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Dong J, Abou Hachem M, Wang Y, Li X, Zhang B, Pijning T, Svensson B, Dijkhuizen L, Jin Z, Bai Y. Tailor-Made α-Glucans by Engineering the Processivity of α-Glucanotransferases via Tunnel-Cleft Active Center Interconversions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11041-11050. [PMID: 38700846 DOI: 10.1021/acs.jafc.4c01842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The function of polysaccharides is intimately associated with their size, which is largely determined by the processivity of transferases responsible for their synthesis. A tunnel active center architecture has been recognized as a key factor that governs processivity of several glycoside hydrolases (GHs), e.g., cellulases and chitinases. Similar tunnel architecture is also observed in the Limosilactobacillus reuteri 121 GtfB (Lr121 GtfB) α-glucanotransferase from the GH70 family. The molecular element underpinning processivity of these transglucosylases remains underexplored. Here, we report the synthesis of the smallest (α1 → 4)-α-glucan interspersed with linear and branched (α1 → 6) linkages by a novel 4,6-α-glucanotransferase from L. reuteri N1 (LrN1 GtfB) with an open-clefted active center instead of the tunnel structure. Notably, the loop swapping engineering of LrN1 GtfB and Lr121 GtfB based on their crystal structures clarified the impact of the loop-mediated tunnel/cleft structure at the donor subsites -2 to -3 on processivity of these α-glucanotransferases, enabling the tailoring of both product sizes and substrate preferences. This study provides unprecedented insights into the processivity determinants and evolutionary diversification of GH70 α-glucanotransferases and offers a simple route for engineering starch-converting α-glucanotransferases to generate diverse α-glucans for different biotechnological applications.
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Affiliation(s)
- Jingjing Dong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Yanli Wang
- College of Food Sciences and Engineering, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Xiaoxiao Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Bo Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tjaard Pijning
- Biomolecular X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Lubbert Dijkhuizen
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
- CarbExplore Research BV, 9747 AA Groningen, The Netherlands
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuxiang Bai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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2
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The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Nat Commun 2022; 13:5577. [PMID: 36151080 PMCID: PMC9508125 DOI: 10.1038/s41467-022-33180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/03/2022] [Indexed: 11/08/2022] Open
Abstract
In the barley β-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures β-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric β-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-β-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.
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Dowd B, McDonnell D, Tuohy MG. Current Progress in Optimising Sustainable Energy Recovery From Cattle Paunch Contents, a Slaughterhouse Waste Product. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.722424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Paunch contents are the recalcitrant, lignocellulose-rich, partially-digested feed present in the rumen of ruminant animals. Cattle forage in Europe is primarily from perennial and Italian ryegrasses and/or white clover, so paunch contents from forage-fed cattle in Europe is enriched in these feedstuffs. Globally, due to its underutilisation, the potential energy in cattle paunch contents annually represents an energy loss of 23,216,548,750–27,804,250,000 Megajoules (MJ) and financial loss of up to ~€800,000,000. Therefore, this review aims to describe progress made to-date in optimising sustainable energy recovery from paunch contents. Furthermore, analyses to determine the economic feasibility/potential of recovering sustainable energy from paunch contents was carried out. The primary method used to recover sustainable energy from paunch contents to-date has involved biomethane production through anaerobic digestion (AD). The major bottleneck in its utilisation through AD is its recalcitrance, resulting in build-up of fibrous material. Pre-treatments partially degrade the lignocellulose in lignocellulose-rich wastes, reducing their recalcitrance. Enzyme systems could be inexpensive and more environmentally compatible than conventional solvent pre-treatments. A potential source of enzyme systems is the rumen microbiome, whose efficiency in lignocellulose degradation is attracting significant research interest. Therefore, the application of rumen fluid (liquid derived from dewatering of paunch contents) to improve biomethane production from AD of lignocellulosic wastes is included in this review. Analysis of a study where rumen fluid was used to pre-treat paper sludge from a paper mill prior to AD for biomethane production suggested economic feasibility for CHP combustion, with potential savings of ~€11,000 annually. Meta-genomic studies of bacterial/archaeal populations have been carried out to understand their ruminal functions. However, despite their importance in degrading lignocellulose in nature, rumen fungi remain comparatively under-investigated. Further investigation of rumen microbes, their cultivation and their enzyme systems, and the role of rumen fluid in degrading lignocellulosic wastes, could provide efficient pre-treatments and co-digestion strategies to maximise biomethane yield from a range of lignocellulosic wastes. This review describes current progress in optimising sustainable energy recovery from paunch contents, and the potential of rumen fluid as a pre-treatment and co-substrate to recover sustainable energy from lignocellulosic wastes using AD.
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Hagen LH, Brooke CG, Shaw CA, Norbeck AD, Piao H, Arntzen MØ, Olson HM, Copeland A, Isern N, Shukla A, Roux S, Lombard V, Henrissat B, O'Malley MA, Grigoriev IV, Tringe SG, Mackie RI, Pasa-Tolic L, Pope PB, Hess M. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISME JOURNAL 2020; 15:421-434. [PMID: 32929206 PMCID: PMC8026616 DOI: 10.1038/s41396-020-00769-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
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Affiliation(s)
- Live H Hagen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.
