrant polysaccharides such as cellulose (β-1,4-linked glucose) and chitin (β-1,4-linked N-acetylglucosamine) by glycoside hydrolases (GHs) is of significant biological and economical importance. In nature, depolymerization is primarily accomplished by processive GHs, which remain attached to the substrate between subsequent hydrolytic reactions. Recent computational efforts have suggested that the processive ability of a GH is directly linked to the ligand binding free energy. The contribution of individual aromatic residues in the active site of these enzymes has been extensively studied. In this study, we offer the first experimental evidence confirming correlation of binding free energy and degree of processivity and evidence that polar residues are essential for maintaining processive ability. Exchanging Thr(276) with Ala in substrate binding subsite -2 in the processive ChiA of Serratia marcescens results in a decrease in both the enthalpy (2.6 and 3.8 kcal/mol) and free energy (0.5 and 2.2 kcal/mol) for the binding to the substrate (GlcNAc)6 and the inhibitor allosamidin, respectively, compared to that of the wild type. Moreover, the initial apparent processivity as measured by [(GlcNAc)2]/[GlcNAc] ratios (17.1 ± 0.4) and chitin degradation efficiency (20%) are greatly reduced for ChiA-T276A versus those of the wild type (30.1 ± 1.5 and 75%, respectively). Mutation of Arg(172) to Ala reduces the level of recognition and positioning of the substrate into the active site. Molecular dynamics simulations indicate ChiA-R172A behaves like the wild type, but the dynamics of ChiA-T276A are greatly influenced by mutation, which is reflective of their influence on processivity.
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Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Nicole K Reppert
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences , P.O. Box 5003, N-1432 Ås, Norway
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48
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Kurašin M, Kuusk S, Kuusk P, Sørlie M, Väljamäe P. Slow Off-rates and Strong Product Binding Are Required for Processivity and Efficient Degradation of Recalcitrant Chitin by Family 18 Chitinases. J Biol Chem 2015; 290:29074-85. [PMID: 26468285 DOI: 10.1074/jbc.m115.684977] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Indexed: 12/18/2022] Open
Abstract
Processive glycoside hydrolases are the key components of enzymatic machineries that decompose recalcitrant polysaccharides, such as chitin and cellulose. The intrinsic processivity (P(Intr)) of cellulases has been shown to be governed by the rate constant of dissociation from polymer chain (koff). However, the reported koff values of cellulases are strongly dependent on the method used for their measurement. Here, we developed a new method for determining koff, based on measuring the exchange rate of the enzyme between a non-labeled and a (14)C-labeled polymeric substrate. The method was applied to the study of the processive chitinase ChiA from Serratia marcescens. In parallel, ChiA variants with weaker binding of the N-acetylglucosamine unit either in substrate-binding site -3 (ChiA-W167A) or the product-binding site +1 (ChiA-W275A) were studied. Both ChiA variants showed increased off-rates and lower apparent processivity on α-chitin. The rate of the production of insoluble reducing groups on the reduced α-chitin was an order of magnitude higher than koff, suggesting that the enzyme can initiate several processive runs without leaving the substrate. On crystalline chitin, the general activity of the wild type enzyme was higher, and the difference was magnifying with hydrolysis time. On amorphous chitin, the variants clearly outperformed the wild type. A model is proposed whereby strong interactions with polymer in the substrate-binding sites (low off-rates) and strong binding of the product in the product-binding sites (high pushing potential) are required for the removal of obstacles, like disintegration of chitin microfibrils.
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Affiliation(s)
| | - Silja Kuusk
- From the Institutes of Molecular and Cell Biology and
| | - Piret Kuusk
- Physics, University of Tartu, 51010 Tartu, Estonia and
| | - Morten Sørlie
- the Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1432, Norway
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Borisova AS, Eneyskaya EV, Bobrov KS, Jana S, Logachev A, Polev DE, Lapidus AL, Ibatullin FM, Saleem U, Sandgren M, Payne CM, Kulminskaya AA, Ståhlberg J. Sequencing, biochemical characterization, crystal structure and molecular dynamics of cellobiohydrolase Cel7A from
Geotrichum candidum
3C. FEBS J 2015; 282:4515-37. [DOI: 10.1111/febs.13509] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/13/2015] [Accepted: 09/04/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Anna S. Borisova
- Department of Chemistry and Biotechnology Swedish University of Agricultural Sciences Uppsala Sweden
- National Research Centre «Kurchatov Institute» B.P. Konstantinov Petersburg Nuclear Physics Institute Gatchina Orlova roscha Russia
| | - Elena V. Eneyskaya
- National Research Centre «Kurchatov Institute» B.P. Konstantinov Petersburg Nuclear Physics Institute Gatchina Orlova roscha Russia
| | - Kirill S. Bobrov
- National Research Centre «Kurchatov Institute» B.P. Konstantinov Petersburg Nuclear Physics Institute Gatchina Orlova roscha Russia
| | - Suvamay Jana
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - Anton Logachev
- Theodosius Dobzhansky Center for Genome Bioinformatics St. Petersburg State University Russia
| | - Dmitrii E. Polev
- Research Resource Centre «Molecular and Cell Technologies» St. Petersburg State University Russia
| | - Alla L. Lapidus
- Centre for Algorithmic Biotechnology St. Petersburg Academic University Russia
| | - Farid M. Ibatullin
- National Research Centre «Kurchatov Institute» B.P. Konstantinov Petersburg Nuclear Physics Institute Gatchina Orlova roscha Russia
| | - Umair Saleem
- Department of Chemistry and Biotechnology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Mats Sandgren
- Department of Chemistry and Biotechnology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Christina M. Payne
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - Anna A. Kulminskaya
- National Research Centre «Kurchatov Institute» B.P. Konstantinov Petersburg Nuclear Physics Institute Gatchina Orlova roscha Russia
- Department of Medical Physics Peter the Great St. Petersburg Polytechnic University Russia
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology Swedish University of Agricultural Sciences Uppsala Sweden
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50
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Sørensen TH, Cruys-Bagger N, Borch K, Westh P. Free Energy Diagram for the Heterogeneous Enzymatic Hydrolysis of Glycosidic Bonds in Cellulose. J Biol Chem 2015; 290:22203-11. [PMID: 26183776 DOI: 10.1074/jbc.m115.659656] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 01/25/2023] Open
Abstract
Kinetic and thermodynamic data have been analyzed according to transition state theory and a simplified reaction scheme for the enzymatic hydrolysis of insoluble cellulose. For the cellobiohydrolase Cel7A from Hypocrea jecorina (Trichoderma reesei), we were able to measure or collect relevant values for all stable and activated complexes defined by the reaction scheme and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association and dissociation of the enzyme-substrate complex. The results showed that the kinetics of enzyme-substrate association (i.e. formation of the Michaelis complex) was almost entirely entropy-controlled and that the activation entropy corresponded approximately to the loss of translational and rotational degrees of freedom of the dissolved enzyme. This implied that the transition state occurred early in the path where the enzyme has lost these degrees of freedom but not yet established extensive contact interactions in the binding tunnel. For dissociation, a similar analysis suggested that the transition state was late in the path where most enzyme-substrate contacts were broken. Activation enthalpies revealed that the rate of dissociation was far more temperature-sensitive than the rates of both association and the inner catalytic cycle. Comparisons of one- and two-domain variants showed that the CBM had no influence on the transition state for association but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association.
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Affiliation(s)
- Trine Holst Sørensen
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Nicolaj Cruys-Bagger
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | - Peter Westh
- From Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Roskilde, Denmark and
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