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Gade M, Tan LL, Damry AM, Sandhu M, Brock JS, Delaney A, Villar-Briones A, Jackson CJ, Laurino P. Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. JACS Au 2021; 1:2349-2360. [PMID: 34977903 PMCID: PMC8715544 DOI: 10.1021/jacsau.1c00464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 05/14/2023]
Abstract
Protein conformational changes can facilitate the binding of noncognate substrates and underlying promiscuous activities. However, the contribution of substrate conformational dynamics to this process is comparatively poorly understood. Here, we analyze human (hMAT2A) and Escherichia coli (eMAT) methionine adenosyltransferases that have identical active sites but different substrate specificity. In the promiscuous hMAT2A, noncognate substrates bind in a stable conformation to allow catalysis. In contrast, noncognate substrates sample stable productive binding modes less frequently in eMAT owing to altered mobility in the enzyme active site. Different cellular concentrations of substrates likely drove the evolutionary divergence of substrate specificity in these orthologues. The observation of catalytic promiscuity in hMAT2A led to the detection of a new human metabolite, methyl thioguanosine, that is produced at elevated levels in a cancer cell line. This work establishes that identical active sites can result in different substrate specificity owing to the effects of substrate and enzyme dynamics.
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Affiliation(s)
- Madhuri Gade
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Li Lynn Tan
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Adam M. Damry
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Mahakaran Sandhu
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Joseph S. Brock
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Andie Delaney
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Alejandro Villar-Briones
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, ACT, Australia
- Australian
Research Council Centre of Excellence in Synthetic Biology, Research
School of Chemistry, Australian National
University, Canberra 2601, ACT, Australia
| | - Paola Laurino
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
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Lee S, Akeprathumchai S, Bundidamorn D, Salaipeth L, Poomputsa K, Ratanakhanokchai K, Chang KL, Phitsuwan P. Interplays of enzyme, substrate, and surfactant on hydrolysis of native lignocellulosic biomass. Bioengineered 2021; 12:5110-5124. [PMID: 34369275 PMCID: PMC8806531 DOI: 10.1080/21655979.2021.1961662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tracking enzyme, substrate, and surfactant interactions to reach maximum reducing sugar production during enzymatic hydrolysis of plant biomass may provide a better understanding of factors that limit the lignocellulosic material degradation in native rice straw. In this study, enzymes (Cellic Ctec2 cellulase and Cellic Htec2 xylanase) and Triton X-100 (surfactant) were used as biocatalysts for cellulose and xylan degradation and as a lignin blocking agent, respectively. The response surface model (R2 = 0.99 and R2-adj = 0.97) indicated that Cellic Ctec2 cellulase (p < 0.0001) had significant impacts on reducing sugar production, whereas Cellic Htec2 xylanase and Triton X-100 had insignificant impacts on sugar yield. Although FTIR analysis suggested binding of Triton X-100 to lignin surfaces, the morphological observation by SEM revealed similar surface features (i.e., smooth surfaces with some pores) of rice straw irrespective of Triton X-100. The reducing sugar yields from substrate hydrolysis with or without the surfactant were comparable, suggesting similar exposure of polysaccharides accessible to the enzymes. The model analysis and chemical and structural evidence suggest that there would be no positive effects on enzymatic hydrolysis by blocking lignins with Triton X-100 if high lignin coverage exists in the substrate due to the limited availability of hydrolyzable polysaccharides.
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Affiliation(s)
- Sengthong Lee
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok Thailand.,LigniTech-Lignin Technology Research Group, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok, Thailand
| | - Saengchai Akeprathumchai
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok Thailand
| | - Damkerng Bundidamorn
- LigniTech-Lignin Technology Research Group, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok, Thailand
| | - Lakha Salaipeth
- Natural Resource Management Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok, Thailand
| | - Kanokwan Poomputsa
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok Thailand
| | - Khanok Ratanakhanokchai
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok Thailand
| | - Ken-Lin Chang
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Paripok Phitsuwan
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok Thailand.,LigniTech-Lignin Technology Research Group, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok, Thailand
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Nemmaru B, Ramirez N, Farino CJ, Yarbrough JM, Kravchenko N, Chundawat SPS. Reduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activity. Biotechnol Bioeng 2020; 118:1141-1151. [PMID: 33245142 DOI: 10.1002/bit.27637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/12/2020] [Accepted: 11/15/2020] [Indexed: 12/24/2022]
Abstract
Dissociation of nonproductively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling nonproductive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three models type-A CBMs (Families 1, 3a, and 64) tethered to multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE-CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation were employed to measure CBM adsorption and desorption rate constants k on and k off , respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates ( k off ) and reduced effective adsorption rates ( nk on ), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in nonproductive enzyme binding and develop improved cellulolytic enzymes for industrial applications.
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Affiliation(s)
| | - Nicholas Ramirez
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Cindy J Farino
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - John M Yarbrough
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Nicholas Kravchenko
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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Pham VD, To TA, Gagné-Thivierge C, Couture M, Lagüe P, Yao D, Picard MÈ, Lortie LA, Attéré SA, Zhu X, Levesque RC, Charette SJ, Shi R. Structural insights into the putative bacterial acetylcholinesterase ChoE and its substrate inhibition mechanism. J Biol Chem 2020; 295:8708-8724. [PMID: 32371400 PMCID: PMC7324521 DOI: 10.1074/jbc.ra119.011809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/04/2020] [Indexed: 01/01/2023] Open
Abstract
Mammalian acetylcholinesterase (AChE) is well-studied, being important in both cholinergic brain synapses and the peripheral nervous systems and also a key drug target for many diseases. In contrast, little is known about the structures and molecular mechanism of prokaryotic acetylcholinesterases. We report here the structural and biochemical characterization of ChoE, a putative bacterial acetylcholinesterase from Pseudomonas aeruginosa Analysis of WT and mutant strains indicated that ChoE is indispensable for P. aeruginosa growth with acetylcholine as the sole carbon and nitrogen source. The crystal structure of ChoE at 1.35 Å resolution revealed that this enzyme adopts a typical fold of the SGNH hydrolase family. Although ChoE and eukaryotic AChEs catalyze the same reaction, their overall structures bear no similarities constituting an interesting example of convergent evolution. Among Ser-38, Asp-285, and His-288 of the catalytic triad residues, only Asp-285 was not essential for ChoE activity. Combined with kinetic analyses of WT and mutant proteins, multiple crystal structures of ChoE complexed with substrates, products, or reaction intermediate revealed the structural determinants for substrate recognition, snapshots of the various catalytic steps, and the molecular basis of substrate inhibition at high substrate concentrations. Our results indicate that substrate inhibition in ChoE is due to acetate release being blocked by the binding of a substrate molecule in a nonproductive mode. Because of the distinct overall folds and significant differences of the active site between ChoE and eukaryotic AChEs, these structures will serve as a prototype for other prokaryotic acetylcholinesterases.
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Affiliation(s)
- Van Dung Pham
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Tuan Anh To
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Cynthia Gagné-Thivierge
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Québec, Canada
| | - Manon Couture
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Patrick Lagüe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Deqiang Yao
- iHuman Institute, ShanghaiTech University, Shanghai, P.R. China
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Louis-André Lortie
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
| | - Sabrina A Attéré
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Québec, Canada
| | - Xiaojun Zhu
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Steve J Charette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Québec, Canada
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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