| | | | | | | | - Hailan Piao
- Washington State University, Richland, WA, USA
| | - Magnus Ø Arntzen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Heather M Olson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nancy Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Anil Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Phillip B Pope
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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Yang Y, Liu Y, Ning L, Wang L, Mu Y, Li W. Binding Process and Free Energy Characteristics of Cellulose Chain into the Catalytic Domain of Cellobiohydrolase TrCel7A. J Phys Chem B 2019; 123:8853-8860. [PMID: 31557037 DOI: 10.1021/acs.jpcb.9b05023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It was observed in experiments that the catalytic domain (CD) of Trichoderma reesei Cel7A (TrCel7A) hydrolyzes crystalline cellulose in a processive manner, but the underlying binding mechanism is still unknown. Here, through replica-exchange molecular dynamics simulations, we find that the loading and sucking-in process of the cellulose chain into CD is entropy-driven and enthalpy-unfavorable, which firmly relate to the desolvation of the binding channel of CD. During the loading process, hydrophobic interactions play a dominant role because several aromatic residues have been identified to guide the cellulose chain processing. At the active site, a transition from enthalpy- to entropy-driven is detected for the driving force. Such a finding reveals the indispensability of the catalytic reaction of the glycosidic bond to provide the energy to drive the movements of the cellulose chain. Our study reveals the interaction pictures between the cellulose chain and TrCel7A at the atomic level, which helps better understand the catalytic mechanism of TrCel7A.
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Affiliation(s)
- Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education , Shandong Normal University , Jinan 250014 , China
| | | | - Lulu Ning
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | | | - Yuguang Mu
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
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Tiwari S, Verma T. Cellulose as a Potential Feedstock for Cellulose Enzyme Production. Fungal Biol 2019. [DOI: 10.1007/978-3-030-14726-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Karnaouri A, Matsakas L, Krikigianni E, Rova U, Christakopoulos P. Valorization of waste forest biomass toward the production of cello-oligosaccharides with potential prebiotic activity by utilizing customized enzyme cocktails. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:285. [PMID: 31827613 PMCID: PMC6902470 DOI: 10.1186/s13068-019-1628-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/04/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Production of value-added materials from lignocellulosic biomass residues is an emerging sector that has attracted much attention as it offers numerous benefits from an environmental and economical point of view. Non-digestible oligosaccharides represent a group of carbohydrates that are resistant to gastrointestinal digestion, and therefore, they are considered as potential prebiotic candidates. Such oligosaccharides can derive from the biomass cellulose fraction through a controlled enzymatic hydrolysis that eliminates the yield of monomers. RESULTS In the present study, hydrolysis of organosolv-pretreated forest residues (birch and spruce) was tested in the presence of four cellulases (EG5, CBH7, CBH6, EG7) and one accessory enzyme (LPMO). The optimal enzyme combinations were comprised of 20% EG5, 43% CBH7, 22% TtLPMO, 10% PaCbh6a and 5% EG7 in the case of birch and 35% EG5, 45% CBH7, 10% TtLPMO, 10% PaCbh6a and 5% EG7 in the case of spruce, leading to 22.3% and 19.1 wt% cellulose conversion into cellobiose, respectively. Enzymatic hydrolysis was applied on scale-up reactions, and the produced oligosaccharides (consisted of > 90% cellobiose) were recovered and separated from glucose through nanofiltration at optimized temperature (50 °C) and pressure (10 bar) conditions, yielding a final product with cellobiose-to-glucose ratio of 21.1 (birch) and 20.2 (spruce). Cellobiose-rich hydrolysates were tested as fermentative substrates for different lactic acid bacteria. It was shown that they can efficiently stimulate the growth of two Lactobacilli strains. CONCLUSIONS Controlled enzymatic hydrolysis with processive cellulases, combined with product recovery and purification, as well as enzyme recycling can potentially support the sustainable production of food-grade oligosaccharides from forest biomass.
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Affiliation(s)
- Anthi Karnaouri
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Eleni Krikigianni
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Ulrika Rova
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
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Biochemical characterization, low-resolution SAXS structure and an enzymatic cleavage pattern of BlCel48 from Bacillus licheniformis. Int J Biol Macromol 2018; 111:302-310. [DOI: 10.1016/j.ijbiomac.2017.12.138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/17/2017] [Accepted: 12/25/2017] [Indexed: 12/12/2022]
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Brunecky R, Alahuhta M, Sammond DW, Xu Q, Chen M, Wilson DB, Brady JW, Himmel ME, Bomble YJ, Lunin VV. Natural diversity of glycoside hydrolase family 48 exoglucanases: insights from structure. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:274. [PMID: 29213319 PMCID: PMC5707792 DOI: 10.1186/s13068-017-0951-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/02/2017] [Indexed: 05/27/2023]
Abstract
Glycoside hydrolase (GH) family 48 is an understudied and increasingly important exoglucanase family found in the majority of bacterial cellulase systems. Moreover, many thermophilic enzyme systems contain GH48 enzymes. Deletion of GH48 enzymes in these microorganisms results in drastic reduction in biomass deconstruction. Surprisingly, given their importance for these microorganisms, GH48s have intrinsically low cellulolytic activity but even in low ratios synergize greatly with GH9 endoglucanases. In this study, we explore the structural and enzymatic diversity of these enzymes across a wide range of temperature optima. We have crystallized one new GH48 module from Bacillus pumilus in a complex with cellobiose and cellohexaose (BpumGH48). We compare this structure to other known GH48 enzymes in an attempt to understand GH48 structure/function relationships and draw general rules correlating amino acid sequences and secondary structures to thermostability in this GH family.
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Affiliation(s)
- Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Deanne W. Sammond
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Mo Chen
- Department of Food Science, Cornell University, Ithaca, NY USA
| | - David B. Wilson
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY USA
| | - John W. Brady
- Department of Food Science, Cornell University, Ithaca, NY USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:52. [PMID: 28413443 PMCID: PMC5327597 DOI: 10.1186/s13068-017-0732-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The high crystallinity of cellulosic biomass myofibrils as well as the complexity of their intermolecular structure is a significant impediment for biofuel production. Cloning of celB-, celC-encoded cellulases (cel12B and cel8C) and peh-encoded polygalacturonase (peh28) from Pectobacterium carotovorum subsp. carotovorum (Pcc) was carried out in our previous study using Escherichia coli as a host vector. The current study partially characterizes the enzymes' molecular structures as well as their catalytic performance on different substrates which can be used to improve their potential for lignocellulosic biomass conversion. RESULTS β-Jelly roll topology, (α/α)6 antiparallel helices and right-handed β-helices were the folds identified for cel12B, cel8C, and peh28, respectively, in their corresponding protein model structures. Purifications of 17.4-, 6.2-, and 6.0-fold, compared to crude extract, were achieved for cel12B and cel8C, and peh28, respectively, using specific membrane ultrafiltrations and size-exclusion chromatography. Avicel and carboxymethyl cellulose (CMC) were substrates for cel12B, whereas for cel8C catalytic activity was only shown on CMC. The enzymes displayed significant synergy on CMC but not on Avicel when tested for 3 h at 45 °C. No observed β-glucosidase activities were identified for cel8C and cel12B when tested on p-nitrophenyl-β-d-glucopyranoside. Activity stimulation of 130% was observed when a recombinant β-glucosidase from Pcc was added to cel8C and cel12B as tested for 3 h at 45 °C. Optimum temperature and pH of 45 °C and 5.4, respectively, were identified for all three enzymes using various substrates. Catalytic efficiencies (kcat/Km) were calculated for cel12B and cel8C on CMC as 0.141 and 2.45 ml/mg/s respectively, at 45 °C and pH 5.0 and for peh28 on polygalacturonic acid as 4.87 ml/mg/s, at 40 °C and pH 5.0. Glucose and cellobiose were the end-products identified for cel8C, cel12B, and β-glucosidase acting together on Avicel or CMC, while galacturonic acid and other minor co-products were identified for peh28 action on pectin. CONCLUSIONS This study provides some insight into which parameters should be optimized when application of cel8C, cel12B, and peh28 to biomass conversion is the goal.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Kim D. Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Keith E. Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4 Canada
| | - Ebtesam N. Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Patrick L. Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Jean M. Escudero
- Department of Basic Science, St. Louis College of Pharmacy, St. Louis, MO 63110-1088 USA
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11
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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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Cockburn D, Wilkens C, Dilokpimol A, Nakai H, Lewińska A, Abou Hachem M, Svensson B. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes. PLoS One 2016; 11:e0160112. [PMID: 27504624 PMCID: PMC4978508 DOI: 10.1371/journal.pone.0160112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/13/2016] [Indexed: 01/23/2023] Open
Abstract
Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data.
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Affiliation(s)
- Darrell Cockburn
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Casper Wilkens
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Anna Lewińska
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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13
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Qian M, Guan S, Shan Y, Zhang H, Wang S. Structural and molecular basis of cellulase Cel48F by computational modeling: Insight into catalytic and product release mechanism. J Struct Biol 2016; 194:347-56. [DOI: 10.1016/j.jsb.2016.03.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 11/26/2022]
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14
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Chen M, Bu L, Alahuhta M, Brunecky R, Xu Q, Lunin VV, Brady JW, Crowley MF, Himmel ME, Bomble YJ. Strategies to reduce end-product inhibition in family 48 glycoside hydrolases. Proteins 2016; 84:295-304. [PMID: 26572060 DOI: 10.1002/prot.24965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/02/2015] [Accepted: 11/06/2015] [Indexed: 11/07/2022]
Abstract
Family 48 cellobiohydrolases are some of the most abundant glycoside hydrolases in nature. They are able to degrade cellulosic biomass and therefore serve as good enzyme candidates for biofuel production. Family 48 cellulases hydrolyze cellulose chains via a processive mechanism, and produce end products composed primarily of cellobiose as well as other cellooligomers (dp ≤ 4). The challenge of utilizing cellulases in biofuel production lies in their extremely slow turnover rate. A factor contributing to the low enzyme activity is suggested to be product binding to enzyme and the resulting performance inhibition. In this study, we quantitatively evaluated the product inhibitory effect of four family 48 glycoside hydrolases using molecular dynamics simulations and product expulsion free-energy calculations. We also suggested a series of single mutants of the four family 48 glycoside hydrolases with theoretically reduced level of product inhibition. The theoretical calculations provide a guide for future experimental studies designed to produce mutant cellulases with enhanced activity.
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Affiliation(s)
- Mo Chen
- Department of Food Science, Cornell University, Ithaca, New York
| | - Lintao Bu
- National Renewable Energy Laboratory, Golden, Colorado
| | | | | | - Qi Xu
- National Renewable Energy Laboratory, Golden, Colorado
| | | | - John W Brady
- Department of Food Science, Cornell University, Ithaca, New York
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15
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Tsai LC, Amiraslanov I, Chen HR, Chen YW, Lee HL, Liang PH, Liaw YC. Structures of exoglucanase from Clostridium cellulovorans: cellotetraose binding and cleavage. Acta Crystallogr F Struct Biol Commun 2015; 71:1264-72. [PMID: 26457517 PMCID: PMC4601590 DOI: 10.1107/s2053230x15015915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/25/2015] [Indexed: 11/10/2022] Open
Abstract
Exoglucanase/cellobiohydrolase (EC 3.2.1.176) hydrolyzes a β-1,4-glycosidic bond from the reducing end of cellulose and releases cellobiose as the major product. Three complex crystal structures of the glycosyl hydrolase 48 (GH48) cellobiohydrolase S (ExgS) from Clostridium cellulovorans with cellobiose, cellotetraose and triethylene glycol molecules were solved. The product cellobiose occupies subsites +1 and +2 in the open active-site cleft of the enzyme-cellotetraose complex structure, indicating an enzymatic hydrolysis function. Moreover, three triethylene glycol molecules and one pentaethylene glycol molecule are located at active-site subsites -2 to -6 in the structure of the ExgS-triethylene glycol complex shown here. Modelling of glucose into subsite -1 in the active site of the ExgS-cellobiose structure revealed that Glu50 acts as a proton donor and Asp222 plays a nucleophilic role.
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Affiliation(s)
- Li-Chu Tsai
- Molecular Science and Engineering, National Taipei University of Technology, 1, Section 3, Chung-Hsiao E. Road, Taipei 10608, Taiwan
| | - Imamaddin Amiraslanov
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Hung-Ren Chen
- Molecular Science and Engineering, National Taipei University of Technology, 1, Section 3, Chung-Hsiao E. Road, Taipei 10608, Taiwan
| | - Yun-Wen Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Hsiao-Lin Lee
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Po-Huang Liang
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
| | - Yen-Chywan Liaw
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan
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16
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Nakamura A, Ishida T, Kusaka K, Yamada T, Fushinobu S, Tanaka I, Kaneko S, Ohta K, Tanaka H, Inaka K, Higuchi Y, Niimura N, Samejima M, Igarashi K. "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography. SCIENCE ADVANCES 2015; 1:e1500263. [PMID: 26601228 PMCID: PMC4643802 DOI: 10.1126/sciadv.1500263] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/09/2015] [Indexed: 05/20/2023]
Abstract
Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.
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Affiliation(s)
- Akihiko Nakamura
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takuya Ishida
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Satoshi Kaneko
- Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Kazunori Ohta
- Japanese Experiment Module (JEM) Utilization Center, Japan Aerospace Exploration Agency, Ibaraki 305-8505, Japan
| | | | - Koji Inaka
- Maruwa Foods and Biosciences Inc., Nara 639-1123, Japan
| | - Yoshiki Higuchi
- Department of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Ibaraki 319-1106, Japan
| | - Masahiro Samejima
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Corresponding author. E-mail:
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17
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Momeni MH, Ubhayasekera W, Sandgren M, Ståhlberg J, Hansson H. Structural insights into the inhibition of cellobiohydrolase Cel7A by xylo-oligosaccharides. FEBS J 2015; 282:2167-77. [PMID: 25765184 DOI: 10.1111/febs.13265] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/06/2015] [Accepted: 03/10/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED The filamentous fungus Hypocrea jecorina (anamorph of Trichoderma reesei) is the predominant source of enzymes for industrial saccharification of lignocellulose biomass. The major enzyme, cellobiohydrolase Cel7A, constitutes nearly half of the total protein in the secretome. The performance of such enzymes is susceptible to inhibition by compounds liberated by physico-chemical pre-treatment if the biomass is kept unwashed. Xylan and xylo-oligosaccharides (XOS) have been proposed to play a key role in inhibition of cellobiohydrolases of glycoside hydrolase family 7. To elucidate the mechanism behind this inhibition at a molecular level, we used X-ray crystallography to determine structures of H. jecorina Cel7A in complex with XOS. Structures with xylotriose, xylotetraose and xylopentaose revealed a predominant binding mode at the entrance of the substrate-binding tunnel of the enzyme, in which each xylose residue is shifted ~ 2.4 Å towards the catalytic center compared with binding of cello-oligosaccharides. Furthermore, partial occupancy of two consecutive xylose residues at subsites -2 and -1 suggests an alternative binding mode for XOS in the vicinity of the catalytic center. Interestingly, the -1 xylosyl unit exhibits an open aldehyde conformation in one of the structures and a ring-closed pyranoside in another complex. Complementary inhibition studies with p-nitrophenyl lactoside as substrate indicate mixed inhibition rather than pure competitive inhibition. DATABASE The atomic coordinates and structure factors are available in the Protein Data Bank under accession number 4D5I (H. jecorina Cel7A E212Q variant, complex with xylotriose), 4D5J (H. jecorina Cel7A E217Q variant, complex with xylotriose), 4D5O (H. jecorina Cel7A E212Q variant, complex with xylopentaose), 4D5P (H. jecorina Cel7A E217Q variant, complex with xylopentaose), 4D5Q (wild-type H. jecorina Cel7A, complex with xylopentaose) and 4D5V (H. jecorina Cel7A E217Q variant, complex with xylotetraose).
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Affiliation(s)
- Majid Haddad Momeni
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Wimal Ubhayasekera
- Institute of Medicinal Chemistry, University of Copenhagen, Denmark.,MAX-Lab, Lund University, Sweden
| | - Mats Sandgren
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Henrik Hansson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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18
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C/N ratio drives soil actinobacterial cellobiohydrolase gene diversity. Appl Environ Microbiol 2015; 81:3016-28. [PMID: 25710367 DOI: 10.1128/aem.00067-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/15/2015] [Indexed: 11/20/2022] Open
Abstract
Cellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. The role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. Here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determined by using terminal restriction fragment length polymorphism (T-RFLP) analysis and clone libraries with gene-specific primers. For comparison, the diversity and abundance of general bacteria and fungi were also assessed. Phylogenetic analysis of the nucleotide sequences of 80 clones revealed significant new diversity of actinobacterial GH48 genes, and analysis of translated protein sequences showed that these enzymes are likely to represent functional cellobiohydrolases. The soil C/N ratio was the primary environmental driver of GH48 community compositions across sites and land uses, demonstrating the importance of substrate quality in their ecology. Furthermore, mid-infrared (MIR) spectrometry-predicted humic organic carbon was distinctly more important to GH48 diversity than to total bacterial and fungal diversity. This suggests a link between the actinobacterial GH48 community and soil organic carbon dynamics and highlights the potential importance of actinobacteria in the terrestrial carbon cycle.
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19
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Kari J, Olsen J, Borch K, Cruys-Bagger N, Jensen K, Westh P. Kinetics of cellobiohydrolase (Cel7A) variants with lowered substrate affinity. J Biol Chem 2014; 289:32459-68. [PMID: 25271162 DOI: 10.1074/jbc.m114.604264] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases are exo-active glycosyl hydrolases that processively convert cellulose to soluble sugars, typically cellobiose. They effectively break down crystalline cellulose and make up a major component in industrial enzyme mixtures used for deconstruction of lignocellulosic biomass. Identification of the rate-limiting step for cellobiohydrolases remains controversial, and recent reports have alternately suggested either association (on-rate) or dissociation (off-rate) as the overall bottleneck. Obviously, this uncertainty hampers both fundamental mechanistic understanding and rational design of enzymes with improved industrial applicability. To elucidate the role of on- and off-rates, respectively, on the overall kinetics, we have expressed a variant in which a tryptophan residue (Trp-38) in the middle of the active tunnel has been replaced with an alanine. This mutation weakens complex formation, and the population of substrate-bound W38A was only about half of the wild type. Nevertheless, the maximal, steady-state rate was twice as high for the variant enzyme. It is argued that these opposite effects on binding and activity can be reconciled if the rate-limiting step is after the catalysis (i.e. in the dissociation process).
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Affiliation(s)
- Jeppe Kari
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Johan Olsen
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Nicolaj Cruys-Bagger
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, Bagsværd DK-2880, Denmark
| | - Peter Westh
- From Department of Science, Systems and Models, Research Unit for Functional Biomaterials, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark and
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20
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Stereochemical Differentiation in the Simmons-Smith Reaction for Cyclopropanated Glucopyranose Derivatives as Molecular Probes for Glycosidases. Biosci Biotechnol Biochem 2014; 75:1380-2. [DOI: 10.1271/bbb.110120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Molecular Dynamics and Metadynamics Simulations of the Cellulase Cel48F. Enzyme Res 2014; 2014:692738. [PMID: 24963399 PMCID: PMC4055089 DOI: 10.1155/2014/692738] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/04/2014] [Accepted: 05/01/2014] [Indexed: 12/04/2022] Open
Abstract
Molecular dynamics (MD) and metadynamics techniques were used to study the cellulase Cel48F-sugar. Cellulase is enzyme that breaks cellulose fibers into small sugar units and is potentially useful in second generation alcohol production. In MD simulations, the overall structure of equilibrated Cel48F did not significantly change along the trajectory, retaining root mean square deviation below 0.15 nm. A set of 15 residues interacting with the sugar chains via hydrogen bonding throughout the simulation was observed. The free energy of dissociation (ΔGdiss.) of the chains in the catalytic tunnel of Cel48F was determined by metadynamics. The
ΔGdiss. values of the chains entering and leaving the wild-type Cel48F cavity were 13.9 and 62.1 kcal/mol, respectively. We also mutated the E542 and Q543 to alanine residue and obtained ΔGdiss. of 41.8 and 45.9 kcal/mol, respectively. These mutations were found to facilitate smooth dissociation of the sugar chain across the Cel48F tunnel. At the entry of the Cel48F tunnel, three residues were mutated to alanine: T110, T213, and L274. Contrary to the T110A-Cel48F, the mutants T213-Cel48F and L274-Cel48F prevented the sugar chain from passing across the leaving site. The present results can be a guideline in mutagenesis studies to improve processing by Cel48F.
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22
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Zhang H, Zhang JL, Sun L, Niu XD, Wang S, Shan YM. Molecular dynamics simulation of the processive endocellulase Cel48F fromClostridium cellulolyticum: a novel “water-control mechanism” in enzymatic hydrolysis of cellulose. J Mol Recognit 2014; 27:438-47. [DOI: 10.1002/jmr.2364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 01/14/2014] [Accepted: 01/28/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Hao Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Ji-long Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Lu Sun
- Department of Pharmacy, China-Japan Union Hospital; Jilin University; Changchun 130033 China
| | - Xiao-di Niu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry; Jilin University; Changchun 130023 China
| | - Ya-ming Shan
- College of Life Science; Jilin University; Changchun 130012 China
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23
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Chen M, Kostylev M, Bomble YJ, Crowley MF, Himmel ME, Wilson DB, Brady JW. Experimental and Modeling Studies of an Unusual Water-Filled Pore Structure with Possible Mechanistic Implications in Family 48 Cellulases. J Phys Chem B 2014; 118:2306-15. [DOI: 10.1021/jp408767j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mo Chen
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
| | - Maxim Kostylev
- Department
of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Yannick J. Bomble
- Biosciences
Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401-3393, United States
| | - Michael F. Crowley
- Biosciences
Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401-3393, United States
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401-3393, United States
| | - David B. Wilson
- Department
of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - John W. Brady
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
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24
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Yi Z, Su X, Revindran V, Mackie RI, Cann I. Molecular and biochemical analyses of CbCel9A/Cel48A, a highly secreted multi-modular cellulase by Caldicellulosiruptor bescii during growth on crystalline cellulose. PLoS One 2013; 8:e84172. [PMID: 24358340 PMCID: PMC3865294 DOI: 10.1371/journal.pone.0084172] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/20/2013] [Indexed: 01/24/2023] Open
Abstract
During growth on crystalline cellulose, the thermophilic bacterium Caldicellulosiruptor bescii secretes several cellulose-degrading enzymes. Among these enzymes is CelA (CbCel9A/Cel48A), which is reported as the most highly secreted cellulolytic enzyme in this bacterium. CbCel9A/Cel48A is a large multi-modular polypeptide, composed of an N-terminal catalytic glycoside hydrolase family 9 (GH9) module and a C-terminal GH48 catalytic module that are separated by a family 3c carbohydrate-binding module (CBM3c) and two identical CBM3bs. The wild-type CbCel9A/Cel48A and its truncational mutants were expressed in Bacillus megaterium and Escherichia coli, respectively. The wild-type polypeptide released twice the amount of glucose equivalents from Avicel than its truncational mutant that lacks the GH48 catalytic module. The truncational mutant harboring the GH9 module and the CBM3c was more thermostable than the wild-type protein, likely due to its compact structure. The main hydrolytic activity was present in the GH9 catalytic module, while the truncational mutant containing the GH48 module and the three CBMs was ineffective in degradation of either crystalline or amorphous cellulose. Interestingly, the GH9 and/or GH48 catalytic modules containing the CBM3bs form low-density particles during hydrolysis of crystalline cellulose. Moreover, TM3 (GH9/CBM3c) and TM2 (GH48 with three CBM3 modules) synergistically hydrolyze crystalline cellulose. Deletion of the CBM3bs or mutations that compromised their binding activity suggested that these CBMs are important during hydrolysis of crystalline cellulose. In agreement with this observation, seven of nine genes in a C. bescii gene cluster predicted to encode cellulose-degrading enzymes harbor CBM3bs. Based on our results, we hypothesize that C. bescii uses the GH48 module and the CBM3bs in CbCel9A/Cel48A to destabilize certain regions of crystalline cellulose for attack by the highly active GH9 module and other endoglucanases produced by this hyperthermophilic bacterium.
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Affiliation(s)
- Zhuolin Yi
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xiaoyun Su
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Vanessa Revindran
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Isaac Cann
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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25
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Vaaje-Kolstad G, Horn SJ, Sørlie M, Eijsink VGH. The chitinolytic machinery ofSerratia marcescens- a model system for enzymatic degradation of recalcitrant polysaccharides. FEBS J 2013; 280:3028-49. [DOI: 10.1111/febs.12181] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Svein J. Horn
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Morten Sørlie
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
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Sukharnikov LO, Alahuhta M, Brunecky R, Upadhyay A, Himmel ME, Lunin VV, Zhulin IB. Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48. J Biol Chem 2012; 287:41068-77. [PMID: 23055526 DOI: 10.1074/jbc.m112.405720] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Currently, the cost of cellulase enzymes remains a key economic impediment to commercialization of biofuels. Enzymes from glycoside hydrolase family 48 (GH48) are a critical component of numerous natural lignocellulose-degrading systems. Although computational mining of large genomic data sets is a promising new approach for identifying novel cellulolytic activities, current computational methods are unable to distinguish between cellulases and enzymes with different substrate specificities that belong to the same protein family. We show that by using a robust computational approach supported by experimental studies, cellulases and non-cellulases can be effectively identified within a given protein family. Phylogenetic analysis of GH48 showed non-monophyletic distribution, an indication of horizontal gene transfer. Enzymatic function of GH48 proteins coded by horizontally transferred genes was verified experimentally, which confirmed that these proteins are cellulases. Computational and structural studies of GH48 enzymes identified structural elements that define cellulases and can be used to computationally distinguish them from non-cellulases. We propose that the structural element that can be used for in silico discrimination between cellulases and non-cellulases belonging to GH48 is an ω-loop located on the surface of the molecule and characterized by highly conserved rare amino acids. These markers were used to screen metagenomics data for "true" cellulases.
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Affiliation(s)
- Leonid O Sukharnikov
- BioEnergy Science Center, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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27
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The crystallization and structural analysis of cellulases (and other glycoside hydrolases): strategies and tactics. Methods Enzymol 2012; 510:141-68. [PMID: 22608725 DOI: 10.1016/b978-0-12-415931-0.00008-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The three-dimensional (3-D) structures of cellulases, and other glycoside hydrolases, are a central feature of research in carbohydrate chemistry and biochemistry. 3-D structure is used to inform protein engineering campaigns, both academic and industrial, which are typically used to improve the stability or activity of an enzyme. Examples of classical protein engineering goals include higher thermal stability, reduced metal-ion dependency, detergent and protease resistance, decreased product inhibition, and altered specificity. 3-D structure may also be used to interpret the behavior of enzyme variants that are derived from screening or random mutagenesis approaches, with a view to establishing an iterative design process. In other areas, 3-D structure is used as one of the many tools to probe enzymatic catalysis, typically dovetailing with physical organic chemistry approaches to provide complete reaction mechanisms for enzymes by visualizing catalytic site interactions at different stages of the reaction. Such mechanistic insight is not only fundamentally important, impacting on inhibitor and drug design approaches with ramifications way beyond cellulose hydrolysis, but also provides the framework for the design of enzyme variants to use as biocatalysts for the synthesis of bespoke oligosaccharides. Here we review some of the strategies and tactics that may be applied to the X-ray structure solution of cellulases (and other carbohydrate-active enzymes). The general approach is first to decide why you are doing the work, then to establish correct domain boundaries for truncated constructs (typically the catalytic domain only), and finally to pursue crystallization of pure, homogeneous, and monodisperse protein with appropriate ligand and additive combinations. Cellulase-specific strategies are important for the delineation of domain boundaries, while glycoside hydrolases generally also present challenges and opportunities for the selection and optimization of ligands to both aid crystallization, and also provide structural and mechanistic insight. As the many roles for plant cell wall degrading enzymes increase, so does the need for rapid high-quality structure determination to provide a sound structural foundation for understanding mechanism and specificity, and for future protein engineering strategies.
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28
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Structural basis for entropy-driven cellulose binding by a type-A cellulose-binding module (CBM) and bacterial expansin. Proc Natl Acad Sci U S A 2012; 109:14830-5. [PMID: 22927418 DOI: 10.1073/pnas.1213200109] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Components of modular cellulases, type-A cellulose-binding modules (CBMs) bind to crystalline cellulose and enhance enzyme effectiveness, but structural details of the interaction are uncertain. We analyzed cellulose binding by EXLX1, a bacterial expansin with ability to loosen plant cell walls and whose domain D2 has type-A CBM characteristics. EXLX1 strongly binds to crystalline cellulose via D2, whereas its affinity for soluble cellooligosaccharides is weak. Calorimetry indicated cellulose binding was largely entropically driven. We solved the crystal structures of EXLX1 complexed with cellulose-like oligosaccharides to find that EXLX1 binds the ligands through hydrophobic interactions of three linearly arranged aromatic residues in D2. The crystal structures revealed a unique form of ligand-mediated dimerization, with the oligosaccharide sandwiched between two D2 domains in opposite polarity. This report clarifies the molecular target of expansin and the specific molecular interactions of a type-A CBM with cellulose.
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29
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Sørlie M, Zakariassen H, Norberg AL, Eijsink VGH. Processivity and substrate-binding in family 18 chitinases. BIOCATAL BIOTRANSFOR 2012. [DOI: 10.3109/10242422.2012.676282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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30
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Santhanam N, Badri DV, Decker SR, Manter DK, Reardon KF, Vivanco JM. Lignocellulose Decomposition by Microbial Secretions. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-23047-9_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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31
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Abstract
There are two types of processive cellulases, exocellulases and processive endoglucanases. There are also two classes of exocellulases, ones that attack the reducing ends of cellulose chains and ones that attack the nonreducing ends. There are a number of ways of assaying processivity but none of them are ideal. It appears that exocellulases, all of which have their active sites in a tunnel, couple movement along a cellulose chain with cleavage of cellobiose from the end of the cellulose molecule. There are two sets of structures that suggest how an exocellulase might move along a cellulose chain. For family 48 exocellulases there are two different ways that a chain can be bound in the active site while for family 6 exocellulases there are several different ligand-bound structures. Site-directed mutagenesis of Thermobifida fusca exocellulases Cel48A and Cel6B and the processive endoglucanase Cel9A have identified some mutations that increase processivity and some that decrease processivity. In addition a mutation in Cel6B was identified that appears to allow the mutant enzyme to move along a cellulose chain in the absence of cleavage.
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Affiliation(s)
- David B Wilson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.
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32
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Abstract
Natural cellulolytic enzyme systems as well as leading commercial cellulase cocktails are dominated by enzymes that degrade cellulose chains in a processive manner. Despite the abundance of processivity among natural cellulases, the molecular basis as well as the biotechnological implications of this mechanism are only partly understood. One of the major limitations lies in the fact that it is not straightforward to measure and quantify processivity in what essentially are biphasic experimental systems. Here, we describe and discuss both well-established methods and newer methods for measuring cellulase processivity. In addition, we discuss recent insights from studies on chitinases that may help direct further studies on processivity in cellulases.
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Affiliation(s)
- Svein J Horn
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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33
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Moréra S, Vigouroux A, Stubbs KA. A potential fortuitous binding of inhibitors of an inverting family GH9 β-glycosidase derived from isofagomine. Org Biomol Chem 2011; 9:5945-7. [PMID: 21785782 DOI: 10.1039/c1ob05766a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using structural insight, the binding mode of isofagomine-derived inhibitors with family GH9 glycosidases is achieved via the study of Alicyclobacillus acidocaldarius (AaCel9A) endoglucanase. In contrast to what was observed in the first report using these compounds with inverting glycosidases from family GH6, these inhibitors do not adopt a distorted conformation in the active site.
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Affiliation(s)
- Solange Moréra
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France.
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34
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Determination of the catalytic base in family 48 glycosyl hydrolases. Appl Environ Microbiol 2011; 77:6274-6. [PMID: 21764975 DOI: 10.1128/aem.05532-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The catalytic base in family 48 glycosyl hydrolases has not been previously established experimentally. Based on structural and modeling data published to date, we used site-directed mutagenesis and azide rescue activity assays to show definitively that the catalytic base in Thermobifida fusca Cel48A is aspartic acid 225. Of the tested mutants, only Cel48A with the D225E mutation retained partial activity on soluble and insoluble substrates. In azide rescue experiments, only the D225G mutation, in the smallest residue tested, showed an increase in activity with added azide.
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35
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Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams PD. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol 2010; 172:372-9. [DOI: 10.1016/j.jsb.2010.06.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/16/2010] [Accepted: 06/23/2010] [Indexed: 11/29/2022]
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36
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Saharay M, Guo H, Smith JC. Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS. PLoS One 2010; 5:e12947. [PMID: 20967294 PMCID: PMC2953488 DOI: 10.1371/journal.pone.0012947] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 08/20/2010] [Indexed: 12/02/2022] Open
Abstract
The hydrolysis of cellulose is the bottleneck in cellulosic ethanol production. The cellobiohydrolase CelS from Clostridium thermocellum catalyzes the hydrolysis of cello-oligosaccharides via inversion of the anomeric carbon. Here, to examine key features of the CelS-catalyzed reaction, QM/MM (SCCDFTB/MM) simulations are performed. The calculated free energy profile for the reaction possesses a 19 kcal/mol barrier. The results confirm the role of active site residue Glu87 as the general acid catalyst in the cleavage reaction and show that Asp255 may act as the general base. A feasible position in the reactant state of the water molecule responsible for nucleophilic attack is identified. Sugar ring distortion as the reaction progresses is quantified. The results provide a computational approach that may complement the experimental design of more efficient enzymes for biofuel production.
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Affiliation(s)
- Moumita Saharay
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Hong Guo
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
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37
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Fontes CMGA, Gilbert HJ. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annu Rev Biochem 2010; 79:655-81. [PMID: 20373916 DOI: 10.1146/annurev-biochem-091208-085603] [Citation(s) in RCA: 362] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes can be described as one of nature's most elaborate and highly efficient nanomachines. These cell bound multienzyme complexes orchestrate the deconstruction of cellulose and hemicellulose, two of the most abundant polymers on Earth, and thus play a major role in carbon turnover. Integration of cellulosomal components occurs via highly ordered protein:protein interactions between cohesins and dockerins, whose specificity allows the incorporation of cellulases and hemicellulases onto a molecular scaffold. Cellulosome assembly promotes the exploitation of enzyme synergism because of spatial proximity and enzyme-substrate targeting. Recent structural and functional studies have revealed how cohesin-dockerin interactions mediate both cellulosome assembly and cell-surface attachment, while retaining the spatial flexibility required to optimize the catalytic synergy within the enzyme complex. These emerging advances in our knowledge of cellulosome function are reviewed here.
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Affiliation(s)
- Carlos M G A Fontes
- CIISA, Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, 1300-477 Lisboa, Portugal.
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38
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Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, Adams PD. Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:744-50. [PMID: 19622857 PMCID: PMC2714717 DOI: 10.1107/s0907444909012773] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 04/03/2009] [Indexed: 11/10/2022]
Abstract
The production of biofuels using biomass is an alternative route to support the growing global demand for energy and to also reduce the environmental problems caused by the burning of fossil fuels. Cellulases are likely to play an important role in the degradation of biomass and the production of sugars for subsequent fermentation to fuel. Here, the crystal structure of an endoglucanase, Cel9A, from Alicyclobacillus acidocaldarius (Aa_Cel9A) is reported which displays a modular architecture composed of an N-terminal Ig-like domain connected to the catalytic domain. This paper describes the overall structure and the detailed contacts between the two modules. Analysis suggests that the interaction involving the residues Gln13 (from the Ig-like module) and Phe439 (from the catalytic module) is important in maintaining the correct conformation of the catalytic module required for protein activity. Moreover, the Aa_Cel9A structure shows three metal-binding sites that are associated with the thermostability and/or substrate affinity of the enzyme.
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Affiliation(s)
- Jose Henrique Pereira
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rajat Sapra
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551, USA
| | - Joanne V. Volponi
- Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551, USA
| | - Carol L. Kozina
- Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551, USA
| | - Blake Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, CA 94720, USA
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39
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Ishida T, Fushinobu S, Kawai R, Kitaoka M, Igarashi K, Samejima M. Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J Biol Chem 2009; 284:10100-9. [PMID: 19193645 DOI: 10.1074/jbc.m808122200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Glycoside hydrolase family 55 consists of beta-1,3-glucanases mainly from filamentous fungi. A beta-1,3-glucanase (Lam55A) from the Basidiomycete Phanerochaete chrysosporium hydrolyzes beta-1,3-glucans in the exo-mode with inversion of anomeric configuration and produces gentiobiose in addition to glucose from beta-1,3/1,6-glucans. Here we report the crystal structure of Lam55A, establishing the three-dimensional structure of a member of glycoside hydrolase 55 for the first time. Lam55A has two beta-helical domains in a single polypeptide chain. These two domains are separated by a long linker region but are positioned side by side, and the overall structure resembles a rib cage. In the complex, a gluconolactone molecule is bound at the bottom of a pocket between the two beta-helical domains. Based on the position of the gluconolactone molecule, Glu-633 appears to be the catalytic acid, whereas the catalytic base residue could not be identified. The substrate binding pocket appears to be able to accept a gentiobiose unit near the cleavage site, and a long cleft runs from the pocket, in accordance with the activity of this enzyme toward various beta-1,3-glucan oligosaccharides. In conclusion, we provide important features of the substrate-binding site at the interface of the two beta-helical domains, demonstrating an unexpected variety of carbohydrate binding modes.
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Affiliation(s)
- Takuya Ishida
- Departments of Biomaterials Sciences and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